Tweaks to PDep convergence checking.

Only compare numerical values if you're looking at the same reaction,
and correct the thresholds so that slight worsening is allowed near the start.
Change badness definition to max abs log error.
Add __reduce__ method to rmgpy.rmg.pdep.RDepReaction (for pickling).

Hopefully closes #114
Check restart file exists near start of --restart job.

This should save some time.