Update thermo by 12Chao · Pull Request #672 · ReactionMechanismGenerator/RMG-database

12Chao · 2024-12-10T02:30:12Z

This PR has the database used for CO methanation model generation with coverage-dependent thermodynamics. Can be used for testing the coverage-dependent thermo PR in RMG-Py ReactionMechanismGenerator/RMG-Py#2646

ssun30 · 2025-01-28T01:35:56Z

This PR will temporarily use the corresponding sister PR for RMG-Py for CI. I'm assuming we are in the same situation as electrochemistry where we have to make sure everything runs correctly on both RMG-Py and RMG-database, and then revert the changes to the CI workflow file and merge manually.

Revert this change after the sister PR is merged.

github-actions · 2025-01-28T03:24:52Z

Regression Testing Results

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): 00:00:01:06
Current: Execution time (DD:HH:MM:SS): 00:00:01:07
Reference: Memory used: 2766.43 MB
Current: Memory used: 2770.08 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 Failed Edge Comparison ❌

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

Non-identical thermo! ❌
original: C=CC1C=CC2=CC1C=C2
tested: C=CC1C=CC2=CC1C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
83.22	84.16	35.48	45.14	53.78	61.40	73.58	82.20	95.08
83.22	82.78	35.48	45.14	53.78	61.40	73.58	82.20	95.08

Identical thermo comments:
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentadiene)

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): 00:00:02:19
Current: Execution time (DD:HH:MM:SS): 00:00:02:20
Reference: Memory used: 2893.93 MB
Current: Memory used: 2895.47 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 1590 reactions.
Test model has 1593 reactions. ❌
The original model has 4 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(31) <=> [OH](22) + CCCC(C)=O(28) origin: intra_H_migration
rxn: C[CH]CCCOO(63) <=> [OH](22) + CCCCC=O(60) 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
The tested model has 7 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: CCCC[CH]OO(96) <=> C[CH]CCCOO(63) 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
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC([O])CC(C)OO(110) + CC([O])CCCOO(123) 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(115) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination

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): 00:00:01:25
Reference: Memory used: 2888.09 MB
Current: Memory used: 2893.61 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): 00:00:02:26
Current: Execution time (DD:HH:MM:SS): 00:00:02:26
Reference: Memory used: 2761.57 MB
Current: Memory used: 2760.87 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: 2866.12 MB
Current: Memory used: 2860.90 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): 00:00:00:35
Current: Execution time (DD:HH:MM:SS): 00:00:00:35
Reference: Memory used: 2947.11 MB
Current: Memory used: 2951.72 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): 00:00:02:23
Current: Execution time (DD:HH:MM:SS): 00:00:02:23
Reference: Memory used: 3481.11 MB
Current: Memory used: 3493.02 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): 00:00:06:11
Current: Execution time (DD:HH:MM:SS): 00:00:06:13
Reference: Memory used: 3475.73 MB
Current: Memory used: 3465.35 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 ✅

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ssun30 force-pushed the update_thermo branch from ee66f8f to 82f1a12 Compare January 28, 2025 01:18

12Chao added 7 commits January 27, 2025 20:19

data for cov-dep thermo test

bd1c905

Add in the cov-dep thermo paraemter for CO on Ni

8f3befe

Add in the cov dep kinetics from doi.org/10.1021/acs.iecr.1c00389 ref 36

b49f4e6

correct the cov dep data to be consistent with the literature

41565c1

Add reactions from for methanation on Ni from literature

94b0dd9

Add coverage dependent thermo models

b1fcda7

Separate the new library from the old

c228d3d

ssun30 force-pushed the update_thermo branch from 82f1a12 to c228d3d Compare January 28, 2025 01:19

TMP: Switch CI to cov_dep_thermo branch of RMG-Py

44077f2

Revert this change after the sister PR is merged.

ssun30 force-pushed the update_thermo branch from 93d566a to 44077f2 Compare January 28, 2025 01:40

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Update thermo#672

Update thermo#672
12Chao wants to merge 8 commits intoReactionMechanismGenerator:mainfrom
12Chao:update_thermo

12Chao commented Dec 10, 2024

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ssun30 commented Jan 28, 2025

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github-actions bot commented Jan 28, 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:

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12Chao commented Dec 10, 2024

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ssun30 commented Jan 28, 2025

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github-actions bot commented Jan 28, 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:

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