When searching for polycyclic ring correction, select correction covering most atoms

Polycylic correction should use the largest possible ring correction found.
Overrides previous usage which was to find the deepest stack, which then gave
reproducibility errors when there are two group values of the same depth and
RMG chooses the first one it finds (random).
When searching for polycyclic ring correction, select correction covering most atoms

Polycylic correction should use the largest possible ring correction found.
Overrides previous usage which was to find the deepest stack, which then gave
reproducibility errors when there are two group values of the same depth and
RMG chooses the first one it finds (random).
New JP10 library JP10calculated = older JP10seedmech + JP10
Merge branch 'aaron' of https://github.com/agvandeputte/RMG-Java into jp10
Fix printing of thermo comments in output files.
Flagged out one of the older cycloaddition rate rules.
Added one rate coefficient to JP10BetaScission Library. JR5BS2
Updating rate rules for intra H migration from alkoxy radical

Rate rules derived from following reactions at BMK/cbsb7 level

CH2OH = CH3O,

CH2CH2CH2OH = CH2CH2CH2O
Updating rate rules for beta scission of alpha-Hydroxyethyl
Correcting rate rules which were incorrectly assigned when the tree was
restructured

Because we merged in Aaron's tree it caused butanol rate coefficients were
now assigned to butene system instead. SSM had used website to figure out
where rate rules should go and had defined it in a more general definition
instead I should have made a more specific node in the first place to avoid
confusion and errors like these.
Small corrections to database, adding some reactions from the JP10rxnlib to JP10calculated
Changes in database to account for O and O2 addition to double
Keto enol reaction family
Cyclic ether formation updated
B-scission in birads
H_Abstraction prepared for merging with AG Vandeputte database
Small changes to databases:
- recalculated one of the polyring corrections
- R_Addition_Multiple bond got rid of O=O
Intra_H_migration same approach as for other intramolecular reactions (thermodynamic consistency)
Reversed some changes made priorly:
- recognition of Cb bonds (problems with radical sites that did not loose their free electron when converted to Cb)
- QM on polycyclics: we recently added a feature to do QM on bicyclics (even when rings are not fused) but results indicate
that in particular for saturated rings, QM underestimate the enthalpy of formation with ~10 kcal/mol
Merge branch 'aaron' of github.com:agvandeputte/RMG-Java

Conflicts:
	databases/RMG_database/kinetics_groups/H_Abstraction/dictionary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/tree.txt
	databases/RMG_database/kinetics_groups/Intra_R_Add_Endocyclic/rateLibrary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/rateLibrary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/tree.txt
	databases/RMG_database/kinetics_groups/families.txt
	databases/RMG_database/kinetics_groups/intra_H_migration/rateLibrary.txt
	databases/RMG_database/kinetics_libraries/JP10BetaScission/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10calculated/species.txt
	databases/RMG_database/thermo_libraries/JP10/Dictionary.txt
	databases/RMG_database/thermo_libraries/JP10/Library.txt
	source/RMG/jing/chemUtil/Graph.java