Fix bug in electrons initialization for depository reaction data #2775

jonwzheng · 2025-03-28T21:47:28Z

This PR fixes a small bug:

Reaction expects electrons to be an integer, but the constructor for Depository reactions initializes electrons as None. This can lead to crashes (as was observed for the RMG-website: TypeError when searching kinetics RMG-website#288)
This PR simply changes the constructor to use a default value of 0 rather than None like other classes that inherit from Reaction.

Reactions expect electrons to be an integer, but the previous constructor for Depository reactions initialized it as None, which can lead to crashes

JacksonBurns · 2025-03-28T22:13:43Z

I see that the default value in Reaction is already zero (here) - this change makes sense to me.

github-actions · 2025-03-29T00:17:05Z

Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:07
Current: Execution time (DD:HH:MM:SS): 00:00:01:07
Reference: Memory used: 2785.49 MB
Current: Memory used: 2786.97 MB

aromatics Passed Core Comparison ✅

Original model has 15 species.
Test model has 15 species. ✅
Original model has 11 reactions.
Test model has 11 reactions. ✅

aromatics Passed Edge Comparison ✅

Original model has 106 species.
Test model has 106 species. ✅
Original model has 358 reactions.
Test model has 358 reactions. ✅

Details

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:20
Current: Execution time (DD:HH:MM:SS): 00:00:02:21
Reference: Memory used: 2907.19 MB
Current: Memory used: 2896.61 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 241 reactions.
Test model has 241 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1593 reactions.
Test model has 1590 reactions. ❌
The original model has 6 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> [OH](22) + CCCC(C)=O(29) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112) origin: intra_H_migration
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC([O])CC(C)OO(110) + CC([O])CCCOO(122) origin: Peroxyl_Disproportionation
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CC(C)OO(105) + CC(O)CCCOO(152) origin: Peroxyl_Termination
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CCCOO(112) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination
The tested model has 3 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(33) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCC(CC)O[O](37) + CCCCCO[O](35) <=> oxygen(1) + CCC([O])CC(67) + CCCCC[O](69) origin: Peroxyl_Disproportionation
tested:
rxn: CCC(CC)O[O](36) + CCCCCO[O](35) <=> oxygen(1) + CCC([O])CC(69) + CCCCC[O](67) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	3.54	4.28	4.73	5.02	5.39	5.62	5.91	6.06
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.064,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing

Details

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:25
Current: Execution time (DD:HH:MM:SS): 00:00:01:26
Reference: Memory used: 2900.00 MB
Current: Memory used: 2900.88 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 360 reactions. ✅

nitrogen Passed Edge Comparison ✅

Original model has 133 species.
Test model has 133 species. ✅
Original model has 983 reactions.
Test model has 983 reactions. ✅

Details

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:25
Current: Execution time (DD:HH:MM:SS): 00:00:02:30
Reference: Memory used: 2772.73 MB
Current: Memory used: 2768.10 MB

oxidation Passed Core Comparison ✅

Original model has 59 species.
Test model has 59 species. ✅
Original model has 694 reactions.
Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species.
Test model has 230 species. ✅
Original model has 1526 reactions.
Test model has 1526 reactions. ✅

Details

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:54
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 2870.43 MB
Current: Memory used: 2858.14 MB

sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Details

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:38
Current: Execution time (DD:HH:MM:SS): 00:00:00:38
Reference: Memory used: 2947.50 MB
Current: Memory used: 2955.29 MB

superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:22
Current: Execution time (DD:HH:MM:SS): 00:00:02:23
Reference: Memory used: 3501.71 MB
Current: Memory used: 3495.37 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:06:16
Current: Execution time (DD:HH:MM:SS): 00:00:06:15
Reference: Memory used: 3487.26 MB
Current: Memory used: 3489.87 MB

RMS_CSTR_liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 202 reactions.
Test model has 202 reactions. ✅

RMS_CSTR_liquid_oxidation Passed Edge Comparison ✅

Original model has 248 species.
Test model has 248 species. ✅
Original model has 2057 reactions.
Test model has 2057 reactions. ✅

Details

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:41
Current: Execution time (DD:HH:MM:SS): 00:00:00:41
Reference: Memory used: 2696.22 MB
Current: Memory used: 2694.95 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

fragment Passed Observable Testing ✅

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:04
Current: Execution time (DD:HH:MM:SS): 00:00:03:04
Reference: Memory used: 3624.16 MB
Current: Memory used: 3647.75 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:44
Current: Execution time (DD:HH:MM:SS): 00:00:00:44
Reference: Memory used: 2875.73 MB
Current: Memory used: 2863.09 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

minimal_surface Passed Observable Testing ✅

beep boop this comment was written by a bot 🤖

change default electrons from None to 0 for depository

1eccdc8

Reactions expect electrons to be an integer, but the previous constructor for Depository reactions initialized it as None, which can lead to crashes

JacksonBurns self-requested a review March 29, 2025 21:43

JacksonBurns approved these changes Mar 29, 2025

View reviewed changes

JacksonBurns merged commit 28c096d into main Mar 29, 2025
9 checks passed

JacksonBurns deleted the fix_electrochem branch March 29, 2025 21:43

jonwzheng mentioned this pull request Mar 31, 2025

TypeError when searching kinetics ReactionMechanismGenerator/RMG-website#288

Open

JacksonBurns mentioned this pull request Jul 10, 2025

RMG-Py Version 3.3.0 #2826

Merged

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Fix bug in electrons initialization for depository reaction data #2775

Fix bug in electrons initialization for depository reaction data #2775

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jonwzheng commented Mar 28, 2025

Uh oh!

JacksonBurns commented Mar 28, 2025

Uh oh!

github-actions bot commented Mar 29, 2025

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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Fix bug in electrons initialization for depository reaction data #2775

Fix bug in electrons initialization for depository reaction data #2775

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jonwzheng commented Mar 28, 2025

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JacksonBurns commented Mar 28, 2025

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github-actions bot commented Mar 29, 2025

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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