Fixing bug of reading thermo from primamry thermo library

When the aromaticity code was changed the chem graph was copied
to a new copy called themo_graph however at that time we did not realize we
also needed to update the attribut to the chem graph like
the boolean is thermo coming from primary thermo library or not.

(Yay to weekly debugging :) )
PM7 for QM calculations on cyclics with MOPAC.
New error message thrown when QM method could not be determined.
Adding rate rules for addition of H rad to C=O both C and O sites
This was done using BMK/cbsb7 + 1D-HR in TS

15 minutes of debugging revealed some bad estimated for addition of H to C=O
Fixing bug for calculating flux when the reaction is given in a reaction
library

For bimolecular reactions coming from reaction libraries
RMG did not check the direction in which the reaction was given.
This led to incorrect flux being calculated.

In Reaction library B + C = A  k1
RMG finds reaction A = B + C
RMG old flux = k1 * [A]
Now it checks the direction and calculates the flux
RMG new flux = k1* Keq * [A]

We havent checked what happens in a pdep reaction!

It must also be noted that if in a reaction library,
duplicates reactions are given in different directions
then this fix will fail, since we only have one boolean
to check for every reaction instance !!
Updated rate coefficient for the reaction H2O + butadiene -> 2-butenol
New estimates from the GA method, older ones had problems with endo addition to conjugated double/triple bonds as those were estimated from the exo-additions
The problem was that exo addition to conjugated bonds is faster while a slowing effect is observed for endo.
Added new reaction in Diels Alder2
C#CC=CC=C -> cyc hexatriene
This might(?) be important for aromatics.
Turning "on" family Intra Diels Alder 2

This family is important for pyrolysis chemistry, large
alkane chains with multiple unsaturated sites can add
on the double bond to lead to rings eventually leading
to aromatics.

Note: Limited testing has shown this family not to break
current RMG usuage. If it breaks normal usuage for users
the default setting should be turned off
Updating rule for npropyl to ipropyl intraH migration

Calculated at CCSD(T)-F12/cc-pVTZ-F12 with 1dHR

Previous rate cofficient came from Sumathy calculation was
more than order of magnitude faster than current rate rule.

This rate affects whether you form H rad or CH3 in your system.
npropyl = CH3 + C2H4
ipropyl = H + C3H6
Correcting minor typo of references due to rearranging of rate rules
Added hydrogen abstraction reactions with allene and propargyl to the H abstraction family tree.
Updated the Diels-Alder additions to include additions of triple bonds to dienes. Calculated two rates for this and corrected on older value.
Adding rate coefficient for vinyl alcohol + propargyl from alcohol group

Method: CBS-QB3 (RRHO) will add hindered rotor corrections later

The reactions for which the rate rules were made are
CH2=CHOH + C#C[CH2] = CH2=CH[O] + C#CC
CH2=CHOH + C#C[CH2] = CH2=CH[O] + C=C=C
Changing head node value for Diels Alder Family

Most of the calculated rates have ~ 20-25 kcal/mol barrier,
SSM thinks the head node is too fast current as it set
barrier less ~ 5E+9. The rank of 0 is a special case
where the family is not averaged and every estimate defaults
to the head node (changing rank to 5 might change this back to 0).
Updating rate rules of di-allylic radical + allylic radical
for disproportionation family

Estimating rate coefficient for cyclopentadienyl radical + butadieneyl radical
NIST estimate for allyl + iso-butyl is 8E+11 at 1000 K, however in our
system the butadieneyl radical is also resonance stabilized
and it will be harder to break the bond to give butadiene +
cyclopentadiene. Currently estimate it to be a factor of 5 slower.

These calculations often require multi-reference calculations, for now I am
making my best estimate!
Modifying R_Addition_Multiple bond dictionary

The One_De nodes specified R as the other group which
means it could be another delocalized group. This caused
RMG not to descend down to correct node.

Example case is Fulvene + H would hit Cds-HH_Cds-OneDe , HJ
instead of Cds-HH_Cds-CdCd , HJ.
Introduced new reaction family for H shifts in cyclopentadiene type rings. 1 rate was taken from H shift in ethyleneCPD.
Fixing bug of reading in thermo for aromatic species in primary thermo
library

Since we converted the thermo_graph to B bonds it would not match the
chemgraph in the thermo library. The current implementation according to me
works this way

1) Create copy of chem_graph and store it in thermo_graph.
2) Check whether thermo_graph is aromatic and convert to B bonds.
3) If thermo_graph is aromatic chem_graph is also aromatic, set the flag.
4) Generate thermo for chem_graph, if this is coming from primary thermo
library then we are set, no need to generate thermo from the B bonded
thermo_graph.
5) If chem_graph is not coming from primary thermo library and chem_graph is
aromatic we need to generate the thermo on the B bonded thermo_graph

When chem_graph is not aromatic and has multiple resonance isomer
we need to check if thermo_graph is from primary library and also update the
attribute for the chem_graph.

Tested for Toluene, Fulvene
Porting over the changes found by Nathan script for Disproportionation
family

1) Made XH_rad more general