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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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PDepException: Tried to determine nonincluded isomer with maximum leak flux, but there are no nonincluded reactions, so no isomer can be identified. #70

Closed rwest closed 14 years ago

rwest commented 14 years ago

I just got this, and am not sure what to do about it:

dupreaction_set[CH4(13) + O2(2) --> CH3(14) + HO2(7)]

jing.rxn.PDepException: Tried to determine nonincluded isomer with maximum leak flux, but there are no nonincluded reactions, so no isomer can be identified.
    at jing.rxn.PDepNetwork.getMaxLeakIsomer(PDepNetwork.java:529)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:320)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:4033)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1419)
    at RMG.main(RMG.java:57)
Tried to determine nonincluded isomer with maximum leak flux, but there are no nonincluded reactions, so no isomer can be identified.
PDepNetwork #18:
    Isomers:
        C2H3O2J(66) (included =true)
        C2H3O2J(65) (included =false)
        CO2(11) + CH3(14) (included =true)
        CH3(14) + CO2JJ(86) (included =true)
        C2H2O2JJ(81) + H(3) (included =true)
        CH3O(18) + CO(10) (included =true)
    Path reactions:
        C2H3O2J(66) (included =true) <=> CO2(11) + CH3(14) (included =true)
        C2H3O2J(66) (included =true) --> CH3(14) + CO2JJ(86) (included =true)
        C2H3O2J(66) (included =true) --> C2H2O2JJ(81) + H(3) (included =true)
        C2H3O2J(66) (included =true) --> C2H3O2J(65) (included =false)
        C2H3O2J(66) (included =true) --> CH3O(18) + CO(10) (included =true)
    Net reactions:
        C2H3O2J(66) (included =true) <=> CO2(11) + CH3(14) (included =true)
    Nonincluded reactions:
rwest commented 14 years ago

Avoid expanding altered PDep networks with multiple reaction systems.

When running with multiple reaction systems, one reaction system may mark a species to be added to the core and another will mark a network to be expanded. Adding the species to the core could alter the network. When the network is then expanded, an error occurs because it has already been expanded (or at least altered).

We now check, before expanding a network, that it has not been altered already in this step.

Closed by ec0562d108416671732b04bf63c938dd44cc7709.

rwest commented 14 years ago

Just got the same error using latest version of code; reopening bug.


jing.rxn.PDepException: Tried to determine nonincluded isomer with maximum leak flux, but there are no nonincluded reactions, so no isomer can be identified.
    at jing.rxn.PDepNetwork.getMaxLeakIsomer(PDepNetwork.java:537)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:333)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:4029)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1415)
    at RMG.main(RMG.java:57)
Tried to determine nonincluded isomer with maximum leak flux, but there are no nonincluded reactions, so no isomer can be identified.
PDepNetwork #123:
    Isomers:
        CH3O(18) (included =true)
        CH2OH(19) (included =true)
        CH2O(20) + H(3) (included =true)
        CH2OJJ(139) + H(3) (included =true)
        O(4) + CH3(14) (included =true)
    Path reactions:
        CH3O(18) (included =true) --> CH2O(20) + H(3) (included =true)
        CH3O(18) (included =true) <=> CH2OJJ(139) + H(3) (included =true)
        CH3O(18) (included =true) --> CH2OH(19) (included =true)
        CH3O(18) (included =true) <=> O(4) + CH3(14) (included =true)
        CH2OH(19) (included =false) --> CH2O(20) + H(3) (included =true)
        CH2OH(19) (included =false) --> CH2OJJ(139) + H(3) (included =true)
    Net reactions:
        CH3O(18) (included =true) <=> CH2O(20) + H(3) (included =true)
        CH3O(18) (included =true) <=> CH2OJJ(139) + H(3) (included =true)
        CH3O(18) (included =true) <=> O(4) + CH3(14) (included =true)
        CH2O(20) + H(3) (included =true) <=> CH2OJJ(139) + H(3) (included =true)
        CH2O(20) + H(3) (included =true) <=> O(4) + CH3(14) (included =true)
        CH2OJJ(139) + H(3) (included =true) <=> O(4) + CH3(14) (included =true)
        CH3O(18) (included =true) --> CH2OH(19) (included =true)
        CH2O(20) + H(3) (included =true) --> CH2OH(19) (included =true)
        CH2OJJ(139) + H(3) (included =true) --> CH2OH(19) (included =true)
    Nonincluded reactions:
rwest commented 14 years ago

Adding reaction to Pdep network sets altered = true

Without this, networks are not reliably marked as altered when merged, and you can end up trying to expand networks that are already fully expanded.

Closed by ab92263524a7c2e5ba54bd9c4584eed411901316 (again!)