Generating an unmarked duplicate Disproportionation reactions

[rwest]

Bug Description

When converting a chemkin file generated by RMG into cantera using ck2cti I got this error:

***********************************************************************
CanteraError thrown by Kinetics::checkDuplicates:
Undeclared duplicate reactions detected:
Reaction 2619: HNO2(571) + HNO2(699) <=> H2NO2(172) + NO2(91)
Reaction 2498: HNO2(571) + HNO2(699) <=> H2NO2(172) + NO2(91)
***********************************************************************

Looking at the annotated chemkin file, sure enough these reactions are unmarked duplicates:

! Reaction index: Chemkin #2498; RMG #3394
! Template reaction: Disproportionation
! Estimated using an average for rate rule [Y_1centerbirad;N3H_s_Rrad]
! Euclidian distance = 0
! family: Disproportionation
HNO2(571)+HNO2(699)=NO2(91)+H2NO2(172)              2.645406e+08 1.500     -0.350   

! Reaction index: Chemkin #2619; RMG #26909
! Template reaction: Disproportionation
! Flux pairs: HNO2(699), NO2(91); HNO2(571), H2NO2(172); 
! Estimated using an average for rate rule [Y_1centerbirad;N3H_s_Rrad]
! Euclidian distance = 0
! family: Disproportionation
HNO2(699)+HNO2(571)=NO2(91)+H2NO2(172)              2.645406e+08 1.500     -0.350   

They even have exactly the same rate rules.
The reactants are listed in a different order, however.

How To Reproduce

The species in question are

HNO2(699)
multiplicity 3
1 O u1 p2 c0 {3,S}
2 O u1 p2 c0 {3,S}
3 N u0 p1 c0 {1,S} {2,S} {4,S}
4 H u0 p0 c0 {3,S}

HNO2(571)
multiplicity 3
1 O u0 p2 c0 {2,S} {3,S}
2 O u0 p2 c0 {1,S} {4,S}
3 N u2 p1 c0 {1,S}
4 H u0 p0 c0 {2,S}

NO2(91)
multiplicity 2
1 O u0 p3 c-1 {3,S}
2 O u0 p2 c0 {3,D}
3 N u1 p0 c+1 {1,S} {2,D}

H2NO2(172)
multiplicity 2
1 O u0 p2 c0 {2,S} {3,S}
2 O u0 p2 c0 {1,S} {4,S}
3 N u1 p1 c0 {1,S} {5,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {3,S}

So hopefully putting the two reactants in an input file will reproduce.

Expected Behavior

Duplicates would be eliminated, merged, or marked as DUPLICATE in the chemkin output.

Installation Information

Describe your installation method and system information.

• OS (include version if known): CentOS 7
• Installation method: from source in anaconda environment
• RMG version information:
  • RMG-Py: 2.4.1-511-gd33df776a
  • RMG-database: 2.4.0-37-gcc0c77f9

Possible links

• No DUPLICATE mark for P-dep and Disproportionation reactions #1624 is about when a Disproportionation and a PDep reaction end up being the same and are not marked as DUPLICATE. But in this case they are both Disproportionation.
• Duplicate family reaction #1336 might be a duplicate of this issue (sorry)

[rwest]

There was one other duplicate pair in the same model (ck2cti only reports them one at a time)

***********************************************************************
CanteraError thrown by Kinetics::checkDuplicates:
Undeclared duplicate reactions detected:
Reaction 2624: HNO2(699) + HNOO(572) <=> H2NO2(172) + NO2(91)
Reaction 2499: HNO2(699) + HNOO(572) <=> H2NO2(172) + NO2(91)
***********************************************************************

! Reaction index: Chemkin #2624; RMG #27079
! Template reaction: Disproportionation
! Flux pairs: HNO2(699), NO2(91); HNOO(572), H2NO2(172); 
! Estimated using an average for rate rule [O_rad/NonDeO;N3H_s_Rrad]
! Euclidian distance = 0
! family: Disproportionation
HNO2(699)+HNOO(572)=NO2(91)+H2NO2(172)              2.900000e+04 2.690     -1.600 

! Reaction index: Chemkin #2499; RMG #3395
! Template reaction: Disproportionation
! Estimated using an average for rate rule [O_rad/NonDeO;N3H_s_Rrad]
! Euclidian distance = 0
! family: Disproportionation
HNOO(572)+HNO2(699)=NO2(91)+H2NO2(172)              2.900000e+04 2.690     -1.600   

[mliu49]

I think #1336 is related.

[rwest]

All recent examples of this have either the reactants or the products in a different order.
eg. A + B = C + D is not detected as a duplicate of A + B = D + C.

The chemkin.mark_duplicate_reaction function does not sort the reactant or product lists before comparing them.

After fixing this, there's a residual problem. The function REMOVES duplicate flags if it thinks they don't belong, but they might belong for a different reason than the one being checked.

Attempts to fix these are in PR #1856

[github-actions]

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