Adding rate rules for abstraction from butanal by HO2 and OH

Reference for Butanal + HO2
DOI: 10.1039/C2SC21090H
Updating H abstractions from branched alcohols by H and CH3

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

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 of
alkenes by OH

The allylic site accounts for over 90% of H abstraction by OH
compared to the vinylic and methyl sites.
Estimating R. + O2 = Alkene + HO2 disproportionation rate
for alpha radical of alcohols.
Adding rate rule for O2 + vinyl = Alkyne + HO2 and O2 + secC-rad = diene +
HO2

The rate rule is derived from the estimate by Westbrook et al.
for C2H3 + O2 = C2H2 + HO2. This affects acetylene production
in many oxidation mechanism.

Also updating rate rule for O2 + allylic = diene + HO2
The estimate is based on secC-rad + O2 = Alkene + HO2 by accounting
for allylic stability (around + 7kcal/mol)
Commiting some changes to disproportionation reactions (mainly with O2) and H_Abstraction reactions (for alcohols) before pulling from master

Conflicts:

	databases/RMG_database/kinetics_groups/Disproportionation/rateLibrary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/tree.txt
Changed the addition of H to a primary double bond
Modfying disproportionation rates for Allyl + rad reactions

This just a estimate, Tsang estimates seem too fast.
Adding a barrier of 6 kcal/mol
Add info on default gfortran-4.6 issue of Ubuntu-12.04 in documentation
Fixing missing thermo comments

Because we made a copy of the chemgraph to get the thermo and
were calling the comments from this new graph, there were cases - when the
molecule was not aromatic it would return an empty string.

We now only call the comments from the thermo_graph if the species is aromatic and not present in a thermo library.

Sigh another Sunday (10:00 pm) bug fix!
Made small changes to the thermolibraries.
a) Modified the Cd-(Cd)(Cd) thermo group which appears to be 7 kcal/mol too low
b) Added a HBI for indenyl
c) Added ring correction for cycloheptatetraene
Adding the option to set max C atoms for a Pdep Network

This option provides more flexibility to determine if we need
to treat a reaction as pressure dependent. Ideally we should not
recommend using this option since whether to treat a reaction as
Pdep or not depends on the total number of atoms in a reaction (i.e net degree
of freedome determines whether a molecule can undergo internal relaxation).

However for some practical consideration when your fuel is unsaturated
and leads to a lot of aromatic species (mostly heavy atoms due to decrease
in saturation) we might want to specify the Carbon number or total number of
Heavy atoms (not yet implemented).
New criterium for intra_R_Add_Endocyclic and intra_R_Add_exocyclic
Consider only addition reactions when the rad and double bond are not part
of two different rings that have 2 or more atoms in common.x
Rate rules for recombination reactions of H with CPDyl (and similar structures)
Merge branch 'master' of github.com:GreenGroup/RMG-Java

Conflicts:
	databases/RMG_database/kinetics_groups/Disproportionation/rateLibrary.txt