Phase/Magnitude of Transmission through Molecular Orbitals

[jalmeida]

Hello,

Please, How can I have access to the phase and transmission contribution of each molecular orbital in a molecular junction? I want to reproduce the pictures 6 and 7 of the paper <https://doi.org/10.1063/5.0141577>. I also attached the images from the paper.

Best,
Joseane

[Anders Blom]

There is a rather old explanation on how to at least project the transmission onto the MPSH states here:
https://docs.quantumatk.com/tutorials/low_level_entities/low_level_entities.html
I hope it still works, but perhaps some small changes in the code lately will require the utility script at least to be updated...

You will have to loop over the energy and record the contribution to the transmission from each MPSH state to make the plot.

The phase is defined the paper through the ratio of the real and imaginary parts of the projected transmission eigenvalues, as I understand it. By default, the transmission eigenvalues computed by QuantumATK are expressed in the basis of the original basis set orbitals (https://docs.quantumatk.com/manual/Types/TransmissionEigenvalues/TransmissionEigenvalues.html), so again one would need to perform a unitary transformation to the space spanned by the MPSH states. I'll check on the best way to do that.

Also see https://docs.quantumatk.com/tutorials/molecular_device/molecular_device.html#the-molecular-projected-self-consistent-hamiltonian-mpsh regarding how to obtain the MPSH spectrum.

[jalmeida]

Thank you very much, I understood the idea. I will do the loop and I am looking forward for the phase information. Here is my email if you need << joseane.almeida@univ-rennes.fr >>

[jalmeida]

Dear Anders Blom  ,

There is a rather old explanation on how to at least project the transmission onto the MPSH states here:
https://docs.quantumatk.com/tutorials/low_level_entities/low_level_entities.html
I hope it still works, but perhaps some small changes in the code lately will require the utility script at least to be updated...

You will have to loop over the energy and record the contribution to the transmission from each MPSH state to make the plot.

1) I projected the transmission onto the MPSH states using the files on the link you sent to me. Which kind of required updates you were talking about? I am working with single molecular junctions. First, I did a MPSH calculation to take the index of the molecular orbitals (MO) that I want to work with. Since my system is open shell, I just change in the inputs the spin for up/down if I want MO up/down.

2) And if I want to make this for a specific k-point (ka, kb), I just need to change the k-point in the python functions vectorToGrid() and scatteringStates() in the utilities.py file, right?

The phase is defined the paper through the ratio of the real and imaginary parts of the projected transmission eigenvalues, as I understand it. By default, the transmission eigenvalues computed by QuantumATK are expressed in the basis of the original basis set orbitals (https://docs.quantumatk.com/manual/Types/TransmissionEigenvalues/TransmissionEigenvalues.html), so again one would need to perform a unitary transformation to the space spanned by the MPSH states. I'll check on the best way to do that.

3) Please, How can I do this?

[jalmeida]

Please, Could you help me with this? Thanks in advance!