Adding new thermo_library to RMG database: CBS_QB3_1dHR

The entries in this library represent the species thermochemistry MRH has
corrected during his work on the butanol isomers.

The species thermochemistry was calculated using CanTherm.  The CBS-QB3 method
was used to calculate the ZPE and optimized geometry.  The frequencies were
calculated using DFT, using the B3LYP/CBSB7 basis set, and then scaled by 0.99
as suggested by Petersson et al.  The 1-d separable hindered rotor
approximation was used for all low-frequency internal rotor modes.
Bond-additivity corrections were used to calculate the reported Hf298.

Units of enthalpy are kcal mol-1.
Units of entropy and heat capacity are cal mol-1 K-1.

The uncertainties are guesses by MRH.
Adding the new Klippenstein H2/O2 thermo library.

The thermo comes from the new new Dryer/Klippenstein (2011) mechanism.
Added new rate in H_abstraction:

HO2 + CH3-CH2-CH2-CH=O = H2O2 + CH3-CH2-CH2-C*=O
from CBS-QB3 calculations

JWA note: Unlike in RMG-Java, I have added this to training since we know
what the reactants and products are.
Modified Cyclic Ether Family to form lactones

Defination of head nodes was changed to include CO with Cd
Additional definination were added to include formation of lactone

Following rates were also added
The rate for CH2CH2CH2CH2C(O)OOH -> 6 membered Lactone + OH
A=1.27E+08 s-1  n=0.77 Ea=18.73 kcal/mol (CBS-QB3)
The rate for CH2C(O)OOH -> 3 membered Lactone + OH
A=1.9E+17 s-1 n=-1.1 Ea=27.2 kcal/mol (Calculated by CFG and JWA)
Added rate rules to intra_H_migration from Sandeep calculations and Atkinson literature.

Sandeep calculations are taken from DOI: 10.1021/jp9098792

The A factor in the paper differs from the ones added to the library as the
paper assumes a slightly different Arrhenius form compared to the default RMG
one. A few new groups were added to the dictionary and tree files to account
for the change in the TS ring size or the H being abstracted. The new library
entries have been checked by performing PopulateReactions jobs with the
original molecules in Sandeep's paper and checking if the right entry is
located.

RMG's previous estimates were based on Curran's estimates for ROO.
isomerizations and were atleast 4 orders of magnitude too slow at about
1000 K when compared with recommendations from NIST, a review by Orlando
et al.(DOI:10.1021/cr020527p) and recent articles that I have looked at
(Veerecken2010(DOI: 10.1039/c0cp00387e) and Somnitz2008(DOI: 10.1039/b711429j)).

The rates added correspond to 1,5 shift only as these are believed to be
faster than others due to ring strain considerations. I have not added
special rates for migration in RC(O)CH2C(O.)R' type of species which can
arise in low temperature oxidation due to cleavage of the O-O bond in
ketohydroperoxides. This is based on a preliminary examination of the
results by Veerecken2010 who report that the presence of the carbonyl
does not significantly alter the rate compared to the base alkoxy radical.
Fixes to the importOldDatabase script to restore it to working order.

This updates things to match the current way the database is stored in
memory (so that we can add entries to the history).
Updated kineticsGroups.py to look for the depositories in the right place.

This script wasn't updated when I moved the depositories into the kinetics
families, and so was broken. With this fix it should be back to working
order.
Merge branch 'summer2011'
Merge branch 'master', remote-tracking branch 'josh'
Added Helium thermo to database so you can now run RMG-Py with He.
Fixed units error in HO2_Elimination_From_PeroxyRadical/rules.

This reaction family has only one reactant, but in the importing from the
old database, the rate rules were erroneously given units corresponding to
bimolecular reactions. (Note that only the units were incorrect; the
actual values of the preexponential factors were imported correctly.)
Regenerated group additivity parameters for HO2_Elimination_From_PeroxyRadical.

Oddly, the values only changed for the topmost mode (although the units
changed for all the nodes). Not sure what effect this will have on RMG
jobs.
Removed R!H group from intra_H_migration Cs_H_out_noH and descendants.

Unlike sibling nodes Cs_H_out_2H and Cs_H_out_1H, Cs_H_out_noH was
specifying all four ligands around the central Cs. This is bad because our
isomorphism check does not allow for matches between labeled atoms in
the molecule and unlabeled atoms in the functional group. This means that,
without this fix, these groups were never matched! The fix makes these
groups parallel those of Cs_H_out_2H and Cs_H_out_1H, which at least makes
things consistent.
Moved Cs_H_out_OOH to be child of Cs_H_out_noH in intra_H_migration.

Previously it was a sibling of Cs_H_out_2H, Cs_H_out_1H, and Cs_H_out_noH,
which was problematic because its definition was not mutually exclusive
with its neighbors. By making it a child of Cs_H_out_noH (and changing its
R group to R!H) I think I've removed the issue. Note that the case where
R = H is already handled as a child of Cs_H_out_1H, so we aren't really
losing any specific nodes.

It's probably worth checking that the rate rules involving these nodes
still make sense.
Merge branch 'intra_H_migration'
Fixed kinetics type in H_Abstraction training entry 540.

Training entries should have Arrhenius (or KineticsData) kinetics, but
this one still had ArrheniusEP (back from when it was a rate rule).
Fixes to group Intra_R_Add_Endocyclic definitions

See https://github.com/GreenGroup/RMG-Py/issues/69 for detailed workup.

R5_DS_allenic now has consistent atom types and bonds, i.e. *2 is always a Cdd
with 2 double bonds. *3 cannot be a Ct nor have a triple bond.
multiplebond_intra also now allows *2 to be Cdd
Replace arrheniusHigh with arrheniusLow in ThirdBody reactions.

Third body reactions are all in their low pressure limit when 
they depend on the collider concentration. This change was made in 
RMG-Py in GreenGroup/RMG-Py@2ea65224ada6ec72a32956cc2a7c8061e8ce98fd

See issue GreenGroup/RMG-Database#7
Correct units in ThirdBody and Pressure-dependent reactions

Replace arrhenius coefficient unit 'cm^3/(mol*s)'  with 'cm^6/(mol*s)' 
and 's^-1' with 'cm^3/(mol*s)' in ThirdBody reactions 

See issue GreenGroup/RMG-Database#7
Removed deceptive longDesc comment from Glarborg/C2

This describes something else, and shouldn't be here.
There are probably other examples of this type of thing.