Re: [Phonopy-users] negative frequencies, cp2k interface

[Kadioglu Ö. <ozg...@ep...>]

Hi,


Thanks a lot for your reply Togo.

Looking at the magnitude of the frequencies, I can say that they are not due to numerical noise from cp2k forces. I visualized the phonons in my system and saw that the negative frequencies are due to the vibrations of the benzene rings.

I am looking at the MODULATION tag right now, I understood how to create the tag however I am confused how to choose the q-points to use in the tag. When I use the full k-point path to create the band.yaml file, I have 612 q-points. For each q-position that i specify in the tag, there is one MPOSCAR file with the displacements.

Since I am interested in calculating heat capacities with harmonic approximation, I think I should be focusing on gamma point. Please correct me if i am wrong.

For each negative frequency (band index), I used the modulation tag (at 0, 0, 0) and produced structures with the atoms displaced in accordance with the corresponding eigenvectors. How am i going to proceed after this point? Now I have MPOSCAR files as much as the number of negative frequencies.

If i had one big negative frequency, I would optimize the new structure that I got from modulation tag, but now with 8 MPOSCAR files I got a bit confused about how to proceed. My question might be more related to the theory rather than the implementation of phonopy but I might be misusing the modulation tag as well.

I would be very happy if someone who solved that problem before can help me.

Thanks in advance!
Best,
Özge




---
Özge Kadioglu

Doctoral Assistant
Laboratory of Molecular Simulation (LSMO)
École Polytechnique Fédérale de Lausanne



________________________________
From: Atsushi Togo <atz...@gm...>
Sent: Friday, March 13, 2020 5:36:21 AM
To: phonopy-users
Subject: Re: [Phonopy-users] negative frequencies, cp2k interface

Hi,

This is the reply for the question about eigenvector corresponding to
the imaginary frequency.
A collective displacement of atoms may be written as
https://phonopy.github.io/phonopy/formulation.html#mean-square-displacement
In this equation, what you have to take into account to displace atoms
are, 1/sqrt(omega), eigenvectors, and phase factor exp(iqr). The
amplitude depends on phonon state, but the current purpose is to break
symmetry, so if your code can detect the broken symmetry due to the
collective displacement, it's OK.
You may be able to use this feature of phonopy,
https://phonopy.github.io/phonopy/setting-tags.html#create-modulated-structure.
Honestly I don't like this very much, but in some cases, this is
useful. You have to use this with understanding what you are doing.
In addition, the imaginary frequency may come from numerical noise of
cp2k forces. In this case, you may not obtain a good result that you
expect.

Togo

On Tue, Mar 10, 2020 at 1:04 AM Kadioglu Özge <ozg...@ep...> wrote:
>
> Hello,
>
> I am working on phonon properties of MOFs. There are some challenging structures that I constantly have negative frequencies for. I managed to decrease the number of negative frequencies by pushing the geometry optimization more and using K-points while optimizing on cp2k. However, I still had negative frequencies, then I did cell-optimization but afterwards the number of negative frequencies increased again.
>
> I checked the previous email threads, seems like I should check the eigenvectors corresponding to the negative frequencies. I did that by using --eigvecs tag and got the eigenvectors written in mesh.yaml file. But i do not know how to move on after this point. How do we move the normal modes with negative frequencies before trying a new optimization? If you have any other suggestion for me to check I would be very glad.
>
> Also, with the version 2.4.2, it takes much longer for the displacements to be created. It was only couple of seconds with the previous versions of phonopy, for a system consisting of 200-300 atoms, now it is 1-2 minutes to create cp2k input files with the displacements. May i ask why did it change significantly?
>
> PS: I am using phonon --cp2k interface.
>
> Thanks in advance.
>
>
>
> ---
> Özge Kadioglu
>
> Doctoral Assistant
> Laboratory of Molecular Simulation (LSMO)
> École Polytechnique Fédérale de Lausanne
>
>
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
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--
Atsushi Togo


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