Removing lingering references to LenardJones class

Cantherm was failing because it was still refering to LenardJones
class which is now removed after the transport branch has been merged.

Made the writing of output of measure also consistent to use
TransportModel
Fix to make standalone Cantherm work

Commit 5c4a2da0aec8e7abcc0153e4bfd62f84fe9f88d6 would
modify the label in the input file causing Cantherm to crash
when its trying to calculate kinetics for that reaction.
Fix typo in function name convertInitialKeysToSpeciesObjects
Save mole fractions instead of concentrations (easier comparison with chemkin)
Do not compute reverse rate coefficients in solver if the rxn is irreversible.

Apparently we were still considering reactions as reversible even when
they are irreversible.
Bug fix for internal mode projection for Cantherm

We were not following the Gaussian white paper formulae and this resulted
in some cases where our projection was completely wrong.

This bug fix has been provided by @agvandeputte
Correcting the ZPE after projection

After projecting the hindered rotors we need to recalculate the ZPE
according to the projected frequencies. Since  'ideally" only the modes with
a small wave number are projected out this should not be that different from
the ZPE coming before projections.
Merge branch 'master' into cantherm

Conflicts:
	rmgpy/cantherm/statmech.py