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How to determine the actual positions of interstitial atoms in Ovito

Wigner-Seitz (WS) defect analysis in Ovito only provides the interstitial atoms sites and their number as per the description given in Ovito. How can one determine the real positions of the interstitial atoms?

I want to use that to carryout defects cluster analysis. This is because, to carry out cluster analysis, one needs to make a selection of the desired particles. However, if WS function is active the particles selected are not defects since WS uses reference (defect-free) crystal and the results of the cluster analysis may therefore be wrong under such circumstance.

Thank you.

Hi,

you might find my last post in this forum discussion helpful,
https://www.ovito.org/forum/topic/problems-writing-xyz-from-dl_poly-history-file/

which explains the difference between the "Atoms" and "Sites" output modes of the Wigner-Seitz defect analysis modifier.
https://www.ovito.org/docs/current/particles.modifiers.wigner_seitz_analysis.php

What you need to use in your case is the "Atoms" mode. Just note that it's not trivial to "only" select the interstitial atoms, since all atoms that occupy one interstitial site will share the same Occupancy number (i.e. number of interstitials + 1).

-Constanze

I find the post quite helpful. Thank you.

 

-Shehu

Hi,

I am so sorry for bothering you. I can't seem to find the 'site' and 'atoms' features I have highlighted in the attached image in the origin I am using. The second image is the screenshot of the Ovito I am currently using showing the only features I can find. Perhaps the version of origin I am using does not have those features.

Thank you.

-Shehu

 

Uploaded files:
  • Ovito_support.PNG
  • Ovito_Support2.PNG

Hi,

no worries, that's what this forum is made for. You're right, in the 2.9 release the "Atoms" output mode is not available. Please upgrade to the developer version if you would like to use that feature.

-Constanze

Hi,

Thank you for your prompt response to my enquiries. I will upgrade to the newest version as soon as possible.

-Shehu