how to get the data of vibration eignvectors ?

[berlin]

We can use "Vibration Visualizer" plugin to see the vibration eignvectors. But how to get or save numerical data of vibration eignvectors ?

What i can do now is to read the nc file, and  get some data from "VibrationalMode_gID00*_eigenvectors_real"  and "VibrationalMode_gID00*_eigenvectors_imag". However, I do not know the units of those data. It sames not be  Angstrom. And more, those have been divided by sqrt(mass_of_atom) or not?

[Jess Wellendorff]

You should use the "eigenvectors" method of the VibrationalMode analyser: http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.vibrationalmode.html. The returned eigenvector is the solution to an eigernvalue problem involving the Dynamical Matrix, so please also see the documentation for the DynamicalMatrix analysis object: http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.dynamicalmatrix.html

[berlin]

I got the method from the first url:

mode(mode_index, temperature): Return the vibrational mode with the specified mode_index. The eigenmode,v, is obtained from the eigenvectors,u, as v = u/sqrt(M)*s, where the scaling factor s = sqrt(kB*T)/omega gives the amplitude of a classical oscillator with frequency omega.

But the scaling factor is defined as
s = sqrt(kB*T)/omega
which may only make sense when kB*T >> omega,

For low tempture, any suggestion？

[Jess Wellendorff]

"s" is just a scaling factor for all the eigenmodes, which is useful for visualization purposes. You may scale all your eigenmodes by some constant, they will still be the vibrational eigenmodes.