Updated atom energies for CCSD(T)-F12 jobs

Previous bond energies were calculated using
the F12b method,updated them to now use the F12a energies.

These energies have been provided by Caleb Class
and Beat Buesser.
Add corrections for various model chem in cantherm

All these values are still a work-in-prgress obtained from Beat.
However, the recent updates for cantherm made by Shamel and I are a bit
incomplete without these.

Atomic energy corrections are provided for:
CCSD(T)-F12/cc-pVDZ-F12_H-TZ
CCSD(T)-F12/cc-pVDZ-F12
CCSD(T)-F12/cc-pCVDZ-F12
CCSD(T)-F12/aug-cc-pVDZ
B-CCSD(T)-F12/cc-pVDZ-F12
B-CCSD(T)-F12/cc-pCVDZ-F12
B-CCSD(T)-F12/aug-cc-pVDZ
DFT_ks_b3lyp
MP2_rmp2_pVDZ
MP2_rmp2_pVTZ
MP2_rmp2_pVQZ
CCSD_DZ
CCSD_TZ
CCSD_QZ
CCSD_core_DZ

Bond energy corrections were added for CCSD(T)-F12/cc-pVDZ-F12

Additionally, there were bug fixes and additional unit tests for the
Molepro parser.
Tidy up thermo comments in chemkin files.

-Removed unecessary declaration line '! Thermo Comments:'
-Added 'Thermo library:' label to thermo originating from thermo libraries.
-Removed the NASA fitting to Wilhoit comments because they clutter up the comments
Tidy up kinetics comments in chemkin files.

-Removed unecessary declation of '! Kinetics comments:'
-Fixed labeling of exact rate rule matches (was falsely labeling some kinetics
as estimates when they were actually exact matches)
-Removed extra line with reaction string using original names.  The chemkin
reaction string should be sufficient.
-Removed line commenting on flux pairs (generates clutter and not super useful)

Concern:
- When merging RMG models together, a lot of comments will be duplicated.
This should be fixed later.
Added Chlorine to allowed atoms for Cantherm.
Fixed transcription error for Sulfur experimental enthalpy of formation at 0K.

Now matches http://www.gaussian.com/g_whitepap/thermo.htm
Cantherm: added energy corrections for Chlorine for CBS-QB3 methods.
Added BAC for H-Cl bond for CBS-QB3 method.
Adding Chlorine to the allowed atomtypes for RMG-Py.

Can now add species including chlorine to your input files either
using smiles or adjacency lists.  RMG families currently cannot handle
chlorine, but they can be added as either inerts or reactive species
if a reaction library is given.
Fixed bug of mutating reactionDict list, causing large memory spikes.

Due to extending my_reactionList with ownReverse reactions, we were mutating
the reactionDict on accident.  This led to my_reactionList having billions of
reactions when there should only be around 10 reactions.  We saw huge
memory spikes due to this.
Fix missing variable reference in rmgpy.data.kinetics.groups
Always add training reactions to the rate rules, unless explicitly told not to.

Unless the user specifies '!training' in the kineticsDepositories list within
the input file, always add training reactions to rate rules automatically.
Store entry history taken from training reaction when saving to rate rules.

Store the new rate rules directly with the original rate rules.  Not sure what
the previous saving to self.entries did, as when running RMG-Py jobs they would
not pick up the training reactions but instead picked up averaged rates,
see https://github.com/GreenGroup/RMG-Py/issues/150
Clean up kinetics comment for averaged rates.
Save the group objects of the training rate rules so they display on website.

Also save the products of rate rules as empty lists instead of None
to not mess up website.
Indicate the training reaction where the rate rule originated from.
Documentation: added features and credits pages to RMG section.
Documentation: input file creation for RMG-Py.
Added framework for RMG user's guide.
Documentation: Add RMG theory guide.