Water tutorial is now wrong

[pfebrer]

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]

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]

This could be the culprit #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]

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.