Check read() for consistency

[martin-schlipf]

Revisit the read functionality of the various Refinery classes and make sure they behave in a consistent manner. Make a decision when elements are included as None and when they are skipped. A general idea could be that data that is added via a selection input is added whereas if it depends on the VASP setup it is set to None.

[sudarshanv01]

Somewhat related, and writing here to make sure it is documented so I can take a look later: there is an issue with if not self._raw_data.cell.scale.is_none(): line in sturcture.py again. The issue is still the is_none() not applying to a numpy array where VaspData is expected.