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Messages - Afshin

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Dear Alex,

Thank you very much. This is exactly what I am looking for. Currently, it is only producing 2D contours (for example only "vector 1 and 2" in "Bin and reduce" analysis) and I intend to have "vector 1 and 2 and 3" for 3D demonstration. Also, is it possible to save this contours as an animation or separate image files?

Dear Alex,

I am using OVITO to color my structure based on per-atom values (Figure1 in attached files), but to provide a better description to my readers I would like to produce a 3D-contour(map) plot using my results (see Figure2 in attached for an example). Is this possible with OVITO at the moment?
I believe that this kind of image rendering would be interesting for the microscopic simulation practitioners since sometimes 2D/3D contours and maps can be more helpful in describing phenomena.

Support Forum / Re: Wall Visualization in OVITO
« on: April 27, 2018, 10:25:59 PM »

if your wall consists of atoms:

The simplest approach would be using Select Particles and only choose atoms inside that cylindrical wall; then, Color Code the selected particles.
Is there any specific distinction between atoms in the wall and atoms outside it? such as "type" or "range of atomic IDs" or anything else that guides OVITO to select the correct particles.


Alex suggestions seems to be a good solution.

Dear Zahid,

Please use the following steps:

1- Load initial data (remember to check for multiple timesteps option),
2- Use Wigner-Seitz modifier (which will help to identify defects in each timestep based on occupancies),
3- Use Select particles to select between defective or defect-less sites (for example, occupance==1 will let OVITO select sites that neither represents a vacancy or an interstitial),
4- if you choose the defect-less sites, then you can easily delete them using Delete Selected (in this case, only vacancies and interstitials remains at each time step),
5- I suggest using Color Coding (based on occupancy of atomic sites) to make a difference between vacancies and interstitials in your visualization,
6- Finally use export file to save positions and probably numbers of defects in a format that you prefer,

Also, I strongly recommend that you read OVITO manual, which is very clear and can help you a lot in your investigation. Please also feel free to ask if you have any other questions.


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,

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?"
Thank you very much.


Support Forum / Re: how to display dumbbells through W-S defect analysis
« 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.


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