Rename IonSim structs

[marwahaha]

see also #73

There was a discussion about renaming the structs involved. Currently, this is how it works:

• Ion (responsible for the parameters of each ion involved)
• IonConfiguration (responsible for how the ions are stuck together)
• Trap (the entire apparatus!)

If we add multi-species chains and other tools, the proposal was to rename the structs to reflect what they ``actually'' do.

KM suggested:

• IonConfiguration -> IonTrap
• Trap -> Chamber