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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