Duplicate reactions

[alongd]

There are many duplicate reactions in the Chemkin file RMG-Py generates (chem.inp), which amounts to about 10%-20% of total reactions, to my experience. Following's a representative example from my trials:

! Reaction index: Chemkin #56; RMG #556
! Library reaction: Nitrogen_Glarborg_Lucassen_et_al
NCC(1)+CH3(28)=C2H6N(93)+CH4(37) 7.300e+02 2.990 7.950

! Reaction index: Chemkin #60; RMG #1712
! Template reaction: H_Abstraction
! Estimated using template (C_sec;C_methyl) for rate rule (C/H2/NonDeN;C_methyl)
! Multiplied by reaction path degeneracy 2
CH3(28)+NCC(1)=CH4(37)+C2H6N(93) 9.203e-03 4.351 3.987

In the above example you can see two duplicate reactions (#56, #60), the first taken from a defined kinetic library, whereas the second was generated via the kinetic rules. Needless to say, Chemkin will not run unless one of the reactions is deleted or both are marked with "DUP".

At other times in the same file RMG gives a duplicate reaction with kinetic data taken from two different libraries, instead of using by default the earliest defined library:

! Reaction index: Chemkin #19; RMG #480
! Library reaction: combustion_core/version5
H(10)+H(10)+M=H2(11)+M 1.870e+18 -1.000 0.000
CH4(37)/3.00/ N2(3)/0.40/ C2H6(84)/3.00/ H2(11)/0.00/ Ar/0.35/
DUPLICATE

! Reaction index: Chemkin #21; RMG #1641
! Library reaction: Nitrogen_Glarborg_Gimenez_et_al
H(10)+H(10)+M=H2(11)+M 7.000e+17 -1.000 0.000
H2(11)/0.00/ N2(3)/0.00/
DUPLICATE

At least in this example it wrote "DUP" after the reactions, nevertheless the second reactions should have been suppressed.

I'm aware that similar issues were brought up and solved in the past (#49, #83, #146, #334, #337).
Somehow the phenomenon returned.

Any suggestions?

[rwest]

thanks for reporting this!
I would start with some (unit) tests that reveal the regression.
(I'm sad that it seems we don't have these already!).
Then if the cause isn't obvious from that, then a git bisect will help find when it was introduced.

[nickvandewiele]

I think I might have messed up in the latest commits. I will create the tests and fix this.

[nickvandewiele]

The problem still persist, after ReactionMechanismGenerator/RMG-Py#517, for the combination of reaction libraries and template reactions.