Author Topic: Is it possible to fix the positions of select atoms during a trajectory?  (Read 14 times)

Jc112358

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I have a nudged elastic band run that I'm looking into rendering for a paper. However, during the run, several atoms along the periodic boundaries get wrapped to the other side of the cell. I'd like to render a movie of the reaction without this wrapping occurring. Is it possible to fix the positions of the wrapped atoms in Ovito, to correspond to their positions in the first image?

Alexander Stukowski

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Re: Is it possible to fix the positions of select atoms during a trajectory?
« Reply #1 on: February 15, 2018, 08:29:10 AM »
Hi,

Yes, unwrapping the atomic coordinates can be achieved, but it's complicated:

  • First, go to frame 0 of the sequence and make a copy of the current atomic positions using the Freeze Property modifier. Name the copied property "pos0", for example.
  • Use the Displacement Vectors modifier to let Ovito compute the atomic displacements with respect to the initial positions. This is where the minimum image convention comes into play.
  • Finally, use the Compute Property modifier to overwrite the values of the Position property. For the X component, enter the expression "pos0.X+Displacement.X". For the other two components, do correspondingly.