Merge branch 'master', remote-tracking branch 'richard/master'
H_Abstraction/training:309 Atoms were mislabeled!

Atoms were mislabeled!  *1 moved from an O to a C, and *3 from a C to an O.
Not sure how widespread this is. @jwallen, how did you create these training.py files?
New R_Addition_MultipleBond/training/1 reaction: Moved from rules to training, cross-referenced with NIST and PrIMe.

New kinetics/families/R_Addition_MultipleBond/training entry number 1 submitted through RMG website:
Moved from rules to training, cross-referenced with NIST and PrIMe.
Richard West <rwest@mit.edu>
Deleted R_Addition_MultipleBond/rules:328 because I just moved it to training.

Our aim is to identify real molecules and add them to the training set,
which should also mean removing them from the rules once we have identified
them.
I think (?) that these will get put back in the right place when exporting the
database in the old RMG-Java format?
Merge branch 'master', remote-tracking branch 'richard/master'
Merge branch 'master', remote-tracking branch 'richard/master'
Merge branch 'master' of git://github.com/rwest/RMG-database
Fixed bug in Intra_R_Add_Endocyclic group definitions.

The generated reverse template was not completely symmetric with the
forward template (which caused an UndeterminableKineticsException in a
recent RMG-Py methylformate job). The fix is to include Cdd as an allowed
atom type in the *3 position in the general templates.

I suspect this is a problem in Intra_R_Add_Exocyclic as well, but I won't
make the change until we encounter the exception explicitly, in case I am
mistaken.
Merge branch 'master' of git://github.com/jwallen/RMG-database
Removing nitrogen reactions from the comments within GRI-Mech3.0 
reactions since they dirty up the chemkin and output files in RMG.

Nitrogen reactions now temporarily stored in a separate txt file.
Added several scripts to help with generating viable training sets.

convertPrIMe.py reads one of the local PrIMe databases (e.g.
H_Abstraction/PrIMe.py) and generates files in that family's new
training folder for each unique reaction in the set. It does not copy
the kinetics from PrIMe, however, because with all of the errors in our
PrIMe.py files and the lack of valid temperature range makes the PrIMe
kinetics of limited use.

queryNIST.py is used to query the NIST kinetics database for a given
reaction, as loaded from one of these training files. It constructs an
HTML query, sends the query to kinetics.nist.gov, and parses the HTML
output to extract the kinetics (with temperature range!) and reference
information and saves them back to the training input file.

kineticsTraining.py uses the set of kinetics in one of the training files
to fit the best kinetics as a single modified Arrhenius expression. It
automatically searches for and ignores the really crazy outliers, and can
plot the results for a human to evaluate. This will be especially useful
for those reactions for which many literature references exist. Ultimately
the output should be placed in the training.py file so that we can use it
to train kinetics group additivity values.
Revert "H_Abstraction/training:309 Atoms were mislabeled!"

This commit was the result of a misunderstanding of how labeled atoms
are assigned to products in reaction families that are their own
reverse. In particular, when applying the recipe for such families, we
finish by swapping the necessary labels so that we can apply the recipe
again to go back from products to reactants. (Unfortunately, this
requires some hardcoding.)

This reverts commit c249f31865fe1c6cb71def77678f35499b38060e.
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'