Restart fails with error message

[ramanan]

I am running the code in remote git@github.com:ramanan/RMG-Java branch(forRamanan) and version (37e2732). This is very close to the version I started from, without much of my changes.

I then run RMG for the hexadecane/condition.txt. There is this error message when it starts running, but can run fine for ever on its own.

Reading thermochemistry groups Reading radical correction groups Reading ring correction groups Reading other correction groups Reading gauche and 1/5 correction groups Reading Abraham solvation groups ERROR: Error in database: Oss(CdsOd) is not actually a child of CdsH ERROR: Error in database: Cds(Od)Cds=CdsCds(Od) is not actually a child of CdsH ERROR: Error in database: Cds(Od)Cds=CdsCds(Od) is not actually a child of CdsH ERROR: Error in database: Oss(CdsOd) is not actually a child of Cds-noH ERROR: Error in database: Cds(Od)OssH is not actually a child of Cds-noH ERROR: Error in database: Cds(Od)Cds=CdsCds(Od) is not actually a child of Cds-noH ERROR: Error in database: Cds(Od)Cds=CdsCds(Od) is not actually a child of Cds-noH Reading Abraham radical solvation groups

I took for the first restart dump from RMG, then restarted it from there. It fails with this error:

Reacting hex(1) with the core: Cyclic_Ether_Formation Reacting hex(1) with the core: OH+CyclicEther_Form_Alkyl-hydroperoxyl Reacting hex(1) with the core: intra_OH_migration Reacting hex(1) with the core: H_Abstraction Created new reverse H_Abstraction reaction: hex(1) + O2(3) --> C16H33J(4) + HO2J(5) ERROR: java.lang.ClassCastException: jing.chemUtil.TreeNode cannot be cast to jing.chemUtil.HierarchyTreeNode at jing.chemUtil.HierarchyTree.findMatchedPath(HierarchyTree.java:87) at jing.chem.ThermoGAGroupLibrary.findAbrahamGroup(ThermoGAGroupLibrary.java:412) at jing.chem.GATP_Abraham.getABGroup(GATP_Abraham.java:172) at jing.chem.GATP_Abraham.generateAbramData(GATP_Abraham.java:65) at jing.chem.ChemGraph.generateAbramData(ChemGraph.java:1363) at jing.chem.ChemGraph.getAbramData(ChemGraph.java:1874) at jing.chem.ChemGraph.getRadius(ChemGraph.java:1907) at jing.rxn.Reaction.calculatediff(Reaction.java:391) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:323) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:367) at jing.rxn.Reaction.checkRateRange(Reaction.java:626) at jing.rxn.Reaction.repOk(Reaction.java:1374) at jing.rxn.TemplateReaction.repOk(TemplateReaction.java:427) at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:415) at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1203) at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:178) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3712) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3873) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1308) at RMG.main(RMG.java:96)

ERROR: jing.chem.FailGenerateThermoDataException at jing.chem.ChemGraph.generateAbramData(ChemGraph.java:1368) at jing.chem.ChemGraph.getAbramData(ChemGraph.java:1874) at jing.chem.ChemGraph.getRadius(ChemGraph.java:1907) at jing.rxn.Reaction.calculatediff(Reaction.java:391) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:323) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:367) at jing.rxn.Reaction.checkRateRange(Reaction.java:626) at jing.rxn.Reaction.repOk(Reaction.java:1374) at jing.rxn.TemplateReaction.repOk(TemplateReaction.java:427) at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:415) at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1203) at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:178) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3712) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3873) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1308) 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)

[ajalan]

Do you know which species is being processed when this error comes up? That would help diagnose if this is an Abraham group finding bug or something else.

[ramanan]

--snip--

---

User input:

Database: RMG_database

//MaxCarbonNumberPerSpecies: //MaxOxygenNumberPerSpecies: //MaxRadicalNumberPerSpecies: //MaxSulfurNumberPerSpecies: //MaxSiliconNumberPerSpecies: //MaxHeavyAtomPerSpecies:

PrimaryThermoLibrary: Name: GRIMech3.0 Location: GRI-Mech3.0 Name: RMG-old Location: primaryThermoLibrary Name: DFT_QCI_thermo Location: DFT_QCI_thermo Name: CBS_QB3_1dHR Location: CBS_QB3_1dHR END

PrimaryTransportLibrary: Name: GRIMech3.0 Location: GRI-Mech3.0 END

ReadRestart: yes WriteRestart: no

TemperatureModel: Constant (K) 453 PressureModel: Constant (atm) 1

EquationOfState: Liquid

Solvation: on octane

Diffusion: on 0.136e-3

InitialStatus:

hex (mol/cm3) 2.98e-3 1 C 0 {2,S} {13,S} 2 C 0 {1,S} {3,S} 3 C 0 {2,S} {4,S} 4 C 0 {3,S} {5,S} 5 C 0 {4,S} {6,S} 6 C 0 {5,S} {7,S} 7 C 0 {6,S} {8,S} 8 C 0 {7,S} {9,S} 9 C 0 {8,S} {10,S} 10 C 0 {9,S} {11,S} 11 C 0 {10,S} {12,S} 12 C 0 {11,S} {14,S} 13 C 0 {1,S} {15,S} 14 C 0 {12,S} {16,S} 15 C 0 {13,S} 16 C 0 {14,S}

hex-OOH (mol/cm3) 2.00e-6 1 C 0 {2,S} {13,S} {17,S} 2 C 0 {1,S} {12,S} 3 C 0 {4,S} {14,S} 4 C 0 {3,S} {5,S} 5 C 0 {4,S} {6,S} 6 C 0 {5,S} {7,S} 7 C 0 {6,S} {8,S} 8 C 0 {7,S} {9,S} 9 C 0 {8,S} {10,S} 10 C 0 {9,S} {11,S} 11 C 0 {10,S} {12,S} 12 C 0 {2,S} {11,S} 13 C 0 {1,S} {16,S} 14 C 0 {3,S} {15,S} 15 C 0 {14,S} 16 C 0 {13,S} 17 O 0 {1,S} {18,S} 18 O 0 {17,S}

O2 (mol/cm3) 1.102e-5 ConstantConcentration 1 O 1 {2,S} 2 O 1 {1,S}

END

InertGas:

END

SpectroscopicDataEstimator: off PressureDependence: off

//Set tolerance appropriately FinishController: (1) Goal ReactionTime: 3600 (sec) (2) Error Tolerance: 0.5

DynamicSimulator: DASSL TimeStep: AUTO //TerminationTolerance: 1e20 //PruningTolerance: 1.0E-18 //MinSpeciesForPruning: 5000 //MaxEdgeSpeciesAfterPruning: 5000 Atol: 1e-18 Rtol: 1e-8

//Error bars: off //Display sensitivity coefficients: off //Display sensitivity information: //END

PrimaryKineticLibrary:

END

ReactionLibrary:

END

SeedMechanism:

END

ChemkinUnits: A: moles Ea: kcal/mol

---

Reading Primary Thermo Library: GRIMech3.0 Reading Primary Thermo Library: RMG-old Reading Primary Thermo Library: DFT_QCI_thermo Reading Primary Thermo Library: CBS_QB3_1dHR Reading Primary Transport Library: GRIMech3.0 Reading in species from Restart folder

Reading thermo database from /Users/rsf/CodeWork/RMG/databases/RMG_database/thermo_groups/ Reading thermochemistry groups Reading radical correction groups Reading ring correction groups Reading other correction groups Reading gauche and 1/5 correction groups

Reading Lennard-Jones database from /Users/rsf/CodeWork/RMG/databases/RMG_database/transport_groups/

Created new species: hex(1) Created new species: hex-OOH(2) Created new species: O2(3) Created new species: C16H33OJ(61) Created new species: HOJ(62) Created new species: H2O(107) Created new species: C16H33J(4) Created new species: HO2J(5) Created new species: C16H33J(6) Created new species: C16H33J(7) Created new species: C16H33J(8) Created new species: C16H33J(9) Created new species: C16H33J(10) Created new species: C16H33J(11) Created new species: C16H33J(12) Created new species: npropyl(13) Created new species: C13H27J(14) Created new species: C14H29J(15) Created new species: C2H5J(16) Created new species: HJ(17) Created new species: butyl_1(18) Created new species: C12H25J(19) Created new species: C5H11J(20) Created new species: C11H23J(21) Created new species: C6H13J(22) Created new species: C10H21J(23) Created new species: C7H15J(24) Created new species: C9H19J(25) Created new species: C8H17J(26) Created new species: C15H31J(27) Created new species: CH3J(28) Created new species: C16H33O2J(29) Created new species: C16H33O2J(30) Created new species: C16H33O2J(31) Created new species: C16H33O2J(32) Created new species: C16H33O2J(33) Created new species: C16H33O2J(34) Created new species: C16H33O2J(35) Created new species: C16H33O2J(36) Created new species: C16H33O2J(37) Created new species: C16H33O2J(38) Created new species: C16H33O2J(39) Created new species: C16H33O2J(40) Created new species: C16H33O2J(41) Created new species: C16H33O2J(42) Created new species: C16H33O2J(43) Created new species: C16H33O2J(44) Created new species: C16H33O2J(45) Created new species: C3H7O2J(46) Created new species: C14H29O2J(47) Created new species: C4H9O2J(48) Created new species: C13H27O2J(49) Created new species: C14H29O2J(50) Created new species: C12H25O2J(51) Created new species: C11H23O2J(52) Created new species: C10H21O2J(53) Created new species: C9H19O2J(54) Created new species: C8H17O2J(55) Created new species: C7H15O2J(56) Created new species: C6H13O2J(57) Created new species: C5H11O2J(58) Created new species: C15H31O2J(59) Created new species: C15H31O2J(60) Created new species: C16H34O(63) Created new species: C16H32OJJ(64) Created new species: C16H32OJJ(65) Created new species: C16H32OJJ(66) Created new species: C16H32OJJ(67) Created new species: C16H32OJJ(68) Created new species: C16H32OJJ(69) Created new species: C16H32OJJ(70) Created new species: C16H32OJJ(71) Created new species: C16H32OJJ(72) Created new species: C16H32OJJ(73) Created new species: C16H32OJJ(74) Created new species: C16H32OJJ(75) Created new species: C16H32OJJ(76) Created new species: C16H32OJJ(77) Created new species: C16H32OJJ(78) Created new species: C16H32OJJ(79) Created new species: propanal(80) Created new species: C14H28O(81) Created new species: C16H32O(82) Created new species: C3H6OJJ(83) Created new species: C14H28OJJ(84) Created new species: C4H8OJJ(85) Created new species: C13H26OJJ(86) Created new species: C14H28OJJ(87) Created new species: C12H24OJJ(88) Created new species: C11H22OJJ(89) Created new species: C10H20OJJ(90) Created new species: C9H18OJJ(91) Created new species: C8H16OJJ(92) Created new species: C7H14OJJ(93) Created new species: C6H12OJJ(94) Created new species: C5H10OJJ(95) Created new species: C15H30OJJ(96) Created new species: C15H30OJJ(97) Created new species: C16H33OJ(98) Created new species: C16H33OJ(99) Created new species: C16H33OJ(100) Created new species: C16H33OJ(101) Created new species: C16H33OJ(102) Created new species: C16H33OJ(103) Created new species: C16H33OJ(104) Created new species: C16H33OJ(105) Created new species: OJJ(106) Created new species: H2O2(108) Reading reactions from Restart folder Reading seed mechanism from directory /Users/rsf/CodeWork/RMG/run/Restart Equation of state: Liquid. Relying on concentrations in input file to get density correct; not checking PV=NRT Reading Primary Abraham Library: primaryAbrahamLibrary Reading Primary Abraham Library: primaryAbrahamLibrary Reading Solvent Library: SolventLibrary Using solvation corrections to thermochemsitry with solvent properties of octane Using diffusion corrections to kinetics with solvent viscosity of 0.000136 Pa.s. Reading kinetics database from /Users/rsf/CodeWork/RMG/databases/RMG_database/kinetics_groups/

Reading kinetics groups database from: /Users/rsf/CodeWork/RMG/databases/RMG_database/kinetics_groups/

Reading forward template: Cyclic_Ether_Formation Generating reverse template: OH+CyclicEther_Form_Alkyl-hydroperoxyl Reading forward template: intra_OH_migration Reading forward template: H_Abstraction Reading forward template: R_Addition_MultipleBond Generating reverse template: Beta_Scission Reading forward template: R_Recombination Generating reverse template: Bond_Dissociation Reading forward template: Disproportionation Generating reverse template: Molecular_Addition Reading forward template: 1,2_Insertion Generating reverse template: 1,1_Elimination Reading forward template: 1,3_Insertion_CO2 Generating reverse template: 1,2_Elimination_CO2 Reading forward template: 1,3_Insertion_ROR Generating reverse template: 1,2_Elimination_ROR Reading forward template: 1+2_Cycloaddition Generating reverse template: Three_Ring_Cleavage Reading forward template: 2+2_cycloaddition_Cd Generating reverse template: Four_Ring_Cleavage_Cd Reading forward template: 2+2_cycloaddition_CO Generating reverse template: Four_Ring_Cleavage_CO Reading forward template: 2+2_cycloaddition_CCO Generating reverse template: Four_Ring_Cleavage_CCO Reading forward template: Diels_alder_addition Generating reverse template: Retro_Diels_Alder_Addition Reading forward template: intra_H_migration Reading forward template: HO2_Elimination_from_PeroxyRadical Reading forward template: Birad_recombination Generating reverse template: Ring_Open Reading forward template: Oa_R_Recombination Generating reverse template: RO_Bond_Dissociation Reading forward template: R_Addition_COm Generating reverse template: COM_Elimination_From_Carbonyl Reading forward template: Intra_R_Add_Exocyclic Generating reverse template: Ring_Open_Exo_Cycli_Radical Reading forward template: Intra_R_Add_Endocyclic Generating reverse template: Ring_Open_Endo_Cycli_Radical Reading forward template: 1,2-Birad_to_alkene Generating reverse template: Alkene_to_1,2-birad Reading forward template: Intra_Disproportionation Generating reverse template: BiradFromMultipleBond Reading forward template: ROO_Termination Reading forward template: Baeyer_Villiger Reading forward template: Korcek_rxn7 Skipping reaction family: ROO_Propagation Skipping reaction family: HOOQOO_beta_scission

Creating reaction system 1 Liquid phase: Not checking C=P/RT; assuming concentrations are specified correctly Temperature = 453.0 K Pressure = 1.0 atm hex = 2.980e-03 mol/cm^3 hex-OOH = 2.000e-06 mol/cm^3 O2 = 1.102e-05 mol/cm^3

Initializing core-edge reaction model hex(1)+O2(3)=C16H33J(4)+HO2J(5) hex(1)+O2(3)=C16H33J(6)+HO2J(5) hex(1)+O2(3)=C16H33J(7)+HO2J(5) hex(1)+O2(3)=C16H33J(8)+HO2J(5) hex(1)+O2(3)=C16H33J(9)+HO2J(5) hex(1)+O2(3)=SPC(10)+HO2J(5) hex(1)+O2(3)=SPC(11)+HO2J(5) hex(1)+O2(3)=SPC(12)+HO2J(5) hex(1)=SPC(13)+SPC(14) hex(1)=SPC(15)+C2H5J(16) hex(1)=C16H33J(4)+HJ(17) hex(1)=SPC(18)+SPC(19) hex(1)=C16H33J(6)+HJ(17) hex(1)=C5H11J(20)+SPC(21) hex(1)=C16H33J(7)+HJ(17) hex(1)=C6H13J(22)+SPC(23) hex(1)=C16H33J(8)+HJ(17) hex(1)=C7H15J(24)+C9H19J(25) hex(1)=C16H33J(9)+HJ(17) hex(1)=C8H17J(26)+C8H17J(26) hex(1)=SPC(10)+HJ(17) hex(1)=SPC(27)+CH3J(28) hex(1)=SPC(11)+HJ(17) hex(1)=SPC(12)+HJ(17) hex-OOH(2)+O2(3)=SPC(29)+HO2J(5) hex-OOH(2)+O2(3)=SPC(30)+HO2J(5) hex-OOH(2)+O2(3)=SPC(31)+HO2J(5) hex-OOH(2)+O2(3)=SPC(32)+HO2J(5) hex-OOH(2)+O2(3)=SPC(33)+HO2J(5) hex-OOH(2)+O2(3)=SPC(34)+HO2J(5) hex-OOH(2)+O2(3)=SPC(35)+HO2J(5) hex-OOH(2)+O2(3)=SPC(36)+HO2J(5) hex-OOH(2)+O2(3)=SPC(37)+HO2J(5) hex-OOH(2)+O2(3)=SPC(38)+HO2J(5) hex-OOH(2)+O2(3)=SPC(39)+HO2J(5) hex-OOH(2)+O2(3)=SPC(40)+HO2J(5) hex-OOH(2)+O2(3)=SPC(41)+HO2J(5) hex-OOH(2)+O2(3)=SPC(42)+HO2J(5) hex-OOH(2)+O2(3)=SPC(43)+HO2J(5) hex-OOH(2)+O2(3)=SPC(44)+HO2J(5) hex-OOH(2)+O2(3)=SPC(45)+HO2J(5) hex-OOH(2)=SPC(46)+SPC(14) hex-OOH(2)=SPC(47)+C2H5J(16) hex-OOH(2)=C16H33J(4)+HO2J(5) hex-OOH(2)=SPC(29)+HJ(17) hex-OOH(2)=SPC(48)+SPC(19) hex-OOH(2)=SPC(30)+HJ(17) hex-OOH(2)=SPC(49)+SPC(13) hex-OOH(2)=SPC(50)+C2H5J(16) hex-OOH(2)=SPC(31)+HJ(17) hex-OOH(2)=SPC(51)+SPC(18) hex-OOH(2)=SPC(32)+HJ(17) hex-OOH(2)=SPC(52)+C5H11J(20) hex-OOH(2)=SPC(33)+HJ(17) hex-OOH(2)=SPC(53)+C6H13J(22) hex-OOH(2)=SPC(34)+HJ(17) hex-OOH(2)=SPC(54)+C7H15J(24) hex-OOH(2)=SPC(35)+HJ(17) hex-OOH(2)=SPC(55)+C8H17J(26) hex-OOH(2)=SPC(36)+HJ(17) hex-OOH(2)=SPC(56)+C9H19J(25) hex-OOH(2)=SPC(37)+HJ(17) hex-OOH(2)=SPC(57)+SPC(23) hex-OOH(2)=SPC(38)+HJ(17) hex-OOH(2)=SPC(58)+SPC(21) hex-OOH(2)=SPC(39)+HJ(17) hex-OOH(2)=SPC(40)+HJ(17) hex-OOH(2)=SPC(59)+CH3J(28) hex-OOH(2)=SPC(41)+HJ(17) hex-OOH(2)=SPC(60)+CH3J(28) hex-OOH(2)=SPC(42)+HJ(17) hex-OOH(2)=SPC(43)+HJ(17) hex-OOH(2)=SPC(44)+HJ(17) hex-OOH(2)=SPC(45)+HJ(17) hex(1)+SPC(61)=C16H33J(4)+SPC(63) hex(1)+SPC(61)=C16H33J(6)+SPC(63) hex(1)+SPC(61)=C16H33J(7)+SPC(63) hex(1)+SPC(61)=C16H33J(8)+SPC(63) hex(1)+SPC(61)=C16H33J(9)+SPC(63) hex(1)+SPC(61)=SPC(10)+SPC(63) hex(1)+SPC(61)=SPC(11)+SPC(63) hex(1)+SPC(61)=SPC(12)+SPC(63) hex-OOH(2)+SPC(61)=SPC(29)+SPC(63) hex-OOH(2)+SPC(61)=SPC(30)+SPC(63) hex-OOH(2)+SPC(61)=SPC(31)+SPC(63) hex-OOH(2)+SPC(61)=SPC(32)+SPC(63) hex-OOH(2)+SPC(61)=SPC(33)+SPC(63) hex-OOH(2)+SPC(61)=SPC(34)+SPC(63) hex-OOH(2)+SPC(61)=SPC(35)+SPC(63) hex-OOH(2)+SPC(61)=SPC(36)+SPC(63) hex-OOH(2)+SPC(61)=SPC(37)+SPC(63) hex-OOH(2)+SPC(61)=SPC(38)+SPC(63) hex-OOH(2)+SPC(61)=SPC(39)+SPC(63) hex-OOH(2)+SPC(61)=SPC(40)+SPC(63) hex-OOH(2)+SPC(61)=SPC(41)+SPC(63) hex-OOH(2)+SPC(61)=SPC(42)+SPC(63) hex-OOH(2)+SPC(61)=SPC(43)+SPC(63) hex-OOH(2)+SPC(61)=SPC(44)+SPC(63) hex-OOH(2)+SPC(61)=SPC(45)+SPC(63) SPC(61)+O2(3)=SPC(64)+HO2J(5) SPC(61)+O2(3)=SPC(65)+HO2J(5) SPC(61)+O2(3)=SPC(66)+HO2J(5) SPC(61)+O2(3)=SPC(67)+HO2J(5) SPC(61)+O2(3)=SPC(68)+HO2J(5) SPC(61)+O2(3)=SPC(69)+HO2J(5) SPC(61)+O2(3)=SPC(70)+HO2J(5) SPC(61)+O2(3)=SPC(71)+HO2J(5) SPC(61)+O2(3)=SPC(72)+HO2J(5) SPC(61)+O2(3)=SPC(73)+HO2J(5) SPC(61)+O2(3)=SPC(74)+HO2J(5) SPC(61)+O2(3)=SPC(75)+HO2J(5) SPC(61)+O2(3)=SPC(76)+HO2J(5) SPC(61)+O2(3)=SPC(77)+HO2J(5) SPC(61)+O2(3)=SPC(78)+HO2J(5) SPC(61)+O2(3)=SPC(79)+HO2J(5) SPC(61)+SPC(61)=SPC(64)+SPC(63) SPC(61)+SPC(61)=SPC(65)+SPC(63) SPC(61)+SPC(61)=SPC(66)+SPC(63) SPC(61)+SPC(61)=SPC(67)+SPC(63) SPC(61)+SPC(61)=SPC(68)+SPC(63) SPC(61)+SPC(61)=SPC(69)+SPC(63) SPC(61)+SPC(61)=SPC(70)+SPC(63) SPC(61)+SPC(61)=SPC(71)+SPC(63) SPC(61)+SPC(61)=SPC(72)+SPC(63) SPC(61)+SPC(61)=SPC(73)+SPC(63) SPC(61)+SPC(61)=SPC(74)+SPC(63) SPC(61)+SPC(61)=SPC(75)+SPC(63) SPC(61)+SPC(61)=SPC(76)+SPC(63) SPC(61)+SPC(61)=SPC(77)+SPC(63) SPC(61)+SPC(61)=SPC(78)+SPC(63) SPC(61)+SPC(61)=SPC(79)+SPC(63) SPC(61)=SPC(80)+SPC(14) SPC(61)=SPC(81)+C2H5J(16) SPC(61)=SPC(82)+HJ(17) SPC(61)=SPC(83)+SPC(14) SPC(61)=SPC(84)+C2H5J(16) SPC(61)=SPC(64)+HJ(17) SPC(61)=SPC(85)+SPC(19) SPC(61)=SPC(65)+HJ(17) SPC(61)=SPC(86)+SPC(13) SPC(61)=SPC(87)+C2H5J(16) SPC(61)=SPC(66)+HJ(17) SPC(61)=SPC(88)+SPC(18) SPC(61)=SPC(67)+HJ(17) SPC(61)=SPC(89)+C5H11J(20) SPC(61)=SPC(68)+HJ(17) SPC(61)=SPC(90)+C6H13J(22) SPC(61)=SPC(69)+HJ(17) SPC(61)=SPC(91)+C7H15J(24) SPC(61)=SPC(70)+HJ(17) SPC(61)=SPC(92)+C8H17J(26) SPC(61)=SPC(71)+HJ(17) SPC(61)=SPC(93)+C9H19J(25) SPC(61)=SPC(72)+HJ(17) SPC(61)=SPC(94)+SPC(23) SPC(61)=SPC(73)+HJ(17) SPC(61)=SPC(95)+SPC(21) SPC(61)=SPC(74)+HJ(17) SPC(61)=SPC(75)+HJ(17) SPC(61)=SPC(96)+CH3J(28) SPC(61)=SPC(76)+HJ(17) SPC(61)=SPC(97)+CH3J(28) SPC(61)=SPC(77)+HJ(17) SPC(61)=SPC(78)+HJ(17) SPC(61)=SPC(79)+HJ(17) O2(3)+SPC(61)=HO2J(5)+SPC(82) SPC(61)+SPC(61)=SPC(63)+SPC(82) SPC(61)=SPC(98) SPC(61)=SPC(99) SPC(61)=SPC(100) SPC(61)=SPC(101) SPC(61)=SPC(102) SPC(61)=SPC(103) SPC(61)=SPC(104) SPC(61)=SPC(105) SPC(61)=C16H33J(4)+OJJ(106) hex(1)+HOJ(62)=C16H33J(4)+H2O(107) hex(1)+HOJ(62)=C16H33J(6)+H2O(107) hex(1)+HOJ(62)=C16H33J(7)+H2O(107) hex(1)+HOJ(62)=C16H33J(8)+H2O(107) hex(1)+HOJ(62)=C16H33J(9)+H2O(107) hex(1)+HOJ(62)=SPC(10)+H2O(107) hex(1)+HOJ(62)=SPC(11)+H2O(107) hex(1)+HOJ(62)=SPC(12)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(29)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(30)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(31)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(32)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(33)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(34)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(35)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(36)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(37)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(38)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(39)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(40)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(41)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(42)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(43)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(44)+H2O(107) hex-OOH(2)+HOJ(62)=SPC(45)+H2O(107) SPC(61)+HOJ(62)=SPC(64)+H2O(107) SPC(61)+HOJ(62)=SPC(65)+H2O(107) SPC(61)+HOJ(62)=SPC(66)+H2O(107) SPC(61)+HOJ(62)=SPC(67)+H2O(107) SPC(61)+HOJ(62)=SPC(68)+H2O(107) SPC(61)+HOJ(62)=SPC(69)+H2O(107) SPC(61)+HOJ(62)=SPC(70)+H2O(107) SPC(61)+HOJ(62)=SPC(71)+H2O(107) SPC(61)+HOJ(62)=SPC(72)+H2O(107) SPC(61)+HOJ(62)=SPC(73)+H2O(107) SPC(61)+HOJ(62)=SPC(74)+H2O(107) SPC(61)+HOJ(62)=SPC(75)+H2O(107) SPC(61)+HOJ(62)=SPC(76)+H2O(107) SPC(61)+HOJ(62)=SPC(77)+H2O(107) SPC(61)+HOJ(62)=SPC(78)+H2O(107) SPC(61)+HOJ(62)=SPC(79)+H2O(107) HOJ(62)+HOJ(62)=H2O2(108) HOJ(62)+SPC(61)=H2O(107)+SPC(82) HOJ(62)=OJJ(106)+HJ(17) HOJ(62)+HO2J(5)=H2O(107)+O2(3) HOJ(62)+SPC(63)=H2O(107)+SPC(61) H2O(107)=HJ(17)+HOJ(62) Reacting hex(1) with the core: Cyclic_Ether_Formation Reacting hex(1) with the core: OH+CyclicEther_Form_Alkyl-hydroperoxyl Reacting hex(1) with the core: intra_OH_migration Reacting hex(1) with the core: H_Abstraction Created new reverse H_Abstraction reaction: hex(1) + O2(3) --> C16H33J(4) + HO2J(5) ERROR: java.lang.ClassCastException: jing.chemUtil.TreeNode cannot be cast to jing.chemUtil.HierarchyTreeNode at jing.chemUtil.HierarchyTree.findMatchedPath(HierarchyTree.java:87) at jing.chem.ThermoGAGroupLibrary.findAbrahamGroup(ThermoGAGroupLibrary.java:412) at jing.chem.GATP_Abraham.getABGroup(GATP_Abraham.java:172) at jing.chem.GATP_Abraham.generateAbramData(GATP_Abraham.java:65) at jing.chem.ChemGraph.generateAbramData(ChemGraph.java:1363) at jing.chem.ChemGraph.getAbramData(ChemGraph.java:1874) at jing.chem.ChemGraph.getRadius(ChemGraph.java:1907) at jing.rxn.Reaction.calculatediff(Reaction.java:391) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:323) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:367) at jing.rxn.Reaction.checkRateRange(Reaction.java:626) at jing.rxn.Reaction.repOk(Reaction.java:1374) at jing.rxn.TemplateReaction.repOk(TemplateReaction.java:427) at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:415) at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1203) at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:178) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3712) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3873) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1308) at RMG.main(RMG.java:96)

ERROR: jing.chem.FailGenerateThermoDataException at jing.chem.ChemGraph.generateAbramData(ChemGraph.java:1368) at jing.chem.ChemGraph.getAbramData(ChemGraph.java:1874) at jing.chem.ChemGraph.getRadius(ChemGraph.java:1907) at jing.rxn.Reaction.calculatediff(Reaction.java:391) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:323) at jing.rxn.Reaction.calculateTotalRate(Reaction.java:367) at jing.rxn.Reaction.checkRateRange(Reaction.java:626) at jing.rxn.Reaction.repOk(Reaction.java:1374) at jing.rxn.TemplateReaction.repOk(TemplateReaction.java:427) at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:415) at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1203) at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:178) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3712) at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3873) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1308) 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)

[ajalan]

I tested all 4 species involved in the reaction: hex(1) + O2(3) --> C16H33J(4) + HO2J(5) after which the error occurs and did not have trouble with their thermo estimation. It doesn't look like a problem with the group additivity method being used (unless I mistakenly tested the wrong species and the program isn't even telling us which species it is).

[ramanan]

I will step through this failed restart to get better pointers to where it is failing.