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Creation of an RMGC2 seed mechanism #301

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Creation of an RMGC2 seed mechanism #301

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mjohnson541
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New C2 chemistry seed based on Klippenstein_Glarborg2016 adding in rates from C2H4+O_Klipp2017 and other individual important rates. In addition to the rates in the above libraries I updated the rate for CH3OOH + HCO = CH2O + CH3OO and added rates for HCO + O2 <=> OCHOO, HO2 + OCHOOH <=> OCHOO + H2O2 and HO2 + CH3 <=> CH3OOH. If you have any chemistry you think is important to have in a general C2 seed for combustion of COH compounds that isn't in the above please let me know.

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@jimchu10 is there anything you think would be important to make sure is included in this?

@mjohnson541 mjohnson541 requested a review from alongd October 14, 2018 14:19
@mjohnson541 mjohnson541 self-assigned this Oct 14, 2018
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Overall looking good. Is there anything in particular you think I should look carefully into?
Also, is there any input from @aelong's thesis that you find relevant for this library?
See minor comments below


entry(
index = 1,
label = "H + O2 <=> HO2",
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How does the H2/O2 subset compare to the Burke/Klipp. library? Is all included and relatively updated here?

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All of the reactions that are in both that I've checked look the same or updated, however there are a few missing. I'm unsure why they weren't included in Klippenstein_Glarborg2016. I'll take a look at tit.


entry(
index = 12,
label = "HO2 + H <=> H2 + O2",
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Add elementary_high_p? Or, do we not care about this PES since we assume it's well explored?

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Hmm...do you think there are any risks (increased uncertainty) to running pdep on a well explored surface?

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I don't, I take it back


entry(
index = 52,
label = "HCO + O <=> CO + OH",
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Add elementary_high_p?
Same for 53, 54...

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I tried running with seedMechanisms=['RMGC2','BurkeH2O2inN2'] and it threw my model off pretty badly. It's possible my original run was a fluke, but I think it's much more likely something doesn't play nice between the two libraries.

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alongd commented Oct 21, 2018

And what if you reverse the library order?
BTW, what H/O chemistry isn't in agreement between the two?

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Never mind, I've worked out what the problem was. It seems to be vital that one of the BurkeH2O2 libraries be included during non-pdep model construction because there is at least one not very significant reaction RMG will estimate if it doesn't have a library: O + OH = HO2 that is very pressure dependent and if it isn't estimated pdep the rate is high enough to impact ignition chemistry. The BurkeH2O2 libraries are also the only libraries with a rate for this reaction.

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It may be worth considering having a primaryReactionLibrary for rates of typically insiginficant reactions that RMG will overestimate if not given a value for.

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Note: We need to add an estimate for CH2OH = CH3O in this.

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Note: We need to add an estimate for CH2OH = CH3O in this.

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alongd commented Oct 22, 2018

I think that one of the Burke H/O libs should always be used (and be given priority). We could rename it to primaryH2/O2 or something of that sort as we discussed, or just recommend users to always use it. If we come up with non-H2/O2 rates that should be included in a primary library, then let's make a general primaryKinetics one.

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Note: We need to add an estimate for CH2OH = CH3O in this.

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Note: We need to add an estimate for CH2OH = CH3O in this.

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a rate for CH2OH = CH3O needs added to this

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jimchu10 commented Jan 2, 2019

Sorry, I didn't see your question before.
Have you compared the rates with FFCM rates?
In my methane modeling, I used
thermoLibraries = ['FFCM1(-)','BurkeH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
reactionLibraries = [('FFCM1(-)',False),('BurkeH2O2inArHe',False),('2005_Senosiain_OH_C2H2',False)],

So FFCM is always prioritized than other libraries. It might not be great for all cases, but at least it worked well for rich-methane combustion.

Based from Klippenstein_Glarborg2016 adding in rates from C2H4+O_Klipp2017 and other individual important rates
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@mjohnson541 any interest in getting this merged? From what we can see this got pretty close, just needs one additional reaction?

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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): 00:00:01:07
Current: Execution time (DD:HH:MM:SS): 00:00:01:07
Reference: Memory used: 2769.81 MB
Current: Memory used: 2763.80 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): 00:00:02:09
Current: Execution time (DD:HH:MM:SS): 00:00:02:08
Reference: Memory used: 2909.37 MB
Current: Memory used: 2900.93 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 216 reactions.
Test model has 215 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](31) <=> [OH](22) + CC=O(69) origin: intra_H_migration

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1610 reactions.
Test model has 1610 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](31) <=> [OH](22) + CC=O(69) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](31) <=> C[CH]OO(73) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 3.52 4.27 4.71 5.01 5.39 5.61 5.91 6.06
k(T): 7.79 7.46 7.21 7.00 6.67 6.41 5.94 5.60

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'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=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""")
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
Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.

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): 00:00:01:28
Current: Execution time (DD:HH:MM:SS): 00:00:01:25
Reference: Memory used: 2911.76 MB
Current: Memory used: 2908.32 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 359 reactions. ✅

nitrogen Passed Edge Comparison ✅

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 981 reactions. ✅

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: 2768.08 MB
Current: Memory used: 2765.59 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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:57
Reference: Memory used: 2873.19 MB
Current: Memory used: 2871.96 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): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:40
Reference: Memory used: 2991.20 MB
Current: Memory used: 2966.30 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): 00:00:02:20
Current: Execution time (DD:HH:MM:SS): 00:00:02:22
Reference: Memory used: 3445.23 MB
Current: Memory used: 3469.24 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): 00:00:05:52
Current: Execution time (DD:HH:MM:SS): 00:00:06:00
Reference: Memory used: 3371.97 MB
Current: Memory used: 3371.97 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 1 reactions that the tested model does not have. ❌
rxn: CCO[O](35) <=> C[CH]OO(63) origin: intra_H_migration
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

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 ✅

beep boop this comment was written by a bot 🤖

@mjohnson541
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@alongd do you think this is still as good of an idea as we thought it was six years ago?

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