Saturated the adjacency lists in the NIST.py files of the kinetics
families to be able to extract information about lone electron pairs and
and electronic charges for future nitrogen and sulphur atoms.
Saturated the adjacency lists in the training.py files of the kinetics
families with hydrogen atoms to be able to extract information about
lone electron pairs and electronic charges for future nitrogen and
sulphur atoms.
Saturated the adjacency lists of the kinetics 
libraries with hydrogen atoms to be able to extract information about
lone electron pairs and electronic charges for future nitrogen and
sulphur atoms.
Saturated the adjacency lists of the thermo libraries with hydrogen
atoms
to be able to extract information about lone electron pairs and 
electronic charges for future nitrogen and sulphur atoms.
Added a node for nitrogen atoms at the level L2: and assigned it
preliminarily the values of the Cs-HHHH group to prevent errors about
not finding a group value and as a starting point for future nitrogen
thermo groups.
Introducing frequencies for nitrogen groups

Amide, Imide, Amine, Nitrile, Nitroso, Nitrites, Nitro, Nitrates
GRI-Mech3.0 kinetics library using all nitrogen containing species

(GRI-Mech3.0-N.py)
Adding nitrogen thermo group and ring correction values

Values taken from Benson et al. (Chem. Rev. 69, 279–324 (1969)) and
Ashcraft and Green (J. Phys. Chem. A. 112, 9144–9152 (2008))
GRI-Mech3.0 thermo library using all nitrogen containing species 

(GRI-Mech3.0-N.py)
Adding estimations of Hydrogen abstraction rates by Dean and Bozzelli

Abstraction by NH2 from ethane reference
Abstraction by H, O, OH and CH3 from ammonia reference
Kinetics library of well investigated small nitrogen molecules

Reviewed by Dean and Bozzelli

'Gas-Phase Combustion Chemistry' (ISBN: 978-1-4612-7088-1), chapter 2,
'Combustion Chemistry of Nitrogen', Anthony M. Dean, Joseph W. Bozzelli"
Reverting H-abstraction family back to previous commit c51ce95

Import script is not able to incorporate many of the manual changes made
to the family.
Fixed incorrect import of kinetics in HO2_elimination_from_peroxyradical family
Incorrect definition for group "OJ" corrected.
Minimal extensions to account for nitrogen atoms.
Merge remote-tracking branch 'GreenGroup/master'

Conflicts:
	input/kinetics/families/H_Abstraction/NIST.py
	input/kinetics/families/R_Addition_MultipleBond/NIST.py
	input/kinetics/families/R_Recombination/NIST.py
	input/kinetics/families/Substitution_O/groups.py
A new reaction family describing the conversion of nitro (RNO2) to
nitrite (RONO) compounds and vice versa.
Updates to families from RMG-Java since previous import (Nov 12 2012)

This was done by an automatic import by Connie <connieg@mit.edu>, followed by these corrections:

1) Reverting H-abstraction family back to previous commit
Import script is not able to incorporate many of the manual changes made
to the family.

2) Fixed incorrect import of kinetics in HO2_elimination_from_peroxyradical family

3) Incorrect definition for group "OJ" corrected.

Richard West <r.west@neu.edu> then merged the commits, removed redundant changes that 
confused the diffstats, and wrote the following description.

The net result seems to be

* Cyclic_Ether_Formation:
	New groups so that the top level can match RnOOR as well as RnOOH
    New rules to fill in some data for these new groups.
	Unfortunately the default diff formatting for me makes it hard to see if any of the
	original data were changed, because they are compared against the new data.

* HO2_Elimination_from_PeroxyRadical:
	It is given a reverse name: "HO2_concerted_addition"
	9 new rate rules added.
	Unfortunately these come with very little information about where they are from
	or who did the calculations, or what the species were. (Does "sp, ts, tt, etc. mean something?)
    As we have space to store this metadata, it would be good to add it.

* R_Addition_MultipleBond:
	2 new groups as sub-groups of O_rad/NonDe
	(Irritatingly causing all the other groups to be renumbered. Do we use these numbers?)
	9 new rate rules added.
	Again, these come with very little information about where they are from.

* Substitution_O:
	The Y_1centerbirad group is no longer allowed to be a CO atom type.
	I have no idea why not. Perhaps there's a commit message in the RMG-Java project.

* H_abstraction:
	These changes were reverted, but it looks like there have been some in RMG-Java
Added USC-Mech-ii thermo library.

This is the first concrete output from the chemkin importer project.
Update to prevent problems with nitrates.