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Calculation of vibrational power spectrom

I am interested in a feature that can:

  1. detects the particles on an interface;
  2. calculates  the velocity correlation on a dump file which includes velocities in three directions;
  3. outputs the FFT on step#2 until a certain frequency;
  4. can smoothe the graph.

Hi Dourna,

Thank you for your inquiry. OVITO doesn't provide a built-in function yet to readily deliver all these outputs, but in principle it should be possible to develop a solution without too much effort using OVITO's Python scripting capabilities. We can help you with that if you like.

The Construct Surface Mesh modifier of OVITO provides a function to identify all particle on the surface of a solid. So perhaps this feature could be used to select particles at an interface too -- if there is a way to select and remove all particle on one side of the interface. Please tell us more about the kind of interface you are dealing with.

We have furthermore developed a OVITO Python script for efficiently calculating the velocity auto-correlation function (VACF) from an MD trajectory, ensemble-averaged over the entire trajectory and partitioned into XYZ vector components. It appears that this script, which we would be willing to share with you, solves problem 2 on your list.

Step 3 will require extra development effort. The FFT can probably be done using NumPy functions applied to the VACF data.

I'm not sure what step 4 will entail. Again, one can likely make use of NumPy/SciPy tools to perform a smoothing of the noisy data series if this is what you want.

-Alex

Would it be possible to make the VACF script discussed above public so others finding this thread can refer to it?

Thanks,

Matt

Hi Matt,

We are currently working on finding an appropriate solution to collect and publish scripts like the one mentioned above. Since you are a licensee of OVITO Pro, I will reach out and send it to you via email if you like.

-Constanze

Dear Dr. Stukowski and Dr. Klacher,
Thanks a lot for all the effort devoted to developing ovito and the support given through this forum.
I would like to know where I can find the script to calculate the VACF from ovito?

Thanks and best regards,
Achraf

Dear Achraf,

We haven't made this script publicly available since it is not in a general form that can be distributed without custom support. Let me reach out to you through via email.

-Constanze