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