Correcting Alkene+OH addition rate coefficient. Mirror of https://github.com/GreenGroup/RMG-Java/commit/dcea2490a23e64ee1292bc80a544a197e66d7abf

The previous estimate was x10 too fast, not sure what went wrong.
Probably when I flipped it using the thermochemistry it resulted
in an error. Replacing the rate by Zador et al. propene + OH
rate coefficient.
Rate rules for intra H migrations.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/32e6b3c8c8ecea2cc6025f513815085f880ac1b3

Mainly related to the currently discovered pathways to benzene
from butadiene + allyl.
New estimates from GA method for Intra_R_Add_Endocyclic family.  Partial mirror of https://github.com/GreenGroup/RMG-Java/commit/baa353ec98ca193d608efe4528b134e3a144f3d2

Older method 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.
The new Intra_R_Add_Endocyclic tree. Mirror of https://github.com/GreenGroup/RMG-Java/commit/3a7508818babf256aaef7de8be7e13ff157a822d

Reorganized the tree in order to allow the calculated values to get
priority level 5. I also added some estimates and calculated values
to block strained reactions.

Additional notes:  Had to make some of the groups more general to adapt to
RMG-Py's nitrogen inclusive nodes.  Also removed deprecated groups
so that the travis unit tests would pass.
Updates from RMG-Java for Intra_R_Add_Exocyclic family.  Now up to date with https://github.com/GreenGroup/RMG-Java/commit/bea900d9ee5d3a8a82baa3a4f9b8bd9472ee5217

A lot of new estimates from the GA method.  https://github.com/GreenGroup/RMG-Java/commit/baa353ec98ca193d608efe4528b134e3a144f3d2
older method 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 rate coefficients for the intramolecular exocyclic addition R6_SMS_D
https://github.com/GreenGroup/RMG-Java/commit/9e1669fa2525f192cac5b42898c43160d6f24436

Restructuring of tree. https://github.com/GreenGroup/RMG-Java/commit/bea900d9ee5d3a8a82baa3a4f9b8bd9472ee5217
in order to allow the tree to be filled up by estimates.
I added some estimates and calculated values to block some steric hindered reactions.
Fixes to groups in R_Addition_Multiple_Bond.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/693c071e1f75e9fdda6bd38ab0cbd28e5011bbb6
and https://github.com/GreenGroup/RMG-Java/commit/45228e890af38dc3e3fbf8dc85cb5490e91f8eec

The ligands renamed to Ct and bonds were changed from double to triple.

SJ was made to be more general.
Updates to H_Abstraction groups ONLY.  Up to date with https://github.com/GreenGroup/RMG-Java/commit/c755f210d051118dd8214c16ea1016511d872d2e
Group additivity refittings for H_Abstraction.  Mostly from https://github.com/GreenGroup/RMG-Java/commit/8f47cd2dde3a314782e4a421902d18500a71ba3b

Aaron Vandeputte GAVs.
Adding rate coefficient for vinyl alcohol + propargyl from alcohol group.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/b6d5d598553596cc8b4eb16dbb4127e02659c756
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
Adding rate rules for abstraction from butanal by HO2 and OH.  Rates from https://github.com/GreenGroup/RMG-Java/commit/45f7dc8114a8451b9e77a647a2e03acf7c46d29b

Reference for Butanal + HO2
DOI: 10.1039/C2SC21090H
Updating H abstractions from branched alcohols by H and CH3.  Mirror of rates from https://github.com/GreenGroup/RMG-Java/commit/637df7ca61b6b14715b643550a168e06980f9d5f

These values were updated by AVG, earlier values seem to be
suspiciously slow by factor of 10. SSM doesnt know why but
it could be related to error due to projection in CANTHERM.
Updating nBuOH + OH rate coefficients.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/fe426913f81472430c46197ff6db48a41958894d

Refitting the rate coefficients yo 3 parameter
using the 4 parameter fit  provided in Table 4 of
reference DOI: 10.1021/jp310910f
Adding rate rules for H abstraction from allylic sites.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/577975ad0544aba5d14e138869f20abe7b0e0403

of alkenes by OH

The allylic site accounts for over 90% of H abstraction by OH
compared to the vinylic and methyl sites.
H_Abstraction rate rule changes for alcohols.  Partial mirror of https://github.com/GreenGroup/RMG-Java/commit/c755f210d051118dd8214c16ea1016511d872d2e
Some updates to rate rule groups in H_Abstraction to match RMG-Java.
Adding the H_shift_cyclopentadiene family to the database.  See https://github.com/GreenGroup/RMG-Java/commit/b130d5b230a97ea07beb1d6115cafd77665c2d21

This reaction family helps find the pathways leading to PAHs.
Made file for transition state group training.

Blank groups file copied from the kinetics equivalent,
and will work in the same way as well.
Modules to store TS data and groups for H abstraction.

Copied from the kinetics equivalent and stripped of some
methods not necessary for the ts distances.
Defined distances for first set of transition states.

Building a training set. These are all H abstractions from
a primary carbon. Abstractions from a broader range of atom
types will be required to fill out the tree.
Methods and training sets now correspond with TS group additivity.