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About periodic display issues

Sorry to bother again,I have a issues about periodic display images. I need a image like upload file Picture 1, in the Picture 1, outside the red box is an extension of the periodic structure. I use the Modification function of the Show periodic images in Ovito, the result shows in upload file Picture 2, I don't know why it's not a complete periodic connection, and there are blank space between periodic structures. I want my periodic sturcture like Picture 3. What should I do? I'm waiting for your reply, thanks!

Uploaded files:
  • Picture1.jpg
  • Picture2.jpg
  • Picture3.jpg

Hi HaoYuan,

you are importing data from an xyz file, right? In case you are not using the “extended xyz” format where the correct cell information is included in the header, ovito guesses the cell parameters from the positions of the outermost atoms. I assume this is what causes your problems with the periodic boundary conditions.

Please manually specify the correct cell parameters in ovito by e.g. first adding an Affine Transformation modifier to your pipeline. Alternatively, you should consider switching to the extended-xyz file format for your data, where the header contains additional information like the simulation cell. This may look like this:

Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.0 5.44"

Please see https://libatoms.github.io/QUIP/io.html#extendedxyz for more details on this file format.

Does that work for you?

-Constanze

okay, I will try it, thanks a lot!

Hi Constanze,

I have tried it, it is ok! If I import an xyz file with thousands of steps, that mean I want to observe a dynamic process, do I have to change the second line of each step to 'Lattice=xxxx', to observe the periodic extension of the entire dynamic process? Is there any other simple method?

Thanks for your reply!

Hi HaoYuan,

yes you would have to do that, but there is a trick:
Now that you've imported that information for the first frame, you can simply add an Affine Transformation modifier to your pipeline (while the first frame is the currently visible frame in the GUI) and choose the options "Transform to target box" and "Operate on" --> Simulation Cell. The cell vector parameters should already be correctly filled out and will now be valid for all other frames too.

-Constanze

It's ok!  Wow! What a great software!Thanks for your help!

Best wishes to u!

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