Author Topic: remove atom from spherical system  (Read 327 times)

zahid

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remove atom from spherical system
« on: December 29, 2018, 03:09:38 AM »
Dear Sir

I have a spherical nanoparticle. I have dumped all atoms for radiation damage but for observing the defects, I want to exclude 3-angstrom surface atom. Is it possible in OVITO? Any kind of suggestion or direction will be helpful to me.

Thank you

Alexander Stukowski

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Re: remove atom from spherical system
« Reply #1 on: December 29, 2018, 12:00:39 PM »
Hi,

If your particle is exactly spherical, and if you know its size, you could use the "Expression Selection" modifier of OVITO to select all atoms in the interior of the particle whose coordinates are fall within a spherical region of a given radius.

If the shape of your nanoparticle is not precisely known, you need a way to adaptively determine the atoms that are located outside a certain distance from the particle's surface. A common way to do this is to use the atomic coordination number to select atoms which are fully coordinated and deselect those that are under-coordinated, because they are located close to the surface. In Ovito, you can use the "Coordination Analysis" modifier to compute the number of neighbors of each atom within a given range (let's say 3.0 Angstroms). Subsequently you can use again the Expression Selection modifier to select all bulk atoms having a coordination number above a certain threshold. Let's say 80% of the usual coordination number of bulk atoms in the interior of the nanoparticle.

-Alex

zahid

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Re: remove atom from spherical system
« Reply #2 on: January 10, 2019, 04:04:52 AM »
Dear Sir

Thank you very much for your reply. I have tried below formula where Position.X = Position.Y = Position.Z = 74.516 for center of sphere and 72 is radius but it is not working at all. It does not select any atom.


sqrt(((Position.X)-(Position.X==74.516))^2 + ((Position.Y)-(Position.Y==74.516))^2 + ((Position.Z)-(Position.Z==74.516))^2) == 72

Constanze Kalcher

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Re: remove atom from spherical system
« Reply #3 on: January 10, 2019, 09:58:54 AM »
Hi,

this will select the atoms inside a sphere of radius 72 centered at [74.516, 74.516, 74.516]:

Code: [Select]
(Position.X - 74.516)^2 + (Position.Y - 74.516)^2 + (Position.Z - 74.516)^2 <= 72^2
-Constanze

zahid

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Re: remove atom from spherical system
« Reply #4 on: January 10, 2019, 08:50:49 PM »
thank you very much. It is working now.