error: mass density is Nan when atom types are not recognized

See ISSUE in atomistic parsers for more information.

The mass_density is calculated in normalizing/common.py. The problem is that when atom types here are unknown, and the summed mass is returning Nan from the atom_utils.py function. We need to implement an alternative route in case the atom types are unknown which checks method for the masses and uses those instead. I would argue that this should actually be the default method, since models can be made which purposefully adjust the mass of atoms.