"I want to use Cluster modifier after Wigner-Seitz modifier, I cannot get the cluster distribution in the displaced frame."

Why do you want to obtain by combining the W-S modifier and the cluster modifier ? A simple "coordination analyzes" will not be enough ?

And keep in mind that, while the position of the interstitial being well defined by the position of the interstitial atom, there is by definition no one atom to define the position of the vacancy (only an empty W-S cell corresponding to an atom in the original structure). So, the use of the original structure to display the results of the W-S analyzes is the only way.

In addition, the results in presence of a surface (if you have one) might be tricky to interpret...

"I want to use Cluster modifier after Wigner-Seitz modifier, I cannot get the cluster distribution in the displaced frame."

Why do you want to obtain by combining the W-S modifier and the cluster modifier ? A simple "coordination analyzes" will not be enough ?

And keep in mind that, while the position of the interstitial being well defined by the position of the interstitial atom, there is by definition no one atom to define the position of the vacancy (only an empty W-S cell corresponding to an atom in the original structure). So, the use of the original structure to display the results of the W-S analyzes is the only way.

In addition, the results in presence of a surface (if you have one) might be tricky to interpret...

Hey,

I had the same problem while analyzing my damaged crystals, so I wrote cpp script with a pre-defined cut-off radius to explain the clustering phenomena.

By the way, you may also want to analyze dislocation nucleation and growth in an irradiated box using OVITO. DXA is the solution but it only can detect extrinsic dislocations, i.e.  dislocations made of interstitials, not the intrinsic ones. This tool needs to be modified.

Dear Guénolé,

Thanks very much for your reply!

I want to get the information of how many interstitials and vacancies in my simulation result, and the positions of them, by using Wigner-Seitz Analysis Modifier. After that, I want to use Cluster Analysis Modifier to obtain whether the interstitials or vacancies form several clusters. I also want to know how many clusters are there and how many interstitials or vacancies in each cluster. This information maybe is very often used in the result analysis of radiation damage simulation.

I am very sorry that I cannot quite understand your reply. I am not very familiar with Coordination Analyzes. I checked the manual of OVITO, it seems it gives the Radial distribution function. I think it is not the information I want to get.

My problem is when W-S modifier is applied, it gives the site’s position in the reference frame. It cannot give the positions of interstitials and vacancies in the displaced frame. And then, the Cluster Analysis Modifier cannot give the information of interstitial cluster and vacancy cluster in the displaced frame.

And what does you mean by “So, the use of the original structure to display the results of the W-S analyzes is the only way.”? Could you please give me more instructions?

Thanks very much!

With Best Regards

Liu

Dear Arjhangmehr,

Thanks very much for your help!

You wrote a cpp script yourself to analyze the clusters. Does that mean my problem cannot be solved in OVITO internally? And does that mean I must write a script to obtain the positions of interstitials and vacancies, and then use another script to analyze the clusters distribution all by myself? Could you please give me more information about this?

I have not used DXA modifier before, your suggestion is very helpful! I will check the doc page of this modifier and try to use it.

It seems you research field is radiation damage simulation. I am a beginner of this field. Hoping more communications with you and more advice form you.

Thanks very much for your help!

With My Best Regards

Liu

see doi:10.1016/j.cpc.2010.12.009

Dear Nelasov, Thanks very much for your suggestion. I will read that later.

Dear Wenqiang,

I totally forgot to add a response to your question. The only solution I have for you is to (a) extract the SIAs and vacancies coordination using OVITO, and (b) define a cut-off radius (a minimum distance between defects of identical nature) and then calculate the distance between all defects and find those that form a cluster. Note that all of this can be easily done with a simple cpp (or any other programming utility) script.

if you have further questions, please feel free to contact me on my personal email: [email protected]

Dear, Afshin Arjhangmeh.

How extract the SIAs and vacancies coordination using OVITO? I have written a Fortran program to find of vacancies (according to the method similar doi: 10.1016 / j.cpc.2010.12.009) and SIAs. In OVITO not find function output coordinate of vacancies or visualization (in Wigner-Seitz Analysis Modifier.)

Dear Afshin Arjhangmehr,

Thank you very much for you answer.

In my opion (and I also asked the author of  OVITO), the W-S modifier in OVITO can obtain the number of interstitials and vacancies. However, it can NOT obtain the coordinates of the defects in the damaged configuration. I think this my main problem that must be solved first. Could you please give some more suggestions?

Does that mean I have to write a script myself to achieve my goal?

Dear Nelasov,

I think you should use the Wigner-Seitz modifier in OVITO. Maybe you can read the doc page of this modifier.

If I write python script for OVITO - I will send

Dear Wenqianq and Nelasov,

In the case of vacancies, I believe (and I have used this technique in my papers) that OVITO gives the right coordinate, since WS modifier only considers polyhedral cells with occupancy equal to zero. In the case of SIAs, however, OVITO only gives the coordinate of cells with occupancy equal or more than two. This means that the position of any atoms within a cell can be exported and there is a little chance that one can get the right coordinate of SIAs.

(Note that as far as I know, there is no specific rule in identifying interstitial position within a WS polyhedral cell. One of the atoms is considered the original one, and others as the SIAs)  

Thus, considering this fact, in our cluster analysis, we specify the cutoff radius equal to 2NN distance and eliminate any mis-interpretation due to uncertainty in interstitial coordinate.

Hope this helps,

Greetings from Tehran,

Afshin

Dear Afshin Arjhangmehr,

Thanks very much for your reply! And I am very sorry to reply this late. I did not check my message these days, due to the other things which my boss let me to do.

I understand the vacancy part of your response about. In OVITO, the W-S modifier compares the reference configuration with the displaced configuration. A site at the reference configuration with zero occupancy is a vacancy site. And this vacancy site corresponds to a vacancy in the displaced configuration. So the coordinates of the vacancies can be gained correctly by W-S modifier and could be further used.

However, in the case of interstitials, the site in the ref configuration with occupancy=n (n is greater than 1) represents a site with n-1 interstitials around this site. If I export the coordinates of these sites, it only gives the position of the sites with occupancy greater than one. There is no information about the coordinates of interstitials in the damaged configuration. So, it cannot be further used to analyze the cluster distribution of interstitials.

Do you agree with me? And could you please give me more help on this topic?

Dear Wenqiang,

That is exactly the reason why we use 2NN distance as the cut-off radius, since WS modifier gives the coordinate of cell with occupancy>=2.

Let me explain it in another way, consider one atom in a polyhedral WS cell which illustrates "before" damage event. Then, consider another cell with two atoms, which represents "after" damage event (one as the reference atom and the other as the SIA).

Now, can you state clearly which one is the "original" and which one is the "interstitial"? Some might say, the atom that is closer to "the polyhedral center" is the original one and the other should be considered as SIA, or vice versa. 

So, the best solution is to consider the center coordinate of the cell as "position" of the interstitial, and define a cut-off radius in a way that eliminates this uncertainty. 

I hope this helps.

Dear Afshin Arjhangmehr,

Thanks very much your reply! But I am sorry I do not fully understand what you mean yet.

I think you are trying to say it is very hard to define which atoms in a W-S cell, which contain more than one atom, are the interstitials. I understand this point.

I think my problem is, in OVITO, form the W-S modifier I only can get the coordinates of the cell of which the occupancy is greater than 1. But in cluster analysis of the interstitials, what I need is the coordinates of the interstitials in the damaged configuration. A cell of occupancy equal n represents n-1 interstitials around the cell, however, I do not know where exactly there are.

So, I do not quite understand the last paragraph of your reply. I think the cut-off radius is applied to the coordinates of the interstitials. How can I apply the cut-off to the coordinates of the cells?

With My Best Regards

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