Author Topic: how to display dumbbells through W-S defect analysis  (Read 514 times)

zeroz

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how to display dumbbells through W-S defect analysis
« on: December 28, 2017, 09:06:30 AM »
Hi,all:
I want to use W-S defect analysis modifier to do point defect analysis,but as mentioned in manual,once the W-S analysis is performed,the reference configuration will replace the original
displaced configuration,and Interstitial positions(Occupancy==2) display as sphere instead of a dumbbell structure or a interstitial.

How can I show accurate sturcture in interstitial positons(such as dumbells toward different directions)  rather than the rough sphere?
Thank you very much.

Xtof

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Re: how to display dumbbells through W-S defect analysis
« Reply #1 on: December 28, 2017, 05:19:25 PM »
Interesting question. I would also be interested in knowing how to do that.

Best regards,
Christophe

Alexander Stukowski

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Re: how to display dumbbells through W-S defect analysis
« Reply #2 on: January 04, 2018, 04:56:44 PM »
Yes, I agree, this is an interesting question  :) I do not see that the current version of OVITO provides a solution to this problem, which others have been facing before.

Basically, the W-S modifier needs to be extended (requiring code modifications). Here is what I have in mind: We could add an option that turns off the normal behavior of the W-S modifier: Instead of replacing the current configuration with the reference configuration, the current configuration is kept. The occupancy numbers that are assigned to the individual atoms then represent the total occupancy of the sites the atoms have been assigned to. The two atoms forming a dumbbell configuration, for example, would both have Occupancy==2. Of course, in this mode it would not be possible to select vacancies, because there are no atoms occupying vacancy sites. Also, the "Output per-type occupancies" option would not make any sense in this mode.

What do you think?

In principle, it is possible to implement this algorithm using a custom "Wigner-Seitz" modifier written in Python. So if you have an urgent need for this approach, that would be the way to go. Otherwise, let me create an issue for this feature request on our GitLab site and I will try to extend the built-in W-S modifier when I find some time.

Afshin

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Re: how to display dumbbells through W-S defect analysis
« Reply #3 on: February 17, 2018, 09:07:13 PM »
Dear Alex,

Is there any progress regarding this issue? I am really interested to see if finally, OVITO is able to show dumbbell defects.



Thanks

Alexander Stukowski

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Re: how to display dumbbells through W-S defect analysis
« Reply #4 on: February 19, 2018, 04:14:35 PM »
Ok, I took the time today to implement the new output mode and extend the W-S modifier as described above. You can find the extension in the latest development version (dev120).
Note that the user manual hasn't been updated yet, but the scripting documentation already reflects the addition:

http://ovito.org/manual_testing/python/modules/ovito_modifiers.html#ovito.modifiers.WignerSeitzAnalysisModifier.keep_current_config

Let me know if it works (or not).

jezper

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Re: how to display dumbbells through W-S defect analysis
« Reply #5 on: February 28, 2018, 07:40:40 AM »
This is a very useful extension to the W-S modifier and it works perfectly for me. Thank you, Alexander!

Afshin

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Re: how to display dumbbells through W-S defect analysis
« Reply #6 on: March 11, 2018, 06:30:44 PM »
Dear Alex,

Thank you very much. I have a question regarding these new developments; As a test, I have placed an atom in my reference structure to virtually create an interstitial without any vacancy. With new improvements, now I should have two atomic sites with occupancy==2 and so,

- Expression selection -> occupancy==1
- Deleted selected
- (Affine mapping of simulation cell  -> off)
- (Reference configuration source  -> both "upstream pipeline" and "External file --> initial data file" have been tested)

 should keep two atoms which then helps me to find if they make let's say a dumbbell. But I still have only one atom kept, which means WS cell still does not retain both current and initial positions. Could you give me some recommendations?

** I also want to add one more utility suggestion and request. Can you please add the following capability to WS analysis?
"If now I can see both reference atom and the second one which has entered to its polyhedral WS cell, then will it be possible to find out which interstitial site is occupied based on the relative positions?"
a
Thank you very much.


Bests,
Afshin

Alexander Stukowski

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Re: how to display dumbbells through W-S defect analysis
« Reply #7 on: March 20, 2018, 08:41:31 AM »
Dear Afshin,

The steps you describe sound correct. I tried the same, and it worked.  So I'm not sure what the two of us have been doing differently, or if there is a problem in OVITO.

To find out, let me start by sending you my test data files (attached). The reference configuration (config.0.poscar) is a perfect bcc crystal made of 54 atoms. The displaced configuration (config.1.poscar) is the same crystal plus one extra atom positioned somewhere. When I perform the WS analysis on this config, using the new 'Keep current configuration' option, I get exactly two atoms with Occupancy==2. The rest has Occupancy==1.

Can you tell if you have been doing something differently?

Furthermore, I am not sure if I understand your suggestion. Even with the new  'Keep current configuration' option, you won't see both configurations simultaneously. You only have the choice to either work with the reference config or the displaced config. If you really need to work with both configurations simultaneously and need to know exactly which set of atoms from the displaced configuration occupies which site from the reference configuration, then this is beyond the current capabilities of the WS modifier and OVITO's data model. You would probably have to do it yourself using a custom analysis code.

-Alex
« Last Edit: March 20, 2018, 08:45:38 AM by Alexander Stukowski »

Afshin

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Re: how to display dumbbells through W-S defect analysis
« Reply #8 on: March 20, 2018, 09:26:56 PM »
Dear Alex,

Thanks for your response. I do not why I could not see "Keep current configuration" option, which was right in front of my eyes  ;D. This works perfectly and it is a very cool utility.
About the next utility suggestion, I will give you a full explanation in a few days with some examples that are floating in my head.

Best Regards,
Afshin