singlet oxygen getting added to mechanism through decay operation

[sevyharris]

Bug Description

I have a recent butane combustion mechanism that forms singlet oxygen through this R Recombination reaction:

! Reaction index: Chemkin #1259; RMG #87
! Template reaction: R_Recombination
! Flux pairs: OH(15), OH(15); O2(2), OH(15);
! Estimated from node Root_N-1R->H_N-1CNOS->N_1COS->O_Ext-1O-R_N-2R->C_N-3R!H->N_2OS->O in family R_Recombination.
! Multiplied by reaction path degeneracy 2.0
O2(2)+OH(15)<=>O2(52)+OH(15)                        4.000000e+13 0.000     22.540

What happens is it forms the [O]OO radical and then decays according to the rmgpy.rmg.decay template.

This then causes more problems in the mechanism because it starts reacting the singlet oxygen with everything else.

How To Reproduce

chemkin file
input file
RMG log
species dictionary

Expected Behavior

I'm using the Burke O2+H2 seed mechanism, so I don't really want RMG guessing more O2 reactions. I don't expect singlet oxygen to end up in this mechanism.

Installation Information

Describe your installation method and system information.

• OS: Ubuntu
• Installation method: source
• RMG version information:
  • RMG-Py: 6cf97c3
  • RMG-database: 9ccc3952e0acef53cbbc7cd3be7558101da1a016

Additional Context

I'm not sure what the right approach is to fixing this. Some options from what I think are best to worst:

1. Forbid singlet oxygen as a possible decay product in the decay module
2. Forbid the undecayed [O]OO radical as a product in the R Recombination family
3. Add a calculation of this reaction to R Recombination depository (or a copy of the reaction with zero kinetics) so RMG knows the rate should be much slower

[sevyharris]

I've tried regenerating the mechanism using method 1, forbidding the singlet precursor smiles='[O]OO' in the R Recombination family, but the singlet still finds its way into the core through other PDEP reactions. And then it leads to the formation of singlet O2 from triplet O2 as described in this issue: #2848

There will always be more ways for singlet O2 to be discovered, and perhaps it makes sense to forbid these paths as we find them, but we probably also need to deal with the Singlet_Val6_to_triplet becoming reversibility problem separately.

[github-actions]

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