Silence the CoreText PostScript warnings caused by profile graph generation.

On Mac OS X Mavericks, generating the PDF of the profile data generates a lot of 
warnings like this:
CoreText performance note: Client called CTFontCreateWithName() using name "Arial" and got font with PostScript name "ArialMT". For best performance, only use PostScript names when calling this API.
Refactor thermo reading in chemkin files.

Just moving the order of the if/else blocks, to reduce nesting.
Upgrade a few logging lines to warnings when reading chemkin thermo
Check for missing thermo and give better error message.

Closes rwest/RMG-models#26
Better handling and checking of console arguments

Closes rwest/RMG-models#10