[CP2K-user] [CP2K:18625] normal mode analysis on an ab initio trajectory

[Giacomo Melani]

Dear Emma,

You can certainly do a vibrational analysis through the standard input for
such calculation (
https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html).
That will read your selected configuration and perform a diagonalization of
the Hessian matrix to extract the corresponding normal mode frequencies and
eigenvectors. This type of calculation will read a specific geometry. It
can also provide you additional information, like IR/Raman intensities, but
that requires the calculation of transition dipole moments and
polarizabilities.

However, if you already have an AIMD trajectory, you might also want to do
a vibrational analysis by computing a time correlation function. For
instance, you can extract a vibrational density of states by calculating
the time-autocorrelation function of nuclear velocities. For sure, the
combination of NMA and correlation functions will give you the best
assessment of vibrational modes in your system.

I hope this helps.

Best,

Giacomo Melani

Il giorno gio 6 apr 2023 alle ore 12:21 Emma Rossi <
emma.rossi.1 at studenti.unipd.it> ha scritto:

> Dear all,
>
> I would need to assign the bands of an IR spectrum, obtained through AIMD
> simulation.
>
> I would like to perform a normal mode analysis (NMA) on the trajectory I
> have already produced to properly take into account solvation effects as
> well as the correct weight of the sampled conformers.
>
> I guess I could do so retracing the traj.xyz and using the vibrational
> analysis section in the input, but I would be very greatful if you could
> clarify a few issues about this strategy:
>
> 1) is it the most efficient and correct way to do NMA over a trajectory or
> do you suggest any other ways?
>
> 2) how the output with eigenfrequencies and eigenvectors should look like?
> I can figure the typical output for NMA on single configurations, but I
> have no ideas of what should I expect for NMA on trajectories (I suppose
> that the hessian will be diagonalized at each step, but how these info will
> be put together at the end of the process? )
>
> I have read the original paper of CP2K and the pdf presentations available
> online, but I couldn't fix my problem.
>
> I am very willing to understand and learn from anyone who will help.
>
> Thank you very much in advance for your support.
>
> Best regards,
> Emma Rossi
>
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