fix species_to_dict function to use correct parameter as reaction species

[ntietje1]

Motivation or Problem

The yaml_writer_addition branch no longer correctly adds reaction species to the Cantera yaml output file. Species block is always a list of nulls. This issue originated during a rebase of the branch.

Description of Changes

• changes to rmgpy/cantera_.py:
  • species_to_dict() method updated to correctly use the parameter obj as the RMG species object.

Testing

Tested on minimal example and minimal_surface example (minimal_surface errors unless commit feb70e2 is reverted/fixed)

Reviewer Tips

Comment out the temporary "raise exception" calls in to_cantera_kinetics() to test on any example that requires this method.

[ntietje1]

Yes, I agree the variable names are confusing. All of the function parameters are unused besides obj, so I would think they could be removed and obj renamed to species?