Cannot read Hamiltonian with certain atomic coordinates about sisl HOT 3 CLOSED

Hi, thanks for reporting. Generally I would advice against using the HSX file format. It is incomplete is various ways. And if you are insisting on the exact same coordinates, then your only choice is to use the TSHS file format. Simply add TS.HS.Save to your fdf file, and use that file (you shouldn't need to change your script as the fdf file will prefer the TSHS file if present).

Lastly, some comments.

• performance wise it is better to do: denseH_arr = H.Hk(format='array')
• do not use numpy.matrix it is outdated.
• the above changes will be much faster! :)

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@Connor-Herring did it fix your problem?

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@zerothi Yes, thank you! I had been trying to write the TSHS before but it was not working. I realized it's because it only gets written if the scf loop converges and I was previously just running 1 step. Anyway, using the TSHS file is working for me now (with all coordinates).

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