Allow CanTherm to save multiple job outputs to chem.inp.

The resulting chem.inp will not be a complete Chemkin file, but will contain
snippets that can be easily moved into Chemkin files.
Change all Cython attributes marked readonly to public.

This allows us to compile RMG-Py again with the latest version of Cython
(0.19). Cython 0.17.x and 0.18.x still do not work because of another issue.
Despite the change, you should probably still treat these attributes as read-
only.
Updated the requirements.txt file for PIP

Only real change is requiring cython>=0.19
(0.16 works, but 0.17 and 0.18 don't)
Oh, and I added argparse and gprof2dot, for the profiling post-processing.
Besides that it's mostly rearranging and adding comments.
Fixed bug in reading of G3 energies from Gaussian log files.

Apparently the line to search for contains "G3(0 K)", not "G3 (0 K)". That's
what I get for assuming Gaussian is consistent I guess, since the equivalent
line for CBS-QB3 is "CBS-QB3 (0 K)'.
Fixed bug in Network.solveFullME() and Network.solveReducedME().

The total concentration was being calculated in cm^3/mol assuming the
pressure was in bar, since it was originally written when these were true.
However, RMG-Py uses SI units for things, however, so pressures are in Pa
and total concentration should be in m^3/mol. (These two effects very nearly
cancel, but not quite.)
Better error message when unable to determine atom type.

The new error message will now also show the number of each type of bond
that it identified, which is the key means of determining the atom type
besides the element.
Fixed another bug in reading of G3 energies from Gaussian log files.

"0 K", not "O K"
Fixed jacobian in terms of moles.  Added unit test.
Updated atom energies for CCSD(T)-F12/cc-pVTZ-F12

Adding atom energies for CCSD(T)-F12/cc-pVTZ-F12
model chemistry. Calculated by Caleb Class.
Merge branch 'master' of git://github.com/shamelmerchant/RMG-Py