Mod Replaced Pdep Kinetics Trange, and adding
RMSE as diagnostic information

Adding RMSE of fit as diagnostic information to
comment for each CHEB

Modifying the Trange to 2000 to 500 K (hard coded)
so as to improve the fitting. Earlier it was using
Thigh and Tlow of CHEB
RMSE in PDepKinetics is now log10 base

In earlier commit rmse was gased on natural log
k values, now converting them to base 10 so its
easier to tell how off is the fit in order of
magnitude estimae
Updating ReplacePdepKinetics Module to do PLOG

The ReplacePdepKinetics now will convert CHEB to PLOG
The two options now are
1 ARH and Pressure of interest
2 PLOG

For now the pressure for the PLOG have been hardcoded
to 0.1,1,10,100 atm.

Other Minor Changes
1)Did not read the reactions in properly if line "REACTIONS"
had units attached with it, this is not the case now
2)The output filename was too crude, the new name gives
more information and generates a .inp file
CalculateReverseRateCoefiicients

Adding utility to calculate reverse rate coefficients from
chemkin file, for Arrhenius,Plog and CHEB reactions.

Tested against Currans software for
npropyl+O2=npropylOO
Curran REV / 1.4E+18 -1.226 33951
RMG REV / 3.09E+17 -1.025 33717

ipropyl+O2=ipropylOO
Curran REV / 5.11E+22 -2.3821 36374
RMG REV / 6.062E+22 -2.407 36398

Though the parameters are different, the actual rate values
are not that different
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge branch 'master' of github.com:GreenGroup/RMG-Java
This commit adds new rates for the R. + ROO-H = RH + ROO. reaction for
secondary alkyl radicals. These estimates are based on the calculations of
Aguilera-Iparraguirre et al. for HO2 + alkanes and  rate recommendations.

Conflicts:

	databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt
Updated rates rules for R. + O2 = HO2 + alkene

RMG was overestimating the disproportionation reaction
between R. and O2 leading to severe problems in alkane
oxidation models. The corresponding rate rules have
been corrected using recently reported values by
Miyoshi (dx.doi.org/10.1021/jp112152n). It should be
noted that the flux of this reaction is weak at low
temperatures which was not the case with the previous
rate rule which assumed a barrierless reaction.
This commit updates rate rules for the following reactions:
1) R. + ROOH = RH + ROO.
2) ROO. + H-ROOH = ROOH + .QOOH (metastable)
3) RC(O). + ROOH = RC(O)H + ROO.
4) RC(O)C(R)H. + ROOH = RC(O)C(R)H2 + ROO.

These reactions were reported as exothermic by RMG in the
direction shown above. CBS-QB3/1dHR rates for the reverse
reaction were used in conjunction with thermo from
DFT_QCI_thermo library to obtain modified Arrhenius fits
for the RMG rate rules. Some old nodes added by AJ were
removed and will be part of an upcoming commit for deprecated
nodes.

Conflicts:

	databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt
Added new reaction family for step 1 of Korcek sequence.
Added reaction family for step 2 of Korcek sequence.
Rate rule updated with latest calculations using b3lyp/cbsb7 rotor potentials
for all 4 rotors of HOOCH2CH2CH2(=O).
Some more changes to the rate using corrected F12 energies for
HOOCH2CH2CH2(=O).
Merge branch 'database'
Update to H-Abstraction rate rules to resolve conflict

RMG cannot find fg: C/H2/Cb
Merge branch 'database'
tried to correct/clarify Gauche_Library comments