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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 (no included reactions) after pruning after restart #106

Closed stijnvranckx closed 14 years ago

stijnvranckx commented 14 years ago

Procedure:

  1. run a job that doesnt prune until it has 33k edge species, and save the restart files
  2. restart the job, this time with pruning limited to 30k edge species
  3. it restarts ok, prunes ok, tries to expand the network, and fails.

here is the log from the pruning step onwards:

Pruning...

Enlarging reaction model
Time: 0.25024959219943116SEC
Rmin: 3.5124693608984116E-14
Unreacted species C5H5O4J has highest flux: 9.943390717653533E-15
Network 32675 has highest leak flux: 3.5250828797778344E-14
Time: 0.07522356073971229SEC
Rmin: 3.890439195050698E-13
Unreacted species C5H5O4J has highest flux: 1.4004384352264271E-13
Network 32675 has highest leak flux: 3.935178071259548E-13
Time: 0.012642891678376126SEC
Rmin: 1.1142544039149067E-8
Unreacted species C5H7O2J has highest flux: 1.1235156611957599E-8
Network 16599 has highest leak flux: 6.318565853163466E-8
Time: 0.003685911184065576SEC
Rmin: 6.892420539509175E-8
Unreacted species C4H4O has highest flux: 7.190429354635071E-8
Network 15126 has highest leak flux: 3.309667642452336E-7
Time: 9.388362388398836E-4SEC
Rmin: 3.4226628987023254E-7
Unreacted species C4H4O has highest flux: 3.4673604718424735E-7
Network 15126 has highest leak flux: 2.2143105803012184E-6
Time: 1.1122836316989583E-4SEC
Rmin: 6.910902760497209E-7
Unreacted species C4H6JJ has highest flux: 7.013508440548534E-7
Network 12502 has highest leak flux: 1.8602893292621676E-6
Time: 3.468499993037397E-5SEC
Rmin: 8.526112517190814E-6
Unreacted species C4H6JJ has highest flux: 8.625803439186818E-6
Network 16632 has highest leak flux: 2.9310057488783017E-5
Time: 9.14126735751067E-6SEC
Rmin: 9.801745534271978E-5
Unreacted species C4H4O has highest flux: 9.891887248227538E-5
Network 16632 has highest leak flux: 3.7674257552936376E-4
Time: 9.98139015807852E-6SEC
Rmin: 5.944545946860053E-6
Unreacted species C4H6JJ has highest flux: 6.19221466902933E-6
Network 23810 has highest leak flux: 1.2481201916775617E-5
Time: 3.433178356941499E-6SEC
Rmin: 5.076402806838484E-5
Unreacted species C4H6JJ has highest flux: 5.274148737430328E-5
Network 23810 has highest leak flux: 1.1060616309356765E-4
Time: 9.625613417468128E-7SEC
Rmin: 5.384281124048206E-4
Unreacted species C4H5O2J has highest flux: 5.400759548400697E-4
Network 5252 has highest leak flux: 7.681683774355949E-4

Add a new included Species: C5H6O4(33570) (included =false) to network 32675
Generating pressure dependent network for SPC(33570): Cyclic_Ether_Formation
Generating pressure dependent network for SPC(33570): intra_OH_migration
Generating pressure dependent network for SPC(33570): Beta_Scission
Generating pressure dependent network for SPC(33570): Bond_Dissociation
Created new species: C4H5O2J(34787)
Created new reaction: C5H6O4(33570) --> C4H5O2J(34787) + OCHO(71)
Created new species: C5H5O4J(34788)
Created new reaction: C5H6O4(33570) --> C5H5O4J(34788) + H(3)
Created new reaction: C5H6O4(33570) --> C4H5O3J(13065) + HCO(21)
Created new species: C5H5O4J(34789)
Created new reaction: C5H6O4(33570) --> C5H5O4J(34789) + H(3)
Created new species: C3H3O4J(34790)
Created new reaction: C5H6O4(33570) --> C3H3O4J(34790) + C2H3(27)
Created new species: C5H5O4J(34791)
Created new reaction: C5H6O4(33570) --> C5H5O4J(34791) + H(3)
Created new species: C5H5O4J(34792)
Created new reaction: C5H6O4(33570) --> C5H5O4J(34792) + H(3)
Created new species: C5H5O4J(34793)
Created new reaction: C5H6O4(33570) --> C5H5O4J(34793) + H(3)
Generating pressure dependent network for SPC(33570): 1,1_Elimination
Generating pressure dependent network for SPC(33570): 1,2_Elimination_CO2
Created new species: C4H6O2(34794)
Created new reaction: C5H6O4(33570) --> C4H6O2(34794) + CO2(11)
Generating pressure dependent network for SPC(33570): 1,2_Elimination_ROR
Generating pressure dependent network for SPC(33570): Three_Ring_Cleavage
Generating pressure dependent network for SPC(33570): Four_Ring_Cleavage_Cd
Generating pressure dependent network for SPC(33570): Four_Ring_Cleavage_CO
Created new species: C2H2O3(34795)
Created new reaction: C5H6O4(33570) --> C2H2O3(34795) + CH2CHCHO(63)
Generating pressure dependent network for SPC(33570): Four_Ring_Cleavage_CCO
Generating pressure dependent network for SPC(33570): Retro_Diels_Alder_Addition
Generating pressure dependent network for SPC(33570): intra_H_migration
Generating pressure dependent network for SPC(33570): HO2_Elimination_from_PeroxyRadical
Generating pressure dependent network for SPC(33570): Birad_recombination
Generating pressure dependent network for SPC(33570): Ring_Open
Created new reaction: C5H6O4(33570) --> C5H6O4JJ(7488)
Created new species: C5H6O4JJ(34796)
Created new reaction: C5H6O4(33570) --> C5H6O4JJ(34796)
Created new reaction: C5H6O4(33570) --> C5H6O4JJ(11406)
Created new species: C5H6O4JJ(34797)
Created new reaction: C5H6O4(33570) --> C5H6O4JJ(34797)
Generating pressure dependent network for SPC(33570): RO_Bond_Dissociation
Generating pressure dependent network for SPC(33570): COM_Elimination_From_Carbonyl
Generating pressure dependent network for SPC(33570): Intra_R_Add_Exocyclic
Generating pressure dependent network for SPC(33570): Ring_Open_Exo_Cycli_Radical
Generating pressure dependent network for SPC(33570): Intra_R_Add_Endocyclic
Generating pressure dependent network for SPC(33570): Ring_Open_Endo_Cycli_Radical
Generating pressure dependent network for SPC(33570): 1,2-Birad_to_alkene
Generating pressure dependent network for SPC(33570): Alkene_to_1,2-birad
Created new reaction: C5H6O4(33570) --> C5H6O4JJ(33729)
Memory used: 1387003904
Free memory: 290162800
After garbage collection:
Memory used: 1397161984
Free memory: 396369576

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:544)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:334)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3982)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1439)
    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 #16599:
    Isomers:
    Path reactions:
        C5H8O2(1231) + C4H5J(12087) (included =true) --> C9H13O2J(17009) (included =false)
    Net reactions:
    Nonincluded reactions:
mrharper commented 14 years ago

(Restart) BUG FIX: Adding isomers from pathReactionList to network

Isomers were only being added to a PDepNetwork for netReactions and nonIncludedReactions. However, some pdep networks may only contain a single pathReaction (i.e. the network has not been explored beyond A+B-->C). If RMG tried to expand this network, an error would be thrown stating "no isomer can be identified".

This commit resolves the bug.

Closed by b4d02a992abf0332891b1c602160078295ec4cb0