Tidy/unify calculations options

[ElliottKasoar]

At some point before a first release, we probably want to do a pass over all the main calculations, including:

• [x] Possibly converting geom_opt and eos into classes
• [x] Consider the interaction and need for file_prefix and struct_name
  • In some cases e.g. eos, I think they may actually do exactly the same thing
  • I'd propose potentially removing struct_name as an option completely, unless there's a clear benefit, to simplify the setting of file names
• [x] Check other settings are consistent between calculations
• [x] Ensure outputs from ase.io.write are consistent with singlepoint (i.e. results in info, they may or may not also be saved in calc.results)
• [x] Change default output extensions to .extxyz