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Improve R_Recombination Generated Tree #369

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Dec 14, 2019
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mjohnson541
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Improved generated tree using SABIC_aromatics and generating resonance structures before calculating thermo. Should mostly fix #353.

kinetics = ArrheniusBM(A=(5e+07,'m^3/(mol*s)'), n=-1.21605e-07, w0=(173000,'J/mol'), E0=(17300,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.0, var=33.1368631905, Tref=1000.0, N=1, correlation='Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_1C-inRing_Ext-1C-R_Sp-3R!H-1C_2R-inRing',), comment="""BM rule fitted to 2 training reactions at node Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_1C-inRing_Ext-1C-R_Sp-3R!H-1C_2R-inRing
Total Standard Deviation in ln(k): 11.5401827615"""),
label = "Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_Ext-2R-R_Ext-2R-R_Ext-1C-R_6R!H->C",
kinetics = ArrheniusBM(A=(1.53609e+09,'m^3/(mol*s)'), n=-0.946459, w0=(173000,'J/mol'), E0=(17300,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.000724761308015, var=1.22133425516, Tref=1000.0, N=6, correlation='Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_Ext-2R-R_Ext-2R-R_Ext-1C-R_6R!H->C',), comment="""BM rule fitted to 2 training reactions at node Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_Ext-2R-R_Ext-2R-R_E
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This rate rule seems like it could be problematic.

@mliu49
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mliu49 commented Dec 13, 2019

In RMG-tests, there are a lot of reactions which were estimated by rate rules on master but estimated by exact match to training reactions on this branch. Do you have any idea why that would be?

@mjohnson541
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I'll take a look tomorrow, this shouldn't happen and isn't desirable.

@mjohnson541
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Should be fixed now

…erating resonance structures before calculating thermo
@mliu49 mliu49 merged commit ada832e into master Dec 14, 2019
@mliu49 mliu49 deleted the r_comb_thermo_improvements branch December 14, 2019 02:23
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New R_Recombination rules much too fast?
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