[CP2K-user] [CP2K:19630] normal mode analysis on an ab initio trajectory

[Matthew Graneri]

Hi Lucas,

Sorry for resurrecting this issue, but I'm in a similar situation to Emma, 
trying to run the normal coordinate analysis through TRAVIS and am 
absolutely stuck. I get up to the question asking for the reference 
structures and, when I specify the file containing my reference geometry, I 
get told: 'Some atoms are not connected to this molecule // Molecule 
recognition failed'.

My AIMD simulation contains several different molecular species, and I am 
trying to work out which peak corresponds to which vibration for each 
molecule in the system. I've tried using a normal .xyz file containing only 
the molecule I want TRAVIS to analyse, and I've tried using an .xyz file 
containing the entire system from the simulation, but nothing has worked.

The only thing I can think of that might be an issue is that I'm using the 
.emp files from the IR spectrum simulation as the input for the analysis. I 
can't think of what other file TRAVIS would like, though...

If you (or anyone else) has any idea why the analysis might not be working, 
I would very much appreciate any advice you can provide!

Regards,

Matthew

On Monday, April 10, 2023 at 4:26:03 AM UTC+8 Francisco Gámez wrote:

> 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 <eluni... 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.r... 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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