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This repository was archived by the owner on Jun 7, 2024. It is now read-only.
This repository was archived by the owner on Jun 7, 2024. It is now read-only.

HCCO in Glarborg/HighP is forbidden by Carbene_D #249

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@faribas

Description

@faribas

Trying to use Glarborg/HighP as a ReactionLibrary or PrimaryKineticLibrary fails:

Created new species: HCCO(57)
ERROR: jing.chem.ForbiddenStructureException: The molecular structure
1  C 2T {2,D}
2  C 0 {1,D} {3,D}
3  O 0 {2,D}
 is forbidden by Carbene_D, and not allowed.
    at jing.chem.ChemGraph.<init>(ChemGraph.java:139)
    at jing.chem.ChemGraph.make(ChemGraph.java:2437)
    at jing.rxnSys.SeedMechanism.readSpecies(SeedMechanism.java:225)
    at jing.rxn.ReactionLibrary.read(ReactionLibrary.java:135)
    at jing.rxn.ReactionLibrary.appendReactionLibrary(ReactionLibrary.java:111)
    at jing.rxnSys.ReactionModelGenerator.readAndMakeReactionLibrary(ReactionModelGenerator.java:4446)
    at jing.rxnSys.ReactionModelGenerator.initializeReactionSystems(ReactionModelGenerator.java:1080)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1312)
    at RMG.main(RMG.java:96)

ERROR: java.io.IOException: RMG cannot read the "species.txt" file in the ReactionLibrary: GlarborgHighP
The molecular structure
1  C 2T {2,D}
2  C 0 {1,D} {3,D}
3  O 0 {2,D}
 is forbidden by Carbene_D, and not allowed.
    at jing.rxnSys.SeedMechanism.readSpecies(SeedMechanism.java:250)
    at jing.rxn.ReactionLibrary.read(ReactionLibrary.java:135)
    at jing.rxn.ReactionLibrary.appendReactionLibrary(ReactionLibrary.java:111)
    at jing.rxnSys.ReactionModelGenerator.readAndMakeReactionLibrary(ReactionModelGenerator.java:4446)
    at jing.rxnSys.ReactionModelGenerator.initializeReactionSystems(ReactionModelGenerator.java:1080)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1312)
    at RMG.main(RMG.java:96)

ERROR: Error reading reaction system initialization file.
ERROR: java.io.IOException: Input file error: Error reading Reaction Library: GlarborgHighP
Can't read Reaction library.
RMG cannot read the "species.txt" file in the ReactionLibrary: GlarborgHighP
The molecular structure
1  C 2T {2,D}
2  C 0 {1,D} {3,D}
3  O 0 {2,D}
 is forbidden by Carbene_D, and not allowed.
    at jing.rxnSys.ReactionModelGenerator.initializeReactionSystems(ReactionModelGenerator.java:1294)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1312)
    at RMG.main(RMG.java:96)

CRITICAL: Input file error: Error reading Reaction Library: GlarborgHighP
Can't read Reaction library.
RMG cannot read the "species.txt" file in the ReactionLibrary: GlarborgHighP
The molecular structure
1  C 2T {2,D}
2  C 0 {1,D} {3,D}
3  O 0 {2,D}
 is forbidden by Carbene_D, and not allowed.

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