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
Merge remote-tracking branch 'upstream/master'
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 remote-tracking branch 'upstream/master'
Merge branch 'Aromaticity_Perception'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge branch 'RSC'
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Merge remote-tracking branch 'upstream/master'
Merge branch 'master' of github.com:GreenGroup/RMG-Java
updates to InchifyCHEMKINusingDictionary script

added definition of environment variables so cInChI-1 can run; also generalized so that dictionary can have InChI (or other info) on the same line as the species name
updates to ThermoDataEstimator

Updates include:
-don't add ID numbers to species names in ThermoData (this allows easy re-evaluation of the thermo section for an existing Chemkin mechanism without naming issues; I'm not aware of cases where the numbering would be helpful)
-write a thermo block in Chemkin file format to TDEresultsCHEMKIN.dat
-re-organized Chemkin thermo output, including the addition of "SMILES" (InChI) comments
Merge remote-tracking branch 'upstream/master'
Added specfun.f90 to FAME for gamma function.

gamma is only an intrinsic function in gfortran version 4.3 or later. This
commit provides a set of special mathematical functions, including the
gamma function, so that FAME will still build with older compilers.

Note: specfun is licensed under the LGPL which we should note in the
documentation. Website for specfun:

http://people.sc.fsu.edu/~jburkardt/f_src/specfun/specfun.html

Closes #240.
units fixes for Ea in PLOG reactions

a source of persistent confusion to both RMG developers and users is that source of persistent confusion is that CHEMKIN's PLOG format requires Ea parameters to be in units of cal/mol and interprets the values
 accordingly, regardless of the units elsewhere in the file; two errors have been identified in RMG's treatment of Ea for PLOG reactions:
1. RMG's chemkin file writer didn't recognize the chemkin convention and converted the activation energy (stored internally as kcal/mol) into the units of the overall chemkin file whereas it should have multiplied by 1000 to print the value in cal/mol
2. the checkForwardAndReverseRateCoefficients utility calculated k for PLOG expressions assuming the Ea was in the units of the CHEMKIN file
these two issues are addressed in this commit
notes:
1. users should specify PLOG Ea parameters in cal/mol in seed mechanisms, regardless of the units specified elsewhere, in accord with the CHEMKIN convention; this is implemented in the code via SeedMechanism.parsePLOGline()
2. internally, Ea is always stored as kcal/mol, regardless of whether it is PLOG or the units specified elsewhere