Author Topic: How to calculate the defect cluster.  (Read 307 times)

zahid

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How to calculate the defect cluster.
« on: April 18, 2019, 04:13:32 AM »
Hi Ovito User

I know how to use the Wigner-Seitz defect analysis using Expression select.
Occupancy == o (for single vacancy)
Occupancy == 1 (for single intersittial)
Occupancy == 2 (for 2 interstitial)
Occupancy == 3 (for 3 intersittial)

Can you help me to analyze the defect clusters? like vacancy cluster (2 vacancies, 3 vacancies etc) and interstitial cluster ( 2 interstitials, 3 interstitials etc )

Do I need to go with a python script or it is possible with expression selection with the pipeline.
Any kind of suggestion would be helpful for me.

Constanze Kalcher

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Re: How to calculate the defect cluster.
« Reply #1 on: April 23, 2019, 10:47:38 AM »
Hello,

can you explain what you would like to analyze specifically?

-Constanze

zahid

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Re: How to calculate the defect cluster.
« Reply #2 on: April 29, 2019, 04:36:21 AM »
Dear Sir

I want to calculate the vacancy and interstitial cluster. I have tried for measuring the interstitial cluster below the modification pipeline:

W-S defect analysis > expression selection: Occupancy == 2 > cluster analysis (cutoff distance 3 mean 3 angstrom)

is it right approach?

Constanze Kalcher

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Re: How to calculate the defect cluster.
« Reply #3 on: April 29, 2019, 03:05:19 PM »
Hello,

it is still not fully clear to me what you mean by "measuring the interstitial cluster". Also, please carefully read the description of the Wigner-Seitz defect analysis modifier in the manual:
https://ovito.org/manual_testing/particles.modifiers.wigner_seitz_analysis.html
In the "sites" mode, the modifier outputs the sites of the reference configuration together with their computed per-site occupancy numbers. In that case Occupancy == 1 means there is one atom sitting on that site,
so there is no interstitial atom, on the contrary, it is a regular lattice site. Interstitials are only present when you have an occupation number greater than 1.

As for the Cluster analysis: If you activate the option "Use only selected particles" you will restrict the clustering algorithm to your currently selected particles (in your case all single interstitial sites Occupancy == 2).
Unselected particles will be treated as if they do not exist and will be assigned the special cluster ID 0. So if you wanted to get clusters (defined by your cutoff) of that specific defect type, what you did there works.
https://www.ovito.org/manual_testing/particles.modifiers.cluster_analysis.html
Furthermore, in the above manual entry it is explained how to export the cluster sizes.

By the way, if you need to count the number of (specific) defects in the neighborhood of each defect (within a predefined cutoff range) and don't want to write a python script for that you could make use of the Compute property modifier.
https://ovito.org/manual_testing/particles.modifiers.compute_property.html
This modifier allows you to generate new particle properties and use selective and conditional property assignment, e.g.
    Expression:
        0
    Neighbor expression:
        @Occupancy == 2 && Occupancy == 2
    Cutoff Radius:
        3
will count the number of single interstitial sites in the neighborhood (cutoff = 3 Angström) of each interstitial site and store that in the particle property you defined in "Output property".
Let me know if you were asking for something different.

-Constanze