Adapting kinetics for with multiple transition states #323
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…templates. Preliminary fix for #142 Instead of calculating degeneracies first, find reaction templates after generating reactions, then combine degenerate reactions only if reaction templates match. These isomorphic reactions remain separate (unlike in RMG-Java) in case someday we want to calculate the separate transition states. The reactions are added to the core and printed to chemkin as duplicates. Issues still remaining: - How to identify the correct reverse reaction when having multiple TS's. My solution is to match the correct reaction pairs- but this only works in the case of a bimolecular A+B=C+D reaction. If the reaction is unimolecular, the reaction pairs will be the same and the correct path cannot be distinguished. - If kinetics are identical, they should be combined through degeneracy, in this commit they remain as duplicates.
If forward reaction has the same template, then do not include it; if not, then we have found an additional transition state and the reaction should be included. Do not include any reverse reactions if the family has its own reverse otherwise we are including kinetics for more than one direction.
…to figure out which reverse reaction (if there are multiple transition states) matches the forward reaction. This is the best I can do for now. Maybe if there is a way to look at the mappings of the labeled atoms this can be done better. Already we are accounting for multiple TS's in the forward direction, so that is already better than before.
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Updated so that RMG uses the template of the reaction to determine whether the rxn has a different TS. However, it is difficult to determine which reaction to pick for families that are their own reverse. When there are two reverse reactions, which one should be picked? Probably need to use some mapping of the atomlabels with hardcoding for those families.. The specific case that might be looked into is the reaction between these two species reacting in Intra_H_migration. This is for future reference. species( species( |
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This is on hold likely till #1055 gets merged |
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Replaced by #1055. |
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Putting up this pull request so that we don't forget about this issue: #142
In certain families, there are multiple reaction paths that can occur, sometimes with different kinetics. The example found in the issue is that of isobutyl radical + tertbutyl radical reacting to form isobutane and isobutene. There are two possible paths in the Disproportionation family: (C_rad/H2/Cs,Cmethyl_Csrad) or (C_rad/Cs3,C/H/NdNd_Csrad). What is currently found in Java is a randomly chosen version of the kinetics (Sometimes the first template appears, other times the 2nd template appears).
What these commits attempt to do is to calculate degeneracy by allowing identical reactions IF their reaction templates are different (3aea3e5). Then degeneracy is calculated separately for each 'transition state' based on bookkeeping of the reaction pairs.
Remaining issues: