Basically, to be able to simulate electronic transmission through a molecule we use the retarded greens function. So far we are able to simulate the transmission through pi-bonds, but to extend our simulation to transmission through more than just the pi-bonds, we want to use the extended huckel approximation as done by Kienle et al. (Extended Hückel theory for bandstructure, chemistry and transport. I. Carbon Nanotubes). For that we need to use the hamiltonian and overlap matrices calculated by this approximation. We mainly use python scripts for our physics computations and were therefore interested in RDkit. Is there another way to access yaehmop through python on a windows machine and get the hamiltonian and overlap?
Here you can see how our VR platform looks so far: https://www.youtube.com/watch?v=_tIIjYkpzHw Regards Zan ________________________________ Fra: Greg Landrum <greg.land...@gmail.com> Sendt: 13. februar 2020 09:25 Til: Zan Mahmood <s181...@student.dtu.dk> Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net> Emne: Re: [Rdkit-discuss] Extended Huckel Matrices Hi Zan, On Wed, Feb 12, 2020 at 7:57 PM Zan Mahmood via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> wrote: I am currently working on developing a Virtual Reality simulation platform for nanosystems. So far we are able to compute electron transmission through 2D structures consisting of Carbon, but want to extend the capabilities using Extended Huckel. As, there is no manual for usage of Extended Huckel through RDkit in python, i would like to know how one can compute the hamiltonian and overlap matrices of a structure? yeah, there's no real documentation about this (yet) aside from the blog post I did last summer: http://rdkit.blogspot.com/2019/06/doing-extended-hueckel-calculations.html I'm still trying to decide what the most useful information is to provide through the RDKit interface and at the moment it's pretty minimal: You currently don't have access to the hamiltonian or overlap matrices from Python. That's also not something I was planning to support (since those are really the input to the calculation). I'm curious what you would want to use them for? Best, -greg Regards Zan _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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