Warning messages not logged

[ojeda-e]

In surface.py, the messages "Atom outside grid boundaries" in lines 92 and 100 are not logged. The warning doesn't provide further or more detailed information about the atom, i.e. if it's because of negative coordinates, etc.

Thanks @orbeckst for spotting it (see review in notebook)

To fix this issue:

• [x] Add logger.warn(msg).
• [x] Edit message to provide more details.
• [x] Add respective tests.