[CP2K-user] [CP2K:18641] normal mode analysis on an ab initio trajectory

[Francisco Gámez]

Dear all
What I frequently found with the NMA is that I the "normal modes
coordinates" in the molden file after TRAVIS evaluation might be Ok and the
IR spectra is remarkably good, but the visualization of the NM in MOLDEN
shows that the assignments are disparate and make no sense from a chemical
point of view and, obviously, do not match with DFT calculations. Does
somebody has some tips to get correct mode assignment from the BOMD
trajectory?
Kind regards

El sáb., 8 abr. 2023 0:43, Lucas Lodeiro <elunicolomo at gmail.com> escribió:

> Dear Emma,
>
> AFAIK compute the IR spectra through dipole (Berry phase), Wannier or
> Voronoi integration must result in almost the same spectra, I remember Dr.
> Brehm shows the unique difference between them is the relative intensity
> between peaks.and Wannier could be problematic sometimes when there is high
> symmetry. So there is no problem. BTW, you can compute the properties of
> your trajectory using the REFTRAJ option in the MD.
>
> About the IR spectrum on TRAVIS, it can be computed with Voronoi
> integrated electron density (which currently can be done directly in CP2K
> on the fly), with fixed charges or fluctuating charges calculated along the
> AIMD. I used the last one with self-consistent Hirschfeld charges and it
> worked very well.
>
> But the point is, with just your trajectory you can compute the power
> spectrum which can show you some "missing" signals in IR (maybe), and the
> NMA without problem. The other spectral properties need electron densities
> and more.
> In the program, the NMA is called NC (normal coordinate analysis) . When
> the "List of functions" is displayed, in the Spectroscopic Functions
> section there is "nc". This is what you need. Then you need give some
> information and feed with the conrformer's structures (previously optimized
> at the same level).
> I suggest computing first the power spectra with TRAVIS and
> "optimize/play" with the variables and become familiar with them (the
> defaults are good, but sometimes a little change can upgrade the spectrum),
> because for the "nc" the same procedure is done + the reference structures.
>
> Finally you will have something like this:
>      Mode         Integral (K)       Center (cm^-1)
>      ----------------------------------------------
>         1            -0.112446              2735.82
>         2           -0.0757895              1377.51
>         3           -0.0508332               529.47
>         4          -0.00656595               615.81
>         5            0.0120252               542.87
>         6             0.177628              1415.45
>      ----------------------------------------------
>         7                327.5               528.37
>         8              335.364               535.27
>         9              338.557               561.62
>  ...
>        23              319.248              2958.93
>        24              330.046              3163.23
>      ----------------------------------------------
>
> Which list the modes frequencies and their thermalization... The mode
> temperature must be similar to the AIMD mean temperature (the first six
> must be near zero)... and a molden file is printed with the normal modes
> for each reference structure where you can see them. The normal mode
> frequencies must be similar to the peaks in the power spectrum.
> In my experience when a time step over 1fs is used the nc starts to
> fail... also if you have the velocities "trajectory" you can use it (with
> -vel option) to obtain a better velocity autocorrelation function when the
> time step is equal or bigger than 0.5fs.
>
> If you have doubts or need help do not hesitate to write to me, I am not
> an expert but I can help or learn on the way :P.
>
> Regards - Lucas
>
> El vie, 7 abr 2023 a las 6:59, Emma Rossi (<emma.rossi.1 at studenti.unipd.it>)
> escribió:
>
>> Dear Lucas,
>>
>> Thank you very much for your suggestion. I obtained the IR spectrum
>> through the dipole moment of the whole box computed at each step of the
>> trajectory by CP2K. Unfortunately, I couldn't use TRAVIS since I had not
>> printed the electron density during the simulation.
>>
>> However, it would be great if I could use TRAVIS as post processing tool
>> to perform NMA on the trajectory. As far as I have seen in the
>> documentation,  the online tutorials/presentations deal only with the
>> simulation of the spectra, which, indeed, require electron density. I
>> couldn't find any instruction about how to perform the NMA (I've found just
>> the original paper).
>>
>> However, if you have expertise in TRAVIS usage, I would be very grateful
>> if you could answer a doubt about TRAVIS NMA tool.
>>
>> Can I perform NMA on my trajectory without performing as a preliminary
>> step the calculation of the IR spectrum? As I mentioned above, I have not
>> the electron density.
>>
>> Thank you very much for your kind support.
>>
>> Best regards,
>> Emma Rossi
>>
>>
>>
>>
>>
>>
>> Il giorno giovedì 6 aprile 2023 alle 23:59:45 UTC+2 Lucas Lodeiro ha
>> scritto:
>>
>>> Hi Emma,
>>>
>>> I do not know how you managed to obtain the IR spectrum from your
>>> trajectory, but I suggest the TRAVIS program to do it:
>>> http://www.travis-analyzer.de/
>>> There is many ways to accomplish it, and the results are very good.
>>> Also, there is the possibility to obtain the "normal modes" of the
>>> trajectory which are consistent with the trajectory IR/Power spectrum.
>>> There are some tutorials, and the program is self explaining:
>>> https://brehm-research.de/spectroscopy.php
>>>
>>> In the normal modes section you can feed the program with one or more
>>> minimum energy conformer where the trajectory is projected, and
>>> approximated normal modes are obtained.
>>>
>>> Regards - Lucas
>>>
>>> El jue, 6 abr 2023 a las 14:21, Emma Rossi (<emma.r... at studenti.unipd.it>)
>>> escribió:
>>>
>>>> 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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