FIX: Improve Model instantiation

[bocklund]

Two changes here:

1. instantiate_models now returns a dict instead of a default dict to be more explicit. Only phases passed to instantiate_models are included.
2. Fixed a subtle bug in calculate where over-specified models could have led to inconsistent maximum internal degree of freedom between calculate and starting_point because calculate based the internal dof size on all the model instances, while starting_point used the phase records (active phases only).