Author Topic: WS analysis  (Read 75 times)

karthikguda

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WS analysis
« on: May 09, 2019, 08:30:32 PM »
Dear Admin,

I am using OVITO 3.0.0-dev362 version to do WS analysis on my pkA simulations. What I find interesting is that I don't see the same number of interstitials and vacancies in the results file I have exported and when I do an expression select using "Occupancy == 0" or "Occupancy == 2" for the same dump frame. Is this a bug?

regards,
Karthik

Constanze Kalcher

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Re: WS analysis
« Reply #1 on: May 10, 2019, 12:05:49 PM »
Dear Karthik,

sorry I don't understand yet what the issue is. Could you please elaborate the problem?

-Constanze

karthikguda

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Re: WS analysis
« Reply #2 on: May 10, 2019, 09:14:00 PM »
Dear Constanze,

I load my dump frame for WS analysis. I do "export file" for the number of vacancies and interstitials.

I then do an expression select of "Occupancy == 0" for vacancies and "Occupancy == 2" for interstitials in the OVITO gui and the number of interstitials and vacancies that I see in the OVITO window are different from those that are present in my exported file for the same frame.

Could this be a bug?

Best regards,
Karthik

Constanze Kalcher

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Re: WS analysis
« Reply #3 on: May 13, 2019, 11:36:18 AM »
Dear Karthik,
you can upload an example file for me here, if you want me to look into this further.

However, did you export the global attributes WignerSeitz.vacancy_count and WignerSeitz.interstitial_count? Note that the latter
counts the total number of excess atoms, summed over all sites of the reference configuration. A site with occupancy=2 has one excess atom. A site with occupancy=3 has two excess atoms, and so forth.
Is that maybe what causes your confusion?

-Constanze
« Last Edit: May 13, 2019, 12:23:56 PM by Constanze Kalcher »

karthikguda

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Re: WS analysis
« Reply #4 on: May 13, 2019, 07:23:12 PM »
Dear Constanze,

Below is a link to my dump file containing two frames with frame zero being the reference frame. I am unable to attach it here as the system contains 1 million atoms.

After loading the file, I activate the WS analysis modifier and Ovito detect 271 vacancies and 271 interstitials.

In order to isolate vacancies from interstitials, I do an expression select with "Occupancy == 0", then Ovito says that 0 elements have been selected.

For "Occupancy == 2" and "Occupancy == 3" I get 538 and 3 respectively.

Aren't these numbers inconsistent?

Best regards,
Karthik

Link to file: https://www.dropbox.com/s/rvtjovxmsed7ntc/for_ovito.dump?dl=0


Constanze Kalcher

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Re: WS analysis
« Reply #5 on: May 14, 2019, 11:32:54 AM »
Dear Karthik,

thanks for uploading the files for me, now I understand what's causing you problems. Note, that the Wigner Seitz defect analysis modifier has two output modes, i.e. the "sites" and "atoms" output modes.

In "sites" output mode, the modifier outputs the sites of the reference configuration together with their computed per-site occupancy numbers. Each site will be associated with a particle property named Occupancy, telling the number of atoms sitting on that site. This integer property subsequently allows you to identify vacancy and interstitial sites. It is important to realize that in this output mode, the displaced configuration gets completely replaced with the reference configuration after performing the WS algorithm.

In "atoms" output mode, in contrast, the modifier will output the atoms of the displaced configuration. Each atom will be assigned a property named Occupancy, now counting how many atoms in total are occupying the same site as the atom itself. Furthermore, the modifier will assign a property named Site Type, which tells for each atom the type of reference site it has been assigned to by the WS algorithm. This information allows to subsequently identify antisites, for example, by comparing the type of an atom to the type of its site. Finally, the algorithm assigns two additional properties named Site Index and Site Identifier to each atom, specifying the index and the unique identifier (if present) of the site to which the atom has been assigned. This information allows you to subsequently identify atoms which have left their original sites, for example. Note, however, that in "atoms" output mode you will not be able to identify vacancy sites, because only the physical atoms are retained. That's why you find 0 elements when you use the expression selection modifier with "Occupancy == 0".

Maybe it becomes more clear with an example: In your case, the Wigner Seitz defect analysis modifier calculated that you have 271 vacancies and 271 interstitials. You can double check that by using the Expression selection modifier:
If you select the output mode: "Sites" in the WS modifier, and then "Occupancy == 0" as expression selection you will get 271. However, to count the interstitials you need to pay attention to how many atoms occupy a site. As for your specific example "Occupancy > 1" selects 270 atoms. That's doesn't mean that there are only 270 interstitials. You have 269 sites with "Occupancy == 2" and 1 site with "Occupancy == 3". The latter site hosts 2 extra atoms, i.e. 269+2 = 271 interstitials.

Moreover, if you choose the "atoms" output mode you will get 2x269 = 538 sites that have a particle property Occupancy equal to 2, since in that mode the property "Occupancy" now tells you how many atoms share the same site as the atom itself. Consequently, for the one site that hosts 3 atoms, there are 3 atoms that fulfill "Occupancy == 3".

-Constanze

« Last Edit: May 14, 2019, 01:36:10 PM by Constanze Kalcher »

karthikguda

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Re: WS analysis
« Reply #6 on: May 15, 2019, 04:31:29 AM »
Dear Constanze,

I really appreciate your detailed explanation. Things are much clearer now.

regards,
Karthik