Adding Fluoromethane chemistry to RMG kinetic database #624

SiddhaSharma · 2023-06-15T08:12:30Z

kinetics for thermal degradation of Fluoromethanes.

input/kinetics/libraries/Fluoromethane/reactions.py

Nora-Khalil · 2023-06-15T19:02:37Z

Hi Siddha,

With a great deal of help from @ChrisBNEU, I was able to add your commits to halogens_combustion_paper, a branch of RMG database that our lab had been using for halogen chemistry. I'm going to see if things still run smoothly in RMG with your additions on this branch, and how it affects a CH3F model.

Until then, for general house keeping purposes, would you be able to edit this pull request and the long description in the reactions.py file with some more details about how you generated the new data/where it came from? If this data was generated using quantum calculations, we will probably need to know the level of theory, etc. and if from literature, we would like to know the source. Two good examples of what the long description should look like can be found here and here.

Thanks so much for this awesome work!

Nora-Khalil

Thanks for the edits!

ChrisBNEU

This looks good, but before we merge can we rebase and make sure the tests all pass? There was an issue with the database tests but I think it should be resolved now.

ChrisBNEU · 2023-08-16T19:52:35Z

The database tests appear to still be broken, but here's a report from running the database tests locally, they all passed.
htmlcov.zip

Added species CH2FO

Corrected CF3CO Adjacency List

Revised description for the reactions.py file

update

updated

Update NASA7

github-actions · 2024-03-07T23:41:44Z

Regression Testing Results

⚠️ 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): 00:00:01:05
Current: Execution time (DD:HH:MM:SS): 00:00:01:07
Reference: Memory used: 3031.39 MB
Current: Memory used: 3047.77 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. ✅

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): 00:00:02:10
Current: Execution time (DD:HH:MM:SS): 00:00:02:10
Reference: Memory used: 3153.06 MB
Current: Memory used: 3165.10 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 216 reactions.
Test model has 216 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1618 reactions.
Test model has 1613 reactions. ❌
The original model has 5 reactions that the tested model does not have. ❌
rxn: [CH2]CCOO(73) + CCCCCOO(105) <=> CCCOO(35) + CC[CH]CCOO(114) origin: H_Abstraction
rxn: [CH2]CCOO(73) + CCCCCOO(105) <=> CCCOO(35) + CCC[CH]COO(113) origin: H_Abstraction
rxn: [CH2]CCOO(73) + CCCCCOO(105) <=> CCCOO(35) + C[CH]CCCOO(115) origin: H_Abstraction
rxn: [CH2]CCOO(73) + CCCCCOO(105) <=> CCCOO(35) + CCCC[CH]OO(138) origin: H_Abstraction
rxn: CCCOO(35) + [CH2]CCCCOO(116) <=> [CH2]CCOO(73) + CCCCCOO(105) origin: H_Abstraction

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): 00:00:01:22
Current: Execution time (DD:HH:MM:SS): 00:00:01:23
Reference: Memory used: 3164.01 MB
Current: Memory used: 3167.65 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 Failed Edge Comparison ❌

Original model has 132 species.
Test model has 132 species. ✅
Original model has 997 reactions.
Test model has 997 reactions. ✅

Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
141.64	58.66	12.26	12.27	12.09	11.96	12.26	12.72	12.15
116.46	53.90	11.62	12.71	13.49	13.96	14.14	13.85	13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)

Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-66.25	-46.19	-34.19	-26.21	-16.28	-10.36	-2.54	1.31
k(T):	-49.54	-33.65	-24.16	-17.85	-10.01	-5.35	0.80	3.82

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H

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): 00:00:02:27
Current: Execution time (DD:HH:MM:SS): 00:00:02:26
Reference: Memory used: 3014.90 MB
Current: Memory used: 3023.58 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. ✅

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): 00:00:00:54
Reference: Memory used: 3118.06 MB
Current: Memory used: 3128.27 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

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): 00:00:00:34
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 3202.81 MB
Current: Memory used: 3248.90 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): 00:00:02:26
Current: Execution time (DD:HH:MM:SS): 00:00:02:28
Reference: Memory used: 3714.03 MB
Current: Memory used: 3698.95 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. ✅

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): 00:00:06:08
Current: Execution time (DD:HH:MM:SS): 00:00:06:06
Reference: Memory used: 3651.81 MB
Current: Memory used: 3663.75 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 232 reactions.
Test model has 233 reactions. ❌
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](36) <=> [OH](21) + CC=O(62) origin: intra_H_migration

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species.
Test model has 206 species. ✅
Original model has 1508 reactions.
Test model has 1508 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: CCCO[O](36) <=> CC[CH]OO(51) origin: intra_H_migration
rxn: CCO[O](35) <=> C[CH]OO(62) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CCO[O](36) <=> [OH](21) + CC=O(62) origin: intra_H_migration
rxn: CCCO[O](35) <=> [OH](21) + CCC=O(50) origin: intra_H_migration

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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rwest

I suggest we figure out better names for thermo/libraries/Fluorine.py and thermo/libraries/C1_C2_Fluorine.py, but that can come in a separate PR.

rwest requested a review from Nora-Khalil June 15, 2023 12:41

ChrisBNEU self-requested a review June 15, 2023 13:32

Nora-Khalil reviewed Jun 15, 2023

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input/kinetics/libraries/Fluoromethane/reactions.py Outdated Show resolved Hide resolved

Nora-Khalil approved these changes Jul 21, 2023

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ChrisBNEU approved these changes Aug 16, 2023

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ChrisBNEU force-pushed the PFAS_chemistry branch from b4c8569 to a2ac74d Compare August 16, 2023 19:54

ChrisBNEU approved these changes Aug 16, 2023

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JacksonBurns mentioned this pull request Nov 2, 2023

Unable to Estimate Thermochemistry for Phosphine Oxides ReactionMechanismGenerator/RMG-Py#2567

Closed

SiddhaSharma added 8 commits March 7, 2024 16:49

Adding Fluoromethane chemistry to RMG kinetic database

8b5d95e

Update dictionary.txt

0ae5105

Added species CH2FO

Update dictionary.txt

ede66b2

Corrected CF3CO Adjacency List

Update reactions.py

0abf75e

Revised description for the reactions.py file

adding thermo data for C1 and C2 fluorinated species

697e003

Update C1_C2_Fluorine.py

38fb801

update

Update dictionary.txt

912b195

updated

Update C1_C2_Fluorine.py

d382daf

Update NASA7

ChrisBNEU force-pushed the PFAS_chemistry branch from 73ab24c to d382daf Compare March 7, 2024 21:49

rwest approved these changes Mar 8, 2024

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Adding Fluoromethane chemistry to RMG kinetic database #624

Adding Fluoromethane chemistry to RMG kinetic database #624

SiddhaSharma commented Jun 15, 2023

Nora-Khalil commented Jun 15, 2023

Nora-Khalil left a comment

ChrisBNEU left a comment

ChrisBNEU commented Aug 16, 2023

github-actions bot commented Mar 7, 2024

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:

rwest left a comment

Adding Fluoromethane chemistry to RMG kinetic database #624

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Adding Fluoromethane chemistry to RMG kinetic database #624

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SiddhaSharma commented Jun 15, 2023

kinetics for thermal degradation of Fluoromethanes.

Nora-Khalil commented Jun 15, 2023

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ChrisBNEU commented Aug 16, 2023

github-actions bot commented Mar 7, 2024

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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