Author Topic: Moving atoms to the center of the simulation cell  (Read 311 times)

computational

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Moving atoms to the center of the simulation cell
« on: January 11, 2019, 08:27:36 AM »
Hi,
Is there a method to move atoms to the central position of the simulation cell using Ovito?
Thanks

Constanze Kalcher

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Re: Moving atoms to the center of the simulation cell
« Reply #1 on: January 11, 2019, 09:16:23 AM »
Hi,

yes, you can easily do that with the Affine Transformation modifier. Here's the corresponding manual page

http://ovito.org/manual/particles.modifiers.affine_transformation.html

-Constanze

computational

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Re: Moving atoms to the center of the simulation cell
« Reply #2 on: January 11, 2019, 09:50:12 AM »
Thanks,
I have already tried this feature but didn't work me.
Can you please outline the methodology?
I am attaching the jpg of the structure.
Can you please tell me how to move the atoms to the center of the simulation cell?

Constanze Kalcher

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Re: Moving atoms to the center of the simulation cell
« Reply #3 on: January 11, 2019, 10:09:13 AM »
Hi,

what did you have trouble with? It's only a translation that you apply on the particles. Don't forget to unselect the simulation cell.

-Constanze

computational

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Re: Moving atoms to the center of the simulation cell
« Reply #4 on: January 11, 2019, 10:38:22 AM »
While implementing affine transformation to particles, by changing the cell vector or the transformation matrix, I can see that the particle positions get squeezed rather than moving.
I hope you understood what I am trying to say.
I have attached figures to clarify.
Its been made sure that the simulation cell is unchecked.
Thanks.

Constanze Kalcher

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Re: Moving atoms to the center of the simulation cell
« Reply #5 on: January 11, 2019, 10:59:21 AM »
Maybe it's best if you send me a screenshot of the modifier you apply, then I can tell you what's the problem.

computational

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Re: Moving atoms to the center of the simulation cell
« Reply #6 on: January 11, 2019, 11:43:12 AM »
PFA the screenshot.
« Last Edit: January 11, 2019, 11:46:11 AM by computational »

Constanze Kalcher

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Re: Moving atoms to the center of the simulation cell
« Reply #7 on: January 11, 2019, 11:54:16 AM »
Hi,

I recommend you to use the Transformation matrix instead of the Transform to target box.
Note that you need to edit the Transformation matrix - Translation field, which I highlighted for you in the screenshot. In that example here I shifted all atoms upwards by 10 units.

-Constanze

computational

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Re: Moving atoms to the center of the simulation cell
« Reply #8 on: January 11, 2019, 12:01:41 PM »
Thanks....
It worked...