Molecular Energy Spectrum

[Jahanzaib]

I've attached the output file for my system - Fe on the surface of nanoribbons. In output, I have energies with occupation and spinup/down.

I'm interested in plot MO diagram. Is there a way in quantumatk or I need to used python or any other way. Please guide me

[Jahanzaib]

This is MES for fe orbital, and I don't have an idea - how to interpret this. I have already attached output of this in previous message. Guide me

[Anders Blom]

What you are seeing are the molecular orbitals of the assembled molecule. You could compute the levels of the isolated atoms and compare, but generally this only makes sense for very simple molecules, and mostly for educational purposes (cf. https://chem.libretexts.org/Courses/Saint_Marys_College_Notre_Dame_IN/CHEM_342%3A_Bio-inorganic_Chemistry/Readings/Week_3%3A_Metal-Ligand_Interactions_continued..../3.3%3A_Molecule_Orbital_(MO)_Theory/3.3.4%3A_Assembling_a_complete_MO_diagram).

The system you are looking at is not really molecule, so what you trying to learn from the MO diagram? Probably there are other ways to plot/compute that information.

[Jahanzaib]

Thank you Prof. Blom for your response.

I have computed transmission spectra(TS) and DDOS, so I want to compare which peak in TS is associated with which energy level and similar for DDOS? I have already calculated the MPSH for that but could not figure it ?

I also followed the tutorial of Molecular devices (https://docs.quantumatk.com/tutorials/molecular_device/molecular_device.html) but I couldn't figure out

- when MPSH with Atom indices (37,38,39,40,41,42,43,44,45,46) are computed and in next step why quantum number 13, 14, 15, 16 were chosen?

[Anders Blom]

In the tutorial, the point is that the transmission occurs through some particular orbitals of the molecule. I am not sure that is applicable to your situation, it sounded more like you had an ad-atom (Fe) on top of a 2D sheet? Of course could compute the energy spectrum of the Fe atom in the presence of the ribbon (that is what the MPSH will give you). The atom indices for the MPSH define what the "molecule" is (in your case a single atom), where the quantum numbers select the eigenstates of the "molecule".