Author Topic: Two problem about W-S defect analysis  (Read 432 times)

HuanHe

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Two problem about W-S defect analysis
« on: January 25, 2018, 09:21:55 AM »
Hello,
    Firstly, I want to say that Wigner-Seitz defect analysis is a pretty wonderful and effective modifier. I appreciate you because it help me solve some problems and save so much time. But  I have two problems recently when I use it in the visualization.The background is what I am researching is a two component systems. Assume that  they are A and B.
    First one , if I do the expression select (for example, the boolean expression is :ParticleType==1&&Occupancy.1==0&&Occupancy.2==2)after W-S defect in OVITO, I find that in the visualization window, I can only see one atom. And its particletype is A. I think my expression select should present two atoms, and they are both B-atoms. And OVITO presents the center atom. So are there some ways to see the two B atoms in OVITO or some python scripts can get the coordinate?
    And the second problem is not about OVITO. It is about the method. We know that  if one A-atom and one B-atom in A site, we regard it as B interstitial. And if only one B-atom in A site, we regard it as A antisite. But if  there are two B-atoms in A site, how to regard these two B-atoms?  Are they double-interstitial or one antisite and one interstitial. I can't understand this problem.
   Thanks for reading and I am waiting for your reply.
With best regards,
Huan He

Alexander Stukowski

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Re: Two problem about W-S defect analysis
« Reply #1 on: February 01, 2018, 02:13:49 PM »
Hi,
my apologies for the late reply. I was on vacation for a few days and now I am trying to catch up now.

When using the W-S function in OVITO it's important to realize that this function throws away the displaced atomic configuration and replaces it with the perfect crystal configuration. This is explained in the user manual: http://www.ovito.org/manual/particles.modifiers.wigner_seitz_analysis.html

It means that any subsequent selection operation will act on sites from the perfect crystal, not atoms from the displaced configuration (which are all thrown away). The only information on the original atoms that is retained is the count of each species that was occupying each site. So in your case this selection expression

ParticleType==1 && Occupancy.1==0 && Occupancy.2==2

will select A-sites occupied by 0 A-atoms and 2 B-atoms. Notably, it will not select the B-atoms that occupy these sites.

The general problem is that OVITO has to throw away one of configurations, either the reference or the defective one, after the W-S analysis has been performed. Any subsequent selection operation can act only on the retained configuration, not both configurations simultaneously. In the current W-S implementation, the decision has been made to retain the reference site configuration and throw away the defective atom configuration. This allows, for example, to select vacancies (sites with Occupancy==0), which would not be possible if we were retaining the defective configuration, because vacancies do not represent physical atoms.

For a future version of OVITO I am thinking about extending the W-S modifier. Maybe add a switch that allows the user to change this default behavior and instead keep the defective configuration and throw away the reference configuration. This would allow one to explicitly visualize the two or more interstitial atoms that are sitting on the same site. The meaning of the "occupancy" property would be changed then. It would now denote the total number of atoms occupying the same site as the atom to which the property relates.

Best regards,
Alex

HuanHe

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Re: Two problem about W-S defect analysis
« Reply #2 on: February 27, 2018, 01:37:49 PM »
Hi,
  My apologies for the late reply too because I am celebrating Spring Festival which is Chinese New Year . Happy Spring Festival for you and your family!
  And Thanks for your reply a lot. I understand your specific explanation. It helps me a lot.

Best regrads,
Huan He