Tweak the unicode reading of chemkin comments.

Now we preserve crazy characters, but try to encode them
in utf-8, so that things downstream know what to expect
(unfortunately they're not all set up to handle Unicode objects)
Save small molecule matches to the SMILES.txt file
Now skips duplicate thermo entries when reading 
thermo blocks in chemkin files.
Make the path if it doesn't exist for the QM files.
Don't match small species more than once.
Don't trust thermo libraries used for thermo matching
enough to use them for RMG estimates.
Added a warning for very large thermo differences
on matches species.