Author Topic: WS Analysis for Occupancy Plot  (Read 481 times)

dualbeam

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WS Analysis for Occupancy Plot
« on: January 06, 2019, 02:30:05 PM »
Dear Ovito Users,

Greetings!

I have come across an issue during Occupancy calculations using WS Analysis Modifier in Ovito. I am doing cascade simulation of energetic ions incident over a diamond lattice. The Ovito analysis of Lammps results at some particular time-steps show defects around the edges. These defects are not created due to the incident ions and appear out of nowhere, and are away from the cascade region/incident ion location. Please see attached image showing vacancies/interstitials in the central region, which looks normal due to incident ion, and the defects (highlighted) away from cascade.

I am wondering if anyone has come across such issue before? Any lead or suggestion is highly appreciated.

Cheers,
Vivek

Constanze Kalcher

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Re: WS Analysis for Occupancy Plot
« Reply #1 on: January 07, 2019, 10:15:45 AM »
Dear Vivek,

if you upload the simulation data here I could investigate this further.

-Constanze

dualbeam

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Re: WS Analysis for Occupancy Plot
« Reply #2 on: January 07, 2019, 10:55:56 AM »
Dear Constanze,

I have shared the dump data of a cascade simulation from Lammps consisting of 10 time-steps, including the WS Analysis modifier I have used:

https://drive.google.com/drive/u/0/folders/1_xeeyseL1lq8dBZhuuWj29jVuUKbbkUg?ogsrc=32


Thanks,
Vivek

Constanze Kalcher

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Re: WS Analysis for Occupancy Plot
« Reply #3 on: January 07, 2019, 12:15:59 PM »
Dear Vivek,

this seems to be an issue of your simulation setup. Have you noticed that in some of your snapshots, the atoms in the corners clearly drift into one direction?
In the attached snapshot you can see that they have non-negligible displacements with respect to the lattice constant. Since the WS-analysis simply looks for the current number of atoms present in the
WS-cells defined by every atom in the reference structure, it makes sense that the WS analysis will detect a lot of defects in this region.

https://ovito.org/manual/particles.modifiers.wigner_seitz_analysis.html

-Constanze

dualbeam

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Re: WS Analysis for Occupancy Plot
« Reply #4 on: January 07, 2019, 12:43:08 PM »
Dear Constanze,

Thank you for going through the data file and your suggestions. I did notice the movements of the atoms towards corners, however, such movement occurs only at some particular time-steps, which made me think if there is any issue arising out of the WS analysis used. Alos, I found out a past thread discussion mentioning similar issue:

http://forum.ovito.org/index.php?topic=179.0

once again thank you, I will see what is going wrong in the simulations to cause such discrepancy at the corners.

Thanks,
Vivek

Constanze Kalcher

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Re: WS Analysis for Occupancy Plot
« Reply #5 on: January 07, 2019, 01:38:50 PM »
Dear Vivek,

what do you mean by
Quote
...however, such movement occurs only at some particular time-steps, which made me think if there is any issue arising out of the WS analysis used...?
Just take your original data and compare the coordinates of the atoms in the different snapshots, the observed displacement has nothing to do with any of the analyses you applied.

In this previous topic you mentioned and also in a current thread here:
http://forum.ovito.org/index.php?topic=447.0
it is discussed how to deal with the reference structure shifting as whole. In that case you could calculate the drift vector and map the damaged structure back to the reference structure so to say.
However, I'm afraid this won't help you since these artifacts only occur in specific regions.

Constanze

dualbeam

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Re: WS Analysis for Occupancy Plot
« Reply #6 on: January 07, 2019, 05:06:39 PM »
Dear Constanze,

Thanks again for your reply.

Please see the attached image for clarification. The image is obtained at 8th time-step, and does not show any corner defects in contrast to the the image posted before (9th time-step). This is from the same Lammps dump file I had shared.

The defects  away from collision cascade (at corners) and appearing out of nowhere at particular time-steps (such as 9th) are confusing considering these cascade simulations, where the defects are supposed to be building up relative to the ion trajectories, also being observed for particular time-steps (such 8th). I agree this issue may have been arising from the simulation, I am trying to find out.



Thanks,
Vivek