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How to observe defects and specific particle (Primary kinetic atom)

Dear Ovito User

I use Ovito for data analyzation. I have found this software is pretty handy. I want to observe the defect movement with PKA atoms. I have attached ovito state files for pipeline modifier.

my pipeline is

Wigner_Seitz analysis > Expression modifier (Occupancy!=0 && Occupancy!=2 && Particleindentifier!=82639) > delete selected

I have found that particle 82639 is not moving but then I have used only Particleindentifier!=82639) > delete selected and found that single particle is moving.

Can you help me about it? How can i see the defects movement with PKA atom (PKA atom should be different color)

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I also recommend adding to your knowledge base determination difference between atom and molecule for an amateur like in this review https://differencebtwn.com/difference-between-an-atom-and-a-molecule.

Quote from Mohammad Zahidul Khan on June 9, 2020, 2:33 am

Dear Ovito User

I use Ovito for data analyzation. I have found this software is pretty handy. I want to observe the defect movement with PKA atoms. I have attached ovito state files for pipeline modifier.

my pipeline is

Wigner_Seitz analysis > Expression modifier (Occupancy!=0 && Occupancy!=2 && Particleindentifier!=82639) > delete selected

I have found that particle 82639 is not moving but then I have used only Particleindentifier!=82639) > delete selected and found that single particle is moving.

Can you help me about it? How can i see the defects movement with PKA atom (PKA atom should be different color)

Hi Mohammad,

I wonder if you have already solved the problem. From the folder you uploaded, you chose the "Output mode" as "Sites" in the Wigner-Seize analysis, which means that you would see the defects of the "reference configuration" rather the "current configuration". Seeovito.modifiers.WignerSeitzAnalysisModifier.for more information. If you wanna see the movement of PKA atom together with other interstitial atoms, you could choose  the "Output mode" as "Atoms". However, you will not see the movement of the vacancies in this way. There is no easy way to see the movement of the interstitial atoms and vacancies in the displaced configuration simutaneously.

Dear Sir

Thank you very much for your response. I can not use the python script. Can you help me by writing the pipeline? Even for interstitials and PKA atom is good for me.

Hi Mohammad,

It's easy to do it in Ovito's window version. In your pipeline

Wigner_Seitz analysis > Expression modifier (Occupancy!=0 && Occupancy!=2 && Particleindentifier!=82639) > delete selected

just select the "Output mode" as "Atoms" when you add the "Wigner-Seize defect analysis" modification, and you'll get what you want. Of course, a python script would be a better choice if you wanna view the movement of vacancies as well, please refer to

https://www.ovito.org/docs/current/python/modules/ovito_modifiers.php#ovito.modifiers.WignerSeitzAnalysisModifier

for more details.

Dear Sir, Thank you very much. It is working now.