rwest
commented
13 years ago It looks to me that there must have been no structure in the reaction that was being checked by reactionPrunableQ. This occured when iterating over PathReactions from a PDepNetwork, when iterating over all Networks, in order to find which PathReactions to prune. Why could a PathReaction not have a structure? And why did nine path reactions in earlier PDepNetworks have reverse structures not in any ReactionTemplate dictionaries?
@rajeshdparmar, do you still have the log file and pruning folder? If so, please could you point us to the right folder on the server? (And if not, please run it again and keep the results.)
rajeshdparmar
mrharper
gmagoon
faribas
One of the job (out of 6 submitted jobs [3 jobs PM3 ON and 3 jobs PM3 off]) has given me following error. Condition file and error message is as follows: (Note: It is a case of PM3 OFF but pdep is ON)
Error Message
Edge species SPC(34021) has a low maximum flux ratio (5.7e-06) and will be pruned to reduce the edge size to the maximum (15000). Edge species SPC(43569) has a low maximum flux ratio (5.7e-06) and will be pruned to reduce the edge size to the maximum (15000). Edge species SPC(43574) has a low maximum flux ratio (5.7e-06) and will be pruned to reduce the edge size to the maximum (15000). Pruning... Removed path reverse SPC(35105)=SPC(35107) from 0 dictionaries Removed path reverse SPC(15029)=SPC(35107) from 0 dictionaries Removed path reverse SPC(15029)=SPC(35117) from 0 dictionaries Removed path reverse SPC(15029)=SPC(35097) from 0 dictionaries Removed path reverse SPC(15029)=SPC(35101) from 0 dictionaries Removed path reverse SPC(33335)=SPC(36791) from 0 dictionaries Removed path reverse SPC(37616)=SPC(47936) from 0 dictionaries Removed path reverse SPC(37616)=SPC(47946) from 0 dictionaries Removed path reverse SPC(37616)=SPC(47965) from 0 dictionaries ERROR: java.lang.NullPointerException at jing.rxn.Reaction.getReactants(Reaction.java:1091) at jing.rxnSys.ReactionModelGenerator.reactionPrunableQ(ReactionModelGenerator.java:4223) at jing.rxnSys.ReactionModelGenerator.pruneReactionModel(ReactionModelGenerator.java:4111) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1458) at RMG.main(RMG.java:96) Exception in thread "main" java.lang.NullPointerException at jing.rxnSys.Logger.log(Logger.java:160) at jing.rxnSys.Logger.critical(Logger.java:204) at RMG.main(RMG.java:106)condition file
Database: RMG_database MaxCarbonNumberPerSpecies: 20 //MaxOxygenNumberPerSpecies: MaxRadicalNumberPerSpecies: 4 MaxCycleNumberPerSpecies: 100 //MaxSulfurNumberPerSpecies: //MaxSiliconNumberPerSpecies: //MaxHeavyAtomPerSpecies: PrimaryThermoLibrary: Name: RMG_Default Location: primaryThermoLibrary Name: DFT_QCI // used from Dr. Richard West condition file Location: DFT_QCI_thermo Name: GRI-Mech3.0 Location: GRI-Mech3.0 END // 1. Default - used to calculate species thermo properties from Benson's additivity rule // 2. Rwest - // 3. DFT_QCI - unpublished high level quantem chemistry calcualtions from Green group. // 4. GRI-Mech3.0 - Methane combustion optimized mechanism PrimaryTransportLibrary: Name: GRIMech3.0 Location: GRI-Mech3.0 END // This is what RMG comes with // Forbidden structures are used from Dr. Richard West's condition file ForbiddenStructures: // In addition to PM3, B3LYP also seems to want to break this up into CO2 + CO2 + CO. // No record currently in SciFinder, the closest analog is a C3O5 with // slightly different structure discussed in doi:10.1016/S0166-1280(00)00601-1 // It caused Gaussian03 to seg-fault 35 times in a row and then freeze, so I'm forbidding // it so that I can move on. O=C=C1OOC(=O)O1 1 C 0 {2,S} {3,D} {5,S} 2 O 0 {1,S} {6,S} 3 O 0 {1,D} 4 C 0 {5,S} {6,S} {7,D} 5 O 0 {4,S} {1,S} 6 O 0 {4,S} {2,S} 7 C 0 {8,D} {4,D} 8 O 0 {7,D} // O this structure kills the QM calcs // / \ and it is nowhere to be found // C=C in SciFinder, so I am // | | assuming it doesn't exist // O-O and I am forbidding it. // also, Greg reports that it's a saddle point at the PM3 level o1oc2Oc12 1 C 0 {2,S} {3,S} {4,D} 2 O 0 {1,S} {5,S} 3 O 0 {1,S} {4,S} 4 C 0 {5,S} {1,D} {3,S} 5 O 0 {4,S} {2,S} END ReadRestart: no WriteRestart: yes TemperatureModel: Constant (K) 673.15 873.15 1073.15 1273.15 PressureModel: Constant (atm) 1.35 5.0 InChIGeneration: off // Quantum calculations for cyclic species. obtained from Dr. Richard West (MIT) // ThermoMethod: QM both // QMForCyclicsOnly: on // MaxRadNumForQM: 0 // with more than this number of radicals, HBI method is used. InitialStatus: (1) TD (mol/m3) 0.6033 1 C 0 {3,S} 2 C 0 {4,S} 3 C 0 {1,S} {5,S} 4 C 0 {2,S} {6,S} 5 C 0 {3,S} {7,S} 6 C 0 {4,S} {8,S} 7 C 0 {5,S} {9,S} 8 C 0 {6,S} {10,S} 9 C 0 {7,S} {11,S} 10 C 0 {8,S} {12,S} 11 C 0 {9,S} {13,S} 12 C 0 {10,S} {14,S} 13 C 0 {11,S} {14,S} 14 C 0 {12,S} {13,S} (2) H2O (mol/m3) 12.6698 1 O 0 (3) O2 (mol/m3) 1.6893 1 O 1 {2,S} 2 O 1 {1,S} END InertGas: N2 (mol/m3) 10.6185 Ne (mol/m3) 0 He (mol/m3) 0 Ar (mol/m3) 0 END // All other inert gases are kept zero as per the manual // Obtained from Dr. Richard West (MIT) SpectroscopicDataEstimator: FrequencyGroups PressureDependence: ReservoirState // ModifiedStrongCollision PDepKineticsModel: Chebyshev 4 2 TRange: (K) 673.15 1473.15 6 PRange: (atm) 1 5 3 // Specify whether fame calculation should be re-run in the event a // pdep rate exceeds the high-p-limit rate by > 2 (default is off) DecreaseGrainSize: yes FinishController: (1) Goal ReactionTime: 0.6 (sec) (2) Error Tolerance: 0.1 DynamicSimulator: DASSL TimeStep: AUTOPRUNE TerminationTolerance: 1.0E20 PruningTolerance: 1.0E-18 MinSpeciesForPruning: 1000 MaxEdgeSpeciesAfterPruning: 15000 Atol: 1e-20 Rtol: 1e-8 PrimaryKineticLibrary: END // Set to default ReactionLibrary: END // set to default // Seed Mechanism is obtained from Dr. Richard West (MIT) SeedMechanism: Name: GRI-Mech3.0 Location: GRI-Mech3.0 GenerateReactions: yes END ChemkinUnits: Verbose: on A: moles Ea: kcal/mol