[CP2K-user] [CP2K:19680] normal mode analysis on an ab initio trajectory

[Lucas Lodeiro]

Hi Matthew,

To run the normal coordinate analysis you have to feed TRAVIS with the
trajectory file and the velocity file if you have it (this is just an
option to avoid numerical differentiation, which introduce some errors).
Running the normal coordinate analysis needs the same procedure as the
power spectra calculation. In the middle of run, TRAVIS ask you for a
reference structure: AFAIK this structure must be written in the same atom
order as is in  the AIMD  molecule atomic order, and the structure must be
optimized at the same level of theory. With it you can complete the
calculation. Some comments, if your molecule has many and pretty
different accessible conformers, this could be a problem. Also take into
account that hydrogen bonding active modes cannot be protected properly on
one molecule, because those are collective modes.

Also if you want to check from which molecule is the normal mode in the IR,
you can compute the power spectra for the whole system, and also for each
molecule type. This also can be done for the IR, so you can check which
molecule contributes to a given signal... but you cannot know how is that
normal mode, for that you need the normal coordinate analysis.

Regards - Lucas Lodeiro

El mié, 6 dic 2023 a las 2:02, Matthew Graneri (<mhvg1994 at gmail.com>)
escribió:

> Hi Luca,
>
> I'd be happy to give it a go, but I would still like to get the normal
> coordinate analysis from TRAVIS working first, considering that's what I
> generated my IR spectra with. I could definitely use your program as a
> validation/verification method, though. I imagine my systems (there are
> three) would be a good test case, to see how robust your program is.
>
> Perhaps get back to me when the article gets published? There's another
> paper I need to publish before I can start working on this one, so there's
> no serious urgency. Plus, I'm still trying to work out what the AIMD data
> is telling me—this is the only AIMD work anyone in my department (possibly
> the entire university) has ever done, so I'm flying blind (people have only
> ever done proper ab initio/DFT or MD calcs here), so I'd really value any
> advice on getting the normal coordinate analysis on TRAVIS to work...
>
> Regards,
>
> Matthew
>
> On Tuesday, December 5, 2023 at 8:30:17 PM UTC+8 Luca wrote:
>
>> I am currently developing a procedure to resolve complex vibrational
>> spectra. Although the procedure is not yet freely available, and the
>> related paper is currently under review, I can provide you with the
>> preprint of the article. Additionally, I am willing to apply the software
>> to resolve your computed spectra. I am looking for some applications.
>>
>> The procedure requires Cartesian coordinates and velocities from a cp2k
>> molecular dynamics (MD) simulation. The vibrational density of states
>> (VDOS) is calculated from the Fourier transform of the velocity
>> autocorrelation function, obtained by processing ab initio (DFT) molecular
>> dynamics simulations.
>> Within this framework, I have developed a computational tool designed to
>> assign the vibrational mode associated with a specific frequency. The
>> method involves projecting velocities along a specific set of internal
>> coordinates, such as stretching or bending, to calculate a partial VDOS
>> (pVDOS). This partial VDOS accounts only for the vibrations associated with
>> the selected set of internal coordinates. It aids in the interpretation of
>> the total VDOS and the experimental spectra in a meaningful way.
>>
>> Cheers,
>>
>> Luca
>> Il giorno martedì 5 dicembre 2023 alle 12:41:00 UTC+1 Matthew Graneri ha
>> scritto:
>>
>>> 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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