I am trying to find the Kohn Sham Hamiltonian for a large supercell. Based on the band structure it all seems to work however zooming in the Hamiltonian contains a single atom which has 0 hopping to all neighboring atoms.

The calculation takes as input a relaxed structure of which this specific atom has a coordinate which is just above 1 in `atoms.speciesandcoordinates`. Specifically it is 1.000000466000000e+00. Can such a what seems rounding type of error in the input explain these obviously wrong 0 hoppings?

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Re: Hopping zero in Kohn Sham Hamiltonian( No.1 )

Date: 2023/05/18 08:16

Name: T. Ozaki

Hi,

Is the single atom far from the other atoms? Without knowing more about your system, it would be difficult to provide a constructive suggestion.