Closed ezanoelo closed 13 years ago
gmagoon
commented
13 years ago I suspect that this may be related to an error in aromaticity perception, which has produced similar issues in the past. @nickvandewiele, do you agree?
Perhaps you could post the adjacency lists for SPC(6782) and SPC(11865)?
gmagoon
commented
13 years ago I just had a similar issue in my job with a C4H4J species. You can see that it was apparently incorrectly aromatized:
*****Error in Gaussian log file: Error termination via Lnk1e in /opt/g03/l1.exe at Thu Nov 3 17:33:36 2011.
*****Final attempt (#36) on species ITPIBAHFTRGDDL-UHFFFAOYAZ (InChI=1/C4H5/c1-4-2-3-4/h2-3H,1H3) failed.
ChemFormula: C4H4J
1 C 0 {2,S} {5,S} {6,S} {9,S}
2 C 0 {3,B} {4,B} {1,S}
3 C 0 {2,B} {4,B} {8,S}
4 C 0 {3,B} {2,B} {7,S}
5 H 0 {1,S}
6 H 0 {1,S}
7 H 0 {4,S}
8 H 0 {3,S}
9 H 0 {1,S}
HBI-based thermo for GOSMMPKSWSOPRZ-UHFFFAOYAD(InChI=1/C4H4/c1-4-2-3-4/h2-3H,1H2): 1036.4 -4.74 0.75 0.6 0.13 -0.42 -1.41 -2.18 -2.18
Warning: Falling back to group additivity due to repeated failure in QMTP calculations
Warning: Transport group not found: 2
Warning: Transport group not found: 3
Warning: Transport group not found: 4
Created new species: C4H3J(733)
Created new forwards Intra_R_Add_Endocyclic reaction: H2CCCCH(27) --> C4H3J(733)
ERROR: Reaction is not balanced: SPC(27)=C4H3J(733)
ERROR: Invalid Reaction Structure:SPC(27)=C4H3J(733)
ERROR: jing.rxn.InvalidTemplateReactionException
at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:416)
at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:896)
at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:807)
at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:134)
at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:79)
at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3642)
at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3917)
at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1331)
at RMG.main(RMG.java:96)
Any ideas for fixes, @mrharper and @nickvandewiele? If not, I'm thinking about trying to resurrect Sandeep's aromaticity perception approach.
ezanoelo
commented
13 years ago Greg, Thank you for your answer. I am just trying to understand the nomenclature used in the RMG to define the chemical structure of a specie. However, because I believe this specie is not important in our model, I removed it and its entire family from the model. Perhaps, I will have to fix the error in the future.
From: gmagoon [reply@reply.github.com] Sent: Thursday, November 03, 2011 6:32 PM To: Everton Zanoelo Subject: Re: [RMG-Java] reaction no balanced error for intra_R_Add_endocyclic reactions (#225)
I just had a similar issue in my job with a C4H4J species. You can see that it was apparently incorrectly aromatized:
*****Error in Gaussian log file: Error termination via Lnk1e in /opt/g03/l1.exe at Thu Nov 3 17:33:36 2011.
*****Final attempt (#36) on species ITPIBAHFTRGDDL-UHFFFAOYAZ (InChI=1/C4H5/c1-4-2-3-4/h2-3H,1H3) failed.
ChemFormula: C4H4J
1 C 0 {2,S} {5,S} {6,S} {9,S}
2 C 0 {3,B} {4,B} {1,S}
3 C 0 {2,B} {4,B} {8,S}
4 C 0 {3,B} {2,B} {7,S}
5 H 0 {1,S}
6 H 0 {1,S}
7 H 0 {4,S}
8 H 0 {3,S}
9 H 0 {1,S}
HBI-based thermo for GOSMMPKSWSOPRZ-UHFFFAOYAD(InChI=1/C4H4/c1-4-2-3-4/h2-3H,1H2): 1036.4 -4.74 0.75 0.6 0.13 -0.42 -1.41 -2.18 -2.18
Warning: Falling back to group additivity due to repeated failure in QMTP calculations
Warning: Transport group not found: 2
Warning: Transport group not found: 3
Warning: Transport group not found: 4
Created new species: C4H3J(733)
Created new forwards Intra_R_Add_Endocyclic reaction: H2CCCCH(27) --> C4H3J(733)
ERROR: Reaction is not balanced: SPC(27)=C4H3J(733)
ERROR: Invalid Reaction Structure:SPC(27)=C4H3J(733)
ERROR: jing.rxn.InvalidTemplateReactionException
at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:416)
at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:896)
at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:807)
at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:134)
at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:79)
at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeModel(ReactionModelGenerator.java:3642)
at jing.rxnSys.ReactionModelGenerator.initializeCoreEdgeReactionModel(ReactionModelGenerator.java:3917)
at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1331)
at RMG.main(RMG.java:96)
Any ideas for fixes, @mrharper and @nickvandewiele? If not, I'm thinking about trying to resurrect Sandeep's aromaticity perception approach.
Reply to this email directly or view it on GitHub: https://github.com/GreenGroup/RMG-Java/issues/225#issuecomment-2624191
nickvandewiele
commented
13 years ago If the error is thrown based on RMG-Java at the latest commit, the "Reaction not balanced" error definitely smells like an aromaticity perception error due to the incorrect addition/deletion of implicit hydrogens.
Anyways, the aro percept. algo was never tested for C4s; only for a couple of C6/C7/C5s. See previous commit messages / issues for this.
I will have a look at it in the coming days.
nickvandewiele
commented
13 years ago @gmagoon,
I just tried InChI=1/C4H5/c1-4-2-3-4/h2-3H,1H3 with the adjacency list:
C4H5 1 C 0 {2,S} 2 C 1 {1,S} {3,S} {4,S} 3 C 0 {2,S} {4,D} 4 C 0 {2,S} {3,D}
and it returned the following (succesful) ThermoDataEstimator job:
[Console output redirected to file:C:\Documents and Settings\nmvdewie\My Documents\workspaces\myForkedProjectsWorkspace\RMG-Java\propellanes.log]
Note: Overriding default MAX_CARBON_NUM with user-defined value: 10
Note: Overriding default MAX_OXYGEN_NUM with user-defined value: 10
Note: Overriding default MAX_RADICAL_NUM with user-defined value: 10
Note: Overriding default MAX_SULFUR_NUM with user-defined value: 10
Note: Overriding default MAX_SILICON_NUM with user-defined value: 10
Note: Overriding default MAX_HEAVYATOM_NUM with user-defined value: 100
Note: Overriding default MAX_CYCLE_NUM with user-defined value: 10
Reading Primary Thermo Library: RMG-minimal
Reading thermo database from C:\Documents and Settings\nmvdewie\My Documents\workspaces\myForkedProjectsWorkspace\RMG-Java/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
ThreeMember
ThreeMember
Cyclopropene
Value for Stack: 1
ThreeMember
Cyclopropene
ThreeMember
Value for Stack: 1
Reading Lennard-Jones database from C:\Documents and Settings\nmvdewie\My Documents\workspaces\myForkedProjectsWorkspace\RMG-Java/databases/RMG_database/transport_groups\
Created new species: C4H5(1)
ChemFormula: C4H5J
1 C 0 {2,S} {5,S} {6,S} {7,S}
2 C 0 {3,S} {4,D} {1,S}
3 C 1 {2,S} {4,S} {8,S}
4 C 0 {2,D} {3,S} {9,S}
5 H 0 {1,S}
6 H 0 {1,S}
7 H 0 {1,S}
8 H 0 {3,S}
9 H 0 {4,S}
The number of resonance isomers is 2
The NASA data is
!Estimated by RMG using Group Additivity
!Group:Cs-(Cds-Cds)HHH Group:Cds-CdsCsCs Group:Cs-(Cds-Cds)(Cds-Cds)HH Group:Cds-CdsCsH Radical:C=CCJC=C
C4H5(1) C 4H 5 G 250.000 5000.000 995.043 1
9.77543771E+00 1.26618417E-02-3.79923427E-06 5.25625568E-10-2.77831705E-14 2
3.75393292E+04-3.03944038E+01 3.20244423E+00 2.02452677E-03 6.81035865E-05 3
-8.50788533E-08 3.08841880E-11 4.06820987E+04 1.05029646E+01 4
ThermoData is
83.81 62.97 16.55 21.53 25.77 29.15 34.12 37.6 43.64
symmetry number = 3
C4H5J H = 83.81022422
Done!
I am working with the latest version of RMG-Java...
Could you check if your TDE still generates the error for C4H5 after merging in the latest version on github (GreenGroup)Sorry for the delay in getting back to you...the e-mail notification got lost in a deluge of e-mails. I think the species in question is actually C4H3? (whatever the product of intra r-add endocyclic on H2CCCH is). I'll try to figure out what the C3HO species is...
gmagoon
commented
13 years ago OK...figured out the problematic C4H3 case:
Note: Overriding default MAX_CARBON_NUM with user-defined value: 10
Note: Overriding default MAX_OXYGEN_NUM with user-defined value: 10
Note: Overriding default MAX_RADICAL_NUM with user-defined value: 10
Note: Overriding default MAX_SULFUR_NUM with user-defined value: 10
Note: Overriding default MAX_SILICON_NUM with user-defined value: 10
Note: Overriding default MAX_HEAVYATOM_NUM with user-defined value: 100
Note: Overriding default MAX_CYCLE_NUM with user-defined value: 10
Reading Primary Thermo Library: RMG-minimal
Reading thermo database from c:\Users\User1\RMG-Java/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 c:\Users\User1\RMG-Java/databases/RMG_database/transport_groups\
Warning: Transport group not found: 1
Warning: Transport group not found: 2
Warning: Transport group not found: 3
Created new species: C4H3J(1)
ChemFormula: C4H4J
1 C 0 {2,B} {3,B} {8,S}
2 C 0 {1,B} {3,B} {5,S}
3 C 0 {1,B} {2,B} {4,S}
4 C 1 {3,S} {6,S} {7,S}
5 H 0 {2,S}
6 H 0 {4,S}
7 H 0 {4,S}
8 H 0 {1,S}
The number of resonance isomers is 2
The NASA data is
!Estimated by RMG using Group Additivity
!Group:Cb-H Group:Cb-H Group:Cb-Cs Group:Cs-CbHHH Radical:Benzyl_P
C4H3J(1) C 4H 4 G 250.000 5000.000 995.043 1
8.51865999E+00 1.24568770E-02-3.68580599E-06 4.96527830E-10-2.55261901E-14 2
1.52737047E+04-3.50229311E+01 3.21941814E+00 4.54425669E-03 5.22833599E-05 3
-6.65091484E-08 2.42228499E-11 1.77746120E+04-2.21589645E+00 4
ThermoData is
38.31 38.29 16.09 20.46 24.13 27.12 31.65 34.85 40.84
symmetry number = 4
C4H4J H = 38.309999999999995
Done!
gmagoon
commented
13 years ago PS...here's what I specified in the input file:
Database: RMG_database
//QM? true/false
false
//method: both/gaussian03/mopac/mm4/mm4hr
gaussian03
//ForCyclicsOnly? true/false
true
//maxradnumforQM?
0
//CheckConnectivity? off/check/confirm
check
MaxCarbonNumberPerSpecies: 10
MaxOxygenNumberPerSpecies: 10
MaxRadicalNumberPerSpecies: 10
MaxSulfurNumberPerSpecies: 10
MaxSiliconNumberPerSpecies: 10
MaxHeavyAtomNumberPerSpecies: 100
MaxCycleNumberPerSpecies: 10
END
PrimaryThermoLibrary:
Name: RMG-minimal
Location: primaryThermoLibrary
END
C4H3J
1 C 1 {2,D} {3,S}
2 C 0 {1,D} {3,S}
3 C 0 {1,S} {2,S} {4,D}
4 C 0 {3,D}
gmagoon
commented
13 years ago I suspect Everton's C3HOJ species may be this very similar species, which has similar problems:
C3HOJ
1 C 1 {2,D} {3,S}
2 C 0 {1,D} {3,S}
3 C 0 {1,S} {2,S} {4,D}
4 O 0 {3,D}
Created new species: C3HOJ(1)
ChemFormula: C3H2OJ
1 C 0 {2,B} {3,B} {6,S}
2 C 0 {1,B} {3,B} {5,S}
3 C 0 {1,B} {2,B} {4,S}
4 O 1 {3,S}
5 H 0 {2,S}
6 H 0 {1,S}
The number of resonance isomers is 2
The NASA data is
!Estimated by RMG using Group Additivity
!Group:Cb-H Group:Cb-H Group:Cb-Os Group:Os-CbH Radical:COJ
C3HOJ(1) C 3H 2O 1 G 250.000 5000.000 995.043 1
9.71629545E+00 5.84107186E-03-1.80011389E-06 2.52488393E-10-1.34284779E-14 2
5.76099575E+03-3.97684481E+01 3.41098331E+00-5.10190594E-04 5.55583603E-05 3
-7.01917812E-08 2.57289454E-11 8.58504034E+03-1.49503980E+00 4
ThermoData is
19.76 39.12 13.7 17.38 20.33 22.54 25.62 27.53 30.38
symmetry number = 2
C3H2OJ H = 19.759999999999998
gmagoon
commented
13 years ago In case it helps, there didn't seem to be an issue when I tried without the substituent on the C3 ring (C3H3J)
gmagoon
commented
13 years ago @ezanoelo , I'm going to merge in the "aromaticityAlt" branch which should hopefully address this; you can turn your intra_R_Add_endocyclic family back on and if you still have problems, please let me know and/or post a new issue.
ezanoelo
commented
13 years ago Thank you. I am going to try to run the model turning the intra_R_Add_endocyclic family on.
One of my recent isobutanol jobs terminated with this error:
Created new species: C3HOJ(11865) Created new forwards Intra_R_Add_Endocyclic reaction: C3HOJ(6782) --> C3HOJ(11865) ERROR: Reaction is not balanced: SPC(6782)=SPC(11865) ERROR: Invalid Reaction Structure:SPC(6782)=SPC(11865) ERROR: jing.rxn.InvalidTemplateReactionException at jing.rxn.TemplateReaction.makeTemplateReaction(TemplateReaction.java:416) at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:896) at jing.rxn.ReactionTemplate.reactOneReactant(ReactionTemplate.java:807) at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:134) at jing.rxnSys.RateBasedRME.enlargeReactionModel(RateBasedRME.java:150) at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3938) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1487) at RMG.main(RMG.java:96)