Items for source code cleanup

[neil-glikin]

Very roughly in order of priority

• Standardize docstring format
  • Getters/setters: Describe only in terms of struct.field, and let struct's documentation do the rest?
  • How to format explanations of inputs and outputs
  • When to include type of output
  • Sentences?
• Decide what outputs for print/show of IonSim structs should be like
• Decide how to organize files
  • Do different methods of the same function go together or can they be separate? E.g. energy
  • How to mark off sections of files (eg ###### general functions #######)
  • Ordering of stuff like import and export statements in a file
• Make argument variable names for functions consistent
  • (eg prefer ion::Ion over I::Ion)
  • There are still several instances of T standing for a Chamber
• Error messages
  • When/how should they be thrown?
  • Formatting of error messages?
• Use more checks
  • Make sure Ions/Lasers aren't put into different Chambers
• Add sources for all constants (both general and species-specific)
• Have a philosophy on default values in IonSim code. E.g.:
  • An empty Laser construction has a polarization and wavevector already, but wavelength must be set manually
  • VibrationalMode N=10 by default
• Change comments to only be 93 characters(?) long
• Make speciesproperties only a function and not a field of Ion
• Change tests to utilize new style (e.g. instead of chamber.iontrap.ions, use ions(chamber))
• Find a way to stop formatter from enforcing spaces around all operators?