I am working with Fluoro-Graphene (let's assume a fully relaxed monolayer on the XY plane with 16C-1F cell where the F is "covalently" bound to the graphene on top of it with respect to the z axis). I am currently using the 4.0.1 version of SIESTA and doing the post-processing with the 4.1beta4.

I am using (and comparing) both the VIBRA post processing module and the ASE extension to try and get IR active normal modes at the $\Gamma$ point and their respective intensities. With both the ASE module and the VIBRA extension, I can get the frequencies of all the normal modes (with high enough k-point sampling of course).

However, the modes I get with ASE, and their respective IR intensities, correspond much better to the literature and can be much better utilized to extract IR activity than the results of the VIBRA module. In fact, the BC (Born effective charge matrix) used by VIBRA to get these intensities is a null matrix making all the intensities for all modes null. This seems to be a glitch in the VIBRA tool since I have tried changing all the parameters (MESH PSEUDOS XC FORCE DISPLACEMENTS BASIS ...) and still get a null BC matrix.

Can anyone explain how VIBRA calculates the IR intensities in a more clear way than what is done in the SIESTA and VIBRA manuals? How does this differ from the way the ASE module calculates it?

I understand the chemistry and physics of the phenomena but not the computational "translation" of the concepts. I believe a lot of us struggle with this same problem

  • 1
    $\begingroup$ siesta is hosted on GitLab, so if you think its a glitch you can submit an issue report there. $\endgroup$
    – Tyberius
    Feb 15, 2022 at 17:35
  • $\begingroup$ @Tyberius thanks to your advice, it seems that the question has now been asked here. I was going to provide a link to this version on the GitLab thread but forgot which GitHub/email account is associated with my GitLab account haha. Perhaps if the developers at the Siesta GitLab know that the question is here, they might be more motivated to find an answer, due to the possibility to earn rep or bounties. $\endgroup$ Sep 2, 2022 at 21:44
  • $\begingroup$ I'm confused as to why I provided that link in my last comment. This is the link that I think I was intending to put. Sorry about that! I've also now provided a link to this question on that GitLab issue (still haven't been able to get my password for GitLab, but was able to log in through GitHub). $\endgroup$ Nov 1, 2022 at 19:52
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    $\begingroup$ Since it has been marked on GitLab, I'm closing for now since it seems like this functionality is not working yet in the code $\endgroup$
    – Tyberius
    Feb 6, 2023 at 19:54


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