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zerothi / sisl

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations
https://zerothi.github.io/sisl
Mozilla Public License 2.0
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Water tutorial is now wrong #698

Open pfebrer opened 7 months ago

pfebrer commented 7 months ago

When the wavefunction is computed in the water tutorial:

https://sisl.readthedocs.io/en/latest/tutorials/tutorial_siesta_1.html

It gives a warning of atoms not being in the unit cell and the wavefunction doesn't integrate to 1. Previously it was fine. I don't have time to look at it, but is it possible that the boundary conditions are now by default "unknown" instead of "periodic" and that is the reason behind this failure? I don't know if boundary conditions were introduced before the latest release.

zerothi commented 7 months ago

Looks like it was also present in the 0.14.3 release: https://sisl.readthedocs.io/en/v0.14.3/tutorials/tutorial_siesta_1.html

the boundary conditions got added just before 0.14.3.

zerothi commented 7 months ago

This could be the culprit https://github.com/zerothi/sisl/pull/634 I will have a look...

I think we should first define tests that should be correct, that would catch lots of these issues. E.g. how the handling of neighbours are handled.

jfaraudo commented 7 months ago

Hi. I did this tutorial with our undergrad students on 16-March-2023 and it was OK, so it has to be something that changed during this time. The comment by Pol makes sense to me.