Reworked file organization so it all makes more sense

[nateharms]

Changes:

• Created a job folder that contains:
  • job.py
  • submit.sh
• Created a data directory that contains the following:
  • base.py
  • update.py
  • io.py (for saving kinetics results)
• Renamed calculators to calculator
• Renamed calculators/calculator.py to data/io.py
• Added documentation to all files
• Changed imports to accurately reflect changes

Ran a few of the submit scripts that I use for discovery to assert that this works. (Still need to make unit tests)