diff --git a/ipython/data/cpox_methane/chem_annotated-gas.inp b/ipython/data/cpox_methane/chem_annotated-gas.inp new file mode 100644 index 0000000000..f71fc7e055 --- /dev/null +++ b/ipython/data/cpox_methane/chem_annotated-gas.inp @@ -0,0 +1,544 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /17.999/ + N + Ne + Ar + He + Si + S + F + Cl + Br + I + X /195.083/ +END + +SPECIES + Ar ! Ar + Ne ! Ne + N2 ! N2 + CH4(2) ! CH4(2) + O2(3) ! O2(3) + CO2(4) ! CO2(4) + H2O(5) ! H2O(5) + H2(6) ! H2(6) + CO(7) ! CO(7) + C2H6(8) ! C2H6(8) + CH2O(9) ! CH2O(9) + CH3(10) ! CH3(10) + C3H8(11) ! C3H8(11) + H(12) ! H(12) + C2H5(13) ! C2H5(13) + CH3OH(14) ! CH3OH(14) + HCO(15) ! HCO(15) + CH3CHO(16) ! CH3CHO(16) + OH(17) ! OH(17) + C2H4(18) ! C2H4(18) + CH3CH(19) ! CH3CH(19) + CH3OO(20) ! CH3OO(20) +END + + + +THERM ALL + 300.000 1000.000 5000.000 + +! Thermo library: primaryThermoLibrary +Ar Ar 1 G 200.000 6000.000 1000.00 1 + 2.50000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 +-7.45375000E+02 4.37967000E+00 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 4.37967000E+00 4 + +! Thermo library: primaryThermoLibrary +Ne Ne 1 G 200.000 6000.000 1000.00 1 + 2.50000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 +-7.45375000E+02 3.35532000E+00 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 3.35532000E+00 4 + +! Thermo library: primaryThermoLibrary +N2 N 2 G 200.000 6000.000 1000.00 1 + 2.95258000E+00 1.39690000E-03-4.92632000E-07 7.86010000E-11-4.60755000E-15 2 +-9.23949000E+02 5.87189000E+00 3.53101000E+00-1.23661000E-04-5.02999000E-07 3 + 2.43531000E-09-1.40881000E-12-1.04698000E+03 2.96747000E+00 4 + +! Thermo library: primaryThermoLibrary +CH4(2) C 1H 4 G 100.000 5000.000 1084.12 1 + 9.08259430E-01 1.14540962E-02-4.57174412E-06 8.29193029E-10-5.66316007E-14 2 +-9.71997168E+03 1.39931301E+01 4.20541633E+00-5.35558620E-03 2.51123688E-05 3 +-2.13763364E-08 5.97526027E-12-1.01619434E+04-9.21283218E-01 4 + +! Thermo library: primaryThermoLibrary +O2(3) O 2 G 100.000 5000.000 1074.55 1 + 3.15382081E+00 1.67804371E-03-7.69974236E-07 1.51275462E-10-1.08782414E-14 2 +-1.04081728E+03 6.16755832E+00 3.53732243E+00-1.21571647E-03 5.31620254E-06 3 +-4.89446434E-09 1.45846258E-12-1.03858849E+03 4.68368183E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +CO2(4) C 1O 2 G 100.000 5000.000 978.22 1 + 4.67427416E+00 2.60962879E-03-9.85683184E-07 1.95712276E-10-1.49834931E-14 2 +-4.89512168E+04-2.11077406E+00 3.28084453E+00 2.50185640E-03 8.08192142E-06 3 +-1.20510369E-08 4.66542684E-12-4.84008303E+04 6.00081438E+00 4 + +! Thermo library: primaryThermoLibrary +H2O(5) H 2O 1 G 100.000 5000.000 1130.23 1 + 2.84325454E+00 2.75107882E-03-7.81027793E-07 1.07242789E-10-5.79385325E-15 2 +-2.99586146E+04 5.91039666E+00 4.05763524E+00-7.87929225E-04 2.90875322E-06 3 +-1.47516271E-09 2.12832915E-13-3.02815866E+04-3.11361934E-01 4 + +! Thermo library: primaryThermoLibrary +H2(6) H 2 G 100.000 5000.000 1959.07 1 + 2.78818509E+00 5.87615921E-04 1.59022130E-07-5.52762536E-11 4.34328120E-15 2 +-5.96155632E+02 1.12618494E-01 3.43536393E+00 2.12711953E-04-2.78628671E-07 3 + 3.40270013E-10-7.76039045E-14-1.03135983E+03-3.90841661E+00 4 + +! Thermo library: primaryThermoLibrary +CO(7) C 1O 1 G 100.000 5000.000 1571.64 1 + 2.91306239E+00 1.64658456E-03-6.88618210E-07 1.21038081E-10-7.84023563E-15 2 +-1.41808823E+04 6.71048256E+00 3.56838006E+00-8.52126340E-04 2.48917989E-06 3 +-1.56331226E-09 3.13595852E-13-1.42842549E+04 3.57912151E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +C2H6(8) C 2H 6 G 100.000 5000.000 1012.42 1 + 2.82845780E+00 1.73040987E-02-6.73336647E-06 1.23742590E-09-8.65681088E-14 2 +-1.19977975E+04 5.93825672E+00 3.72239865E+00 1.65077010E-03 3.44177937E-05 3 +-3.76861352E-08 1.24451983E-11-1.15575904E+04 4.68245945E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +CH2O(9) C 1H 2O 1 G 100.000 5000.000 1070.44 1 + 2.21174394E+00 7.94262445E-03-3.34191224E-06 6.28467142E-10-4.40427951E-14 2 +-1.42974541E+04 1.13047879E+01 4.12927444E+00-4.08397173E-03 2.03227934E-05 3 +-1.83522494E-08 5.37968433E-12-1.44294638E+04 3.22419750E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +CH3(10) C 1H 3 G 100.000 5000.000 697.61 1 + 3.09511290E+00 5.55429655E-03-1.88158709E-06 3.13334630E-10-2.05194840E-14 2 + 1.65426189E+04 4.20297326E+00 3.96043207E+00 5.92926692E-04 8.78580229E-06 3 +-9.88037299E-09 3.63237783E-12 1.64218817E+04 3.39861761E-01 4 + +! Thermo library: DFT_QCI_thermo +C3H8(11) C 3H 8 G 100.000 5000.000 990.00 1 + 5.60451848E+00 2.19526774E-02-8.22069003E-06 1.50101249E-09-1.05633081E-13 2 +-1.58394533E+04-6.22689747E+00 3.06333162E+00 1.29218175E-02 3.47019889E-05 3 +-4.70929096E-08 1.71376767E-11-1.43905776E+04 1.07836665E+01 4 + +! Thermo library: primaryThermoLibrary +H(12) H 1 G 100.000 5000.000 4879.80 1 + 4.28461071E+00-1.45494649E-03 4.44804306E-07-6.04359642E-11 3.07921551E-15 2 + 2.37230923E+04-1.18931307E+01 2.50000000E+00-3.01680531E-12 3.74582141E-15 3 +-1.50856878E-18 1.86626471E-22 2.54742178E+04-4.44972899E-01 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +C2H5(13) C 2H 5 G 100.000 5000.000 1006.87 1 + 3.53785970E+00 1.37310796E-02-5.29559811E-06 9.71471485E-10-6.80280075E-14 2 + 1.26351580E+04 5.15538097E+00 3.68745362E+00 3.06903728E-03 2.55868151E-05 3 +-2.94070110E-08 9.94048651E-12 1.31153653E+04 6.96689071E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +CH3OH(14) C 1H 4O 1 G 100.000 5000.000 1035.75 1 + 2.79182744E+00 1.15828112E-02-4.51553413E-06 8.21210187E-10-5.67066120E-14 2 +-2.57211607E+04 9.41070357E+00 3.84006541E+00 1.38238147E-03 1.91668527E-05 3 +-2.01570364E-08 6.39109354E-12-2.56083089E+04 5.90976964E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +HCO(15) C 1H 1O 1 G 100.000 5000.000 1112.10 1 + 3.05135670E+00 4.11707280E-03-1.75586905E-06 3.29303911E-10-2.29174920E-14 2 + 3.93008152E+03 7.67467218E+00 4.05936488E+00-1.73847366E-03 9.14984065E-06 3 +-8.01135179E-09 2.25738698E-12 3.84377614E+03 3.32449412E+00 4 + +! Thermo library: DFT_QCI_thermo +CH3CHO(16) C 2H 4O 1 G 100.000 5000.000 1028.81 1 + 4.08563839E+00 1.39061205E-02-5.59370236E-06 1.04609279E-09-7.38738642E-14 2 +-2.20391342E+04 3.76801799E+00 3.57992412E+00 5.18983303E-03 2.26897556E-05 3 +-2.73742720E-08 9.28480001E-12-2.13697374E+04 8.96971515E+00 4 + +! Thermo library: primaryThermoLibrary +OH(17) H 1O 1 G 100.000 5000.000 1145.76 1 + 3.07193724E+00 6.04019839E-04-1.39805930E-08-2.13440813E-11 2.48061367E-15 2 + 3.57938792E+03 4.57801469E+00 3.51456839E+00 2.92734292E-05-5.32150598E-07 3 + 1.01947521E-09-3.85939405E-13 3.41425418E+03 2.10434756E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +C2H4(18) C 2H 4 G 100.000 5000.000 979.36 1 + 3.55666148E+00 1.10626517E-02-4.17013598E-06 7.85573786E-10-5.70050038E-14 2 + 4.32044177E+03 2.17688329E+00 3.97470131E+00-4.75826458E-03 4.16777352E-05 3 +-4.51383971E-08 1.54221033E-11 4.91540809E+03 3.62436102E+00 4 + +! Thermo library: DFT_QCI_thermo +CH3CH(19) C 2H 4 G 100.000 5000.000 960.81 1 + 4.30486414E+00 9.43069145E-03-3.27558933E-06 5.95122108E-10-4.27307267E-14 2 + 4.07091457E+04 1.84203490E+00 3.82362693E+00-9.09524648E-04 3.21380397E-05 3 +-3.73480103E-08 1.33090621E-11 4.13713807E+04 7.10947614E+00 4 + +! Thermo library: thermo_DFT_CCSDTF12_BAC +CH3OO(20) C 1H 3O 2 G 100.000 5000.000 1031.34 1 + 4.35019035E+00 1.07183820E-02-4.26218191E-06 7.89585637E-10-5.53852350E-14 2 +-3.09796253E+02 4.08946553E+00 3.58601551E+00 6.15340433E-03 1.33272147E-05 3 +-1.76585177E-08 6.13226209E-12 2.48233263E+02 9.74093531E+00 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #23 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: H2(6), H(12); H2(6), H(12); +H2(6)+M<=>H(12)+H(12)+M 4.577e+19 -1.400 104.380 +CO(7)/1.90/ H2O(5)/12.00/ H2(6)/2.50/ CO2(4)/3.80/ Ar/0.00/ + +! Reaction index: Chemkin #2; RMG #24 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: H2(6), H(12); Ar, Ar; Ar, H(12); +Ar+H2(6)<=>Ar+H(12)+H(12) 5.840000e+18 -1.100 104.380 + +! Reaction index: Chemkin #3; RMG #21 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: OH(17), H2O(5); H2(6), H(12); +OH(17)+H2(6)<=>H(12)+H2O(5) 2.160000e+08 1.510 3.430 + +! Reaction index: Chemkin #4; RMG #30 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: H2O(5), H(12); H2O(5), OH(17); +H2O(5)+M<=>H(12)+OH(17)+M 6.064e+27 -3.322 120.790 +H2(6)/3.00/ H2O(5)/0.00/ CO(7)/1.90/ CO2(4)/3.80/ O2(3)/1.50/ N2/2.00/ + +! Reaction index: Chemkin #5; RMG #31 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: H2O(5), H2O(5); H2O(5), H(12); H2O(5), OH(17); +H2O(5)+H2O(5)<=>H(12)+OH(17)+H2O(5) 1.006000e+26 -2.440 120.180 + +! Reaction index: Chemkin #6; RMG #45 +! Library reaction: BurkeH2O2inArHe +! Flux pairs: OH(17), O2(3); OH(17), H2(6); +OH(17)+OH(17)<=>O2(3)+H2(6) 2.000000e+11 0.510 50.500 + +! Reaction index: Chemkin #7; RMG #51 +! Template reaction: R_Recombination +! Flux pairs: CH3(10), CH4(2); H(12), CH4(2); +! Matched reaction 57 H + CH3 <=> CH4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R->S_N-2CHNO->H_N-2CNO-inRing_N-2CNO->O] +! family: R_Recombination +H(12)+CH3(10)<=>CH4(2) 1.930000e+14 0.000 0.270 + +! Reaction index: Chemkin #8; RMG #55 +! Template reaction: R_Recombination +! Flux pairs: CH3(10), C2H6(8); CH3(10), C2H6(8); +! Matched reaction 9 CH3 + CH3 <=> C2H6 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing] +! family: R_Recombination +CH3(10)+CH3(10)<=>C2H6(8) 9.450000e+14 -0.538 0.135 + +! Reaction index: Chemkin #9; RMG #56 +! Template reaction: R_Recombination +! Flux pairs: C2H5(13), C2H6(8); H(12), C2H6(8); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R->S_N-2CHNO->H_N-2CNO-inRing_Ext-2CNO-R_N-Sp-3R!H=2CCNNOO_N-2CNO->O_3R!H->C_Sp-3C-2CN] +! family: R_Recombination +H(12)+C2H5(13)<=>C2H6(8) 1.000000e+14 0.000 0.000 + +! Reaction index: Chemkin #10; RMG #57 +! Template reaction: 1,2_Insertion_CO +! Flux pairs: CO(7), CH2O(9); H2(6), CH2O(9); +! Matched reaction 2 H2 + CO <=> CH2O in 1,2_Insertion_CO/training +! This reaction matched rate rule [CO;H2] +! family: 1,2_Insertion_CO +H2(6)+CO(7)<=>CH2O(9) 2.890000e+09 1.160 82.100 + +! Reaction index: Chemkin #11; RMG #58 +! Template reaction: R_Recombination +! Flux pairs: HCO(15), CH2O(9); H(12), CH2O(9); +! Matched reaction 63 H + CHO <=> CH2O in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R->S_N-2CHNO->H_N-2CNO-inRing_Ext-2CNO-R_Sp-3R!H=2CCNNOO_3R!H->O] +! family: R_Recombination +H(12)+HCO(15)<=>CH2O(9) 4.680000e+10 0.000 -4.530 + +! Reaction index: Chemkin #12; RMG #62 +! Template reaction: R_Recombination +! Flux pairs: C2H5(13), C3H8(11); CH3(10), C3H8(11); +! Matched reaction 10 CH3 + C2H5 <=> C3H8 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_Sp-3R!H-2R_3R!H->C_2R->C] +! family: R_Recombination +CH3(10)+C2H5(13)<=>C3H8(11) 1.230000e+15 -0.562 0.021 + +! Reaction index: Chemkin #13; RMG #64 +! Template reaction: Birad_R_Recombination +! Flux pairs: H(12), C2H5(13); CH3CH(19), C2H5(13); +! Estimated using an average for rate rule [H_rad;Birad] +! Euclidian distance = 0 +! family: Birad_R_Recombination +H(12)+CH3CH(19)<=>C2H5(13) 1.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #14; RMG #65 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H4(18), C2H5(13); H(12), C2H5(13); +! Matched reaction 2541 H + C2H4 <=> C2H5-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(12)+C2H4(18)<=>C2H5(13) 4.620000e+08 1.640 1.010 + +! Reaction index: Chemkin #15; RMG #68 +! Template reaction: R_Recombination +! Flux pairs: OH(17), CH3OH(14); CH3(10), CH3OH(14); +! Matched reaction 73 CH3 + OH <=> CH4O in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CNOS->N_1COS->O_2R->C] +! family: R_Recombination +OH(17)+CH3(10)<=>CH3OH(14) 6.030000e+13 0.000 0.000 + +! Reaction index: Chemkin #16; RMG #72 +! Template reaction: R_Addition_COm +! Flux pairs: CO(7), HCO(15); H(12), HCO(15); +! Matched reaction 4 H + CO <=> CHO in R_Addition_COm/training +! This reaction matched rate rule [COm;H_rad] +! family: R_Addition_COm +H(12)+CO(7)<=>HCO(15) 1.180000e+11 0.000 2.720 + +! Reaction index: Chemkin #17; RMG #73 +! Template reaction: 1,2_Insertion_CO +! Flux pairs: CO(7), CH3CHO(16); CH4(2), CH3CHO(16); +! Matched reaction 3 CH4 + CO <=> C2H4O in 1,2_Insertion_CO/training +! This reaction matched rate rule [CO;C_methane] +! family: 1,2_Insertion_CO +CO(7)+CH4(2)<=>CH3CHO(16) 6.560000e+04 2.860 86.900 + +! Reaction index: Chemkin #18; RMG #76 +! Template reaction: R_Recombination +! Flux pairs: HCO(15), CH3CHO(16); CH3(10), CH3CHO(16); +! Matched reaction 71 CH3 + CHO <=> C2H4O in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CNOS->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_N-Sp-3R!H-2R_3R!H->O] +! family: R_Recombination +HCO(15)+CH3(10)<=>CH3CHO(16) 1.810000e+13 0.000 0.000 + +! Reaction index: Chemkin #19; RMG #84 +! Template reaction: R_Recombination +! Flux pairs: CH3OO(20), CH3(10); CH3OO(20), O2(3); +! Matched reaction 0 CH3O2 <=> O2 + CH3 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CNOS->N_1COS->O_Ext-1O-R_2R->C_3R!H->O] +! family: R_Recombination +CH3OO(20)<=>O2(3)+CH3(10) 1.090000e+14 0.250 33.300 + +! Reaction index: Chemkin #20; RMG #86 +! Template reaction: intra_H_migration +! Flux pairs: CH3OO(20), OH(17); CH3OO(20), CH2O(9); +! From training reaction 240 used for R3H_SS_O;O_rad_out;Cs_H_out_2H +! Exact match found for rate rule [R3H_SS_O;O_rad_out;Cs_H_out_2H] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: intra_H_migration +CH3OO(20)<=>OH(17)+CH2O(9) 4.710000e+08 1.450 42.270 + +! Reaction index: Chemkin #21; RMG #125 +! Template reaction: CO_Disproportionation +! Flux pairs: H(12), H2(6); HCO(15), CO(7); +! Matched reaction 0 HCO + H <=> CO + H2 in CO_Disproportionation/training +! This reaction matched rate rule [Root_N-4R->N_4BrCClFHIOPSSi->H] +! family: CO_Disproportionation +H(12)+HCO(15)<=>H2(6)+CO(7) 9.030000e+13 0.000 0.000 + +! Reaction index: Chemkin #22; RMG #128 +! Template reaction: H_Abstraction +! Flux pairs: CH4(2), CH3(10); H(12), H2(6); +! Matched reaction 186 CH4b + H <=> CH3_p1 + H2_p in H_Abstraction/training +! This reaction matched rate rule [H2;C_methyl] +! family: H_Abstraction +H(12)+CH4(2)<=>H2(6)+CH3(10) 4.100000e+03 3.156 8.755 + +! Reaction index: Chemkin #23; RMG #129 +! Template reaction: H_Abstraction +! Flux pairs: C2H6(8), C2H5(13); H(12), H2(6); +! Matched reaction 210 C2H6 + H <=> C2H5b + H2_p in H_Abstraction/training +! This reaction matched rate rule [H2;C_rad/H2/Cs\H3] +! family: H_Abstraction +H(12)+C2H6(8)<=>H2(6)+C2H5(13) 1.150000e+08 1.900 7.530 + +! Reaction index: Chemkin #24; RMG #131 +! Template reaction: H_Abstraction +! Flux pairs: HCO(15), CH2O(9); H2(6), H(12); +! Matched reaction 309 H2 + HCO_r3 <=> CH2O + H in H_Abstraction/training +! This reaction matched rate rule [H2;CO_pri_rad] +! family: H_Abstraction +H2(6)+HCO(15)<=>H(12)+CH2O(9) 1.800000e+06 2.000 48.940 + +! Reaction index: Chemkin #25; RMG #134 +! Template reaction: Disproportionation +! Flux pairs: H(12), H2(6); C2H5(13), C2H4(18); +! Matched reaction 4 H + C2H5 <=> H2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Root_4R->H_Sp-2R!H-1R!H_2R!H-u1_N-1R!H->O_1CN->C_2R!H->C] +! family: Disproportionation +H(12)+C2H5(13)<=>H2(6)+C2H4(18) 1.083000e+13 0.000 0.000 + +! Reaction index: Chemkin #26; RMG #135 +! Template reaction: H_Abstraction +! Flux pairs: CH3CH(19), C2H5(13); H2(6), H(12); +! Estimated using an average for rate rule [H2;Y_1centerbirad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +H2(6)+CH3CH(19)<=>H(12)+C2H5(13) 2.317758e+11 0.750 21.325 + +! Reaction index: Chemkin #27; RMG #186 +! Template reaction: CO_Disproportionation +! Flux pairs: CH3(10), CH4(2); HCO(15), CO(7); +! Matched reaction 3 HCO + CH3 <=> CO + CH4 in CO_Disproportionation/training +! This reaction matched rate rule [Root_N-4R->N_N-4BrCClFHIOPSSi->H_4CO->C] +! family: CO_Disproportionation +HCO(15)+CH3(10)<=>CO(7)+CH4(2) 4.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #28; RMG #189 +! Template reaction: H_Abstraction +! Flux pairs: C2H6(8), C2H5(13); CH3(10), CH4(2); +! Matched reaction 215 C2H6 + CH3_r3 <=> C2H5b + CH4 in H_Abstraction/training +! This reaction matched rate rule [C_methane;C_rad/H2/Cs\H3] +! family: H_Abstraction +CH3(10)+C2H6(8)<=>CH4(2)+C2H5(13) 3.500000e+01 3.440 10.384 + +! Reaction index: Chemkin #29; RMG #191 +! Template reaction: H_Abstraction +! Flux pairs: HCO(15), CH2O(9); CH4(2), CH3(10); +! Matched reaction 318 HCO_r3 + CH4b <=> CH2O + CH3_p1 in H_Abstraction/training +! This reaction matched rate rule [C_methane;CO_pri_rad] +! family: H_Abstraction +HCO(15)+CH4(2)<=>CH2O(9)+CH3(10) 7.280000e+03 2.850 34.250 + +! Reaction index: Chemkin #30; RMG #194 +! Template reaction: H_Abstraction +! Flux pairs: OH(17), H2O(5); CH4(2), CH3(10); +! Matched reaction 188 CH4b + OH <=> CH3_p1 + H2O_p in H_Abstraction/training +! This reaction matched rate rule [C_methane;O_pri_rad] +! family: H_Abstraction +OH(17)+CH4(2)<=>H2O(5)+CH3(10) 1.000000e+06 2.182 2.506 + +! Reaction index: Chemkin #31; RMG #195 +! Template reaction: Disproportionation +! Flux pairs: CH3(10), CH4(2); C2H5(13), C2H4(18); +! Matched reaction 5 CH3_r1 + C2H5 <=> CH4 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_4CNS->C_1CNS->C_Sp-2R!H-1C_2R!H->C] +! family: Disproportionation +CH3(10)+C2H5(13)<=>CH4(2)+C2H4(18) 6.570000e+14 -0.680 0.000 + +! Reaction index: Chemkin #32; RMG #196 +! Template reaction: H_Abstraction +! Flux pairs: CH3CH(19), C2H5(13); CH4(2), CH3(10); +! Estimated using an average for rate rule [C_methane;Y_1centerbirad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +CH4(2)+CH3CH(19)<=>CH3(10)+C2H5(13) 2.006512e+11 0.833 15.521 + +! Reaction index: Chemkin #33; RMG #251 +! Template reaction: CO_Disproportionation +! Flux pairs: OH(17), H2O(5); HCO(15), CO(7); +! Estimated from node Root_N-4R->N_N-4BrCClFHIOPSSi->H_N-4CO->C in family CO_Disproportionation. +OH(17)+HCO(15)<=>H2O(5)+CO(7) 3.010000e+13 0.000 0.000 + +! Reaction index: Chemkin #34; RMG #254 +! Template reaction: H_Abstraction +! Flux pairs: C2H6(8), C2H5(13); OH(17), H2O(5); +! Matched reaction 212 C2H6 + OH <=> C2H5b + H2O_p in H_Abstraction/training +! This reaction matched rate rule [O_pri;C_rad/H2/Cs\H3] +! family: H_Abstraction +OH(17)+C2H6(8)<=>H2O(5)+C2H5(13) 1.610000e+06 2.224 0.741 + +! Reaction index: Chemkin #35; RMG #256 +! Template reaction: H_Abstraction +! Flux pairs: CH2O(9), HCO(15); OH(17), H2O(5); +! Matched reaction 367 OH_p23 + CH2O <=> H2O + HCO_r3 in H_Abstraction/training +! This reaction matched rate rule [O_pri;CO_pri_rad] +! family: H_Abstraction +OH(17)+CH2O(9)<=>H2O(5)+HCO(15) 3.440000e+09 1.180 -0.450 + +! Reaction index: Chemkin #36; RMG #260 +! Template reaction: Disproportionation +! Flux pairs: OH(17), H2O(5); C2H5(13), C2H4(18); +! Matched reaction 13 HO + C2H5 <=> H2O + C2H4 in Disproportionation/training +! This reaction matched rate rule [Root_N-4R->H_4CNOS-u1_N-1R!H->O_4CNOS->O_Sp-2R!H-1CNS_1CNS->C_2R!H->C] +! family: Disproportionation +OH(17)+C2H5(13)<=>H2O(5)+C2H4(18) 7.230000e+13 0.000 0.000 + +! Reaction index: Chemkin #37; RMG #261 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(13), CH3CH(19); OH(17), H2O(5); +! Estimated using template [Xrad_H;O_pri_rad] for rate rule [C_rad_H;O_pri_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +OH(17)+C2H5(13)<=>H2O(5)+CH3CH(19) 6.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #38; RMG #316 +! Template reaction: CO_Disproportionation +! Flux pairs: C2H5(13), C2H6(8); HCO(15), CO(7); +! Matched reaction 12 C2H5 + HCO <=> C2H6 + CO in CO_Disproportionation/training +! This reaction matched rate rule [Root_N-4R->N_N-4BrCClFHIOPSSi->H_Ext-4CO-R_5R!H->C_Sp-5C-4CO_4CO->C] +! family: CO_Disproportionation +HCO(15)+C2H5(13)<=>CO(7)+C2H6(8) 4.300000e+13 0.000 0.000 + +! Reaction index: Chemkin #39; RMG #318 +! Template reaction: CO_Disproportionation +! Flux pairs: HCO(15), CH2O(9); HCO(15), CO(7); +! Matched reaction 5 HCO + HCO_Y <=> CO + CH2O in CO_Disproportionation/training +! This reaction matched rate rule [Root_N-4R->N_N-4BrCClFHIOPSSi->H_Ext-4CO-R_N-5R!H->C_5BrClFINOPSSi->O_4CO->C_N-Sp-5O-4C] +! family: CO_Disproportionation +HCO(15)+HCO(15)<=>CO(7)+CH2O(9) 1.800000e+13 0.000 0.000 + +! Reaction index: Chemkin #40; RMG #322 +! Template reaction: CO_Disproportionation +! Flux pairs: CH3CH(19), C2H5(13); HCO(15), CO(7); +! Estimated from node Root_N-4R->N_N-4BrCClFHIOPSSi->H_Ext-4CO-R_5R!H->C_Sp-5C-4CO_4CO->C in family CO_Disproportionation. +HCO(15)+CH3CH(19)<=>CO(7)+C2H5(13) 4.309140e+13 -0.000 0.000 + +! Reaction index: Chemkin #41; RMG #357 +! Template reaction: H_Abstraction +! Flux pairs: HCO(15), CH2O(9); C2H6(8), C2H5(13); +! Matched reaction 325 HCO_r3 + C2H6 <=> CH2O + C2H5 in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;CO_pri_rad] +! family: H_Abstraction +HCO(15)+C2H6(8)<=>CH2O(9)+C2H5(13) 4.692000e+04 2.720 38.240 + +! Reaction index: Chemkin #42; RMG #360 +! Template reaction: Disproportionation +! Flux pairs: C2H5(13), C2H6(8); C2H5(13), C2H4(18); +! Matched reaction 6 C2H5 + C2H5-2 <=> C2H6 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_Ext-4CNS-R_N-Sp-5R!H#4CCCNNNSSS_N-2R!H->S_N-5R!H->O_Sp-5CS-4CCNSS_1CNS->C] +! family: Disproportionation +C2H5(13)+C2H5(13)<=>C2H4(18)+C2H6(8) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #43; RMG #361 +! Template reaction: H_Abstraction +! Flux pairs: CH3CH(19), C2H5(13); C2H6(8), C2H5(13); +! Estimated using an average for rate rule [C/H3/Cs\H3;Y_1centerbirad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: H_Abstraction +CH3CH(19)+C2H6(8)<=>C2H5(13)+C2H5(13) 1.157245e+11 0.933 12.427 + +! Reaction index: Chemkin #44; RMG #397 +! Template reaction: Disproportionation +! Flux pairs: HCO(15), C2H4(18); C2H5(13), CH2O(9); +! Estimated from node Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_Ext-4CNS-R_N-Sp-5R!H#4CCCNNNSSS_N-2R!H->S_5R!H->O_1CNS->C in family Disproportionation. +! Multiplied by reaction path degeneracy 3.0 +HCO(15)+C2H5(13)<=>CH2O(9)+C2H4(18) 8.670000e+12 0.000 0.000 + +! Reaction index: Chemkin #45; RMG #404 +! Template reaction: H_Abstraction +! Flux pairs: CH3CH(19), C2H5(13); CH2O(9), HCO(15); +! Estimated using an average for rate rule [CO_pri;Y_1centerbirad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +CH2O(9)+CH3CH(19)<=>HCO(15)+C2H5(13) 5.012624e+10 0.285 1.380 + +! Reaction index: Chemkin #46; RMG #456 +! Template reaction: Disproportionation +! Flux pairs: C2H5(13), C2H5(13); CH3CH(19), C2H4(18); +! Estimated from node Root_N-4R->H_N-4CNOS-u1_N-1R!H->O_Sp-2R!H-1CNS_1CNS->C_2R!H->C in family Disproportionation. +! Multiplied by reaction path degeneracy 3.0 +CH3CH(19)+C2H5(13)<=>C2H4(18)+C2H5(13) 9.030000e+13 0.000 0.000 + +END + diff --git a/ipython/data/cpox_methane/chem_annotated-surface.inp b/ipython/data/cpox_methane/chem_annotated-surface.inp new file mode 100644 index 0000000000..aca9dd3881 --- /dev/null +++ b/ipython/data/cpox_methane/chem_annotated-surface.inp @@ -0,0 +1,2523 @@ +SITE/SURF0/ SDEN/2.4830E-09/ ! mol/cm^2 + X(1) ! X(1) + HX(21) ! HX(21) + CO2X(22) ! CO2X(22) + COX(23) ! COX(23) + OX(24) ! OX(24) + CH2X(25) ! CH2X(25) + CH3X(26) ! CH3X(26) + CHX(27) ! CHX(27) + CX(28) ! CX(28) + H2X(29) ! H2X(29) + OHX(30) ! OHX(30) + H2OX(31) ! H2OX(31) + CHOX(32) ! CHOX(32) + XCH2CH3(54) ! XCH2CH3(54) + XCHCH3(64) ! XCHCH3(64) + XCH2XCH2(66)/2/ ! XCH2XCH2(66) + XCHCH2(67) ! XCHCH2(67) + CH2CH2X(68) ! CH2CH2X(68) + XCHXO(70)/2/ ! XCHXO(70) + XCOH(80) ! XCOH(80) + XCHOH(81) ! XCHOH(81) + XCCH3(96) ! XCCH3(96) + XCXCO(105)/2/ ! XCXCO(105) + XCCO(106) ! XCCO(106) + XCHCO(111) ! XCHCO(111) + XCXCH2(118)/2/ ! XCXCH2(118) + XCCH2(119) ! XCCH2(119) + XCH2XCH(122)/2/ ! XCH2XCH(122) + XCHXCH(123)/2/ ! XCHXCH(123) + CHCHX(176) ! CHCHX(176) +END + + + +THERM ALL + 300.000 1000.000 5000.000 + +! Thermo library: surfaceThermoPt111 +X(1) X 1 G 298.000 3000.000 1000.00 1 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 4 + +! Thermo library: surfaceThermoPt111 +HX(21) H 1X 1 G 298.000 2000.000 1000.00 1 + 2.72247960E+00-1.06816957E-03 1.98653534E-06-1.12048346E-09 2.09811447E-13 2 +-5.33834283E+03-1.53207364E+01-2.07570352E+00 1.73580907E-02-2.60920836E-05 3 + 1.89282272E-08-5.38835749E-12-4.28629410E+03 8.15362620E+00 4 + +! Thermo library: surfaceThermoPt111 +CO2X(22) C 1O 2X 1 G 298.000 2000.000 1000.00 1 + 6.98298185E+00-3.09871211E-03 5.62882671E-06-3.07847266E-09 5.62448785E-13 2 +-5.01432130E+04-2.76520082E+01 2.00959624E+00 1.33597621E-02-1.62303952E-05 3 + 1.10029588E-08-3.14484938E-12-4.88915555E+04-2.59292675E+00 4 + +! Thermo library: surfaceThermoPt111 +COX(23) C 1O 1X 1 G 298.000 2000.000 1000.00 1 + 5.48655965E+00-1.68118060E-03 3.09029814E-06-1.71186421E-09 3.15864230E-13 2 +-3.02504824E+04-2.76788160E+01 1.42894816E+00 1.40374567E-02-2.21178962E-05 3 + 1.78659585E-08-5.71478989E-12-2.93377830E+04-7.78264626E+00 4 + +! Thermo library: surfaceThermoPt111 +OX(24) O 1X 1 G 298.000 2000.000 1000.00 1 + 2.90244107E+00-3.38576310E-04 6.43364262E-07-3.66322914E-10 6.90087688E-14 2 +-1.36543831E+04-1.52559382E+01-2.94477587E-01 1.44162684E-02-2.61322747E-05 3 + 2.19005961E-08-6.98019726E-12-1.30665623E+04-1.99436466E-01 4 + +! Thermo library: surfaceThermoPt111 +CH2X(25) C 1H 2X 1 G 298.000 2000.000 1000.00 1 + 6.83459305E+00-5.14925435E-03 9.15490095E-06-4.84916961E-09 8.63765861E-13 2 +-2.66347873E+03-3.62214989E+01-2.23007140E+00 2.92223049E-02-4.33155010E-05 3 + 3.31428200E-08-9.96471660E-12-6.26760839E+02 8.30175061E+00 4 + +! Thermo library: surfaceThermoPt111 +CH3X(26) C 1H 3X 1 G 298.000 2000.000 1000.00 1 + 8.65704488E+00-7.90307727E-03 1.40100433E-05-7.40016052E-09 1.31516588E-12 2 +-1.01605953E+04-4.43352536E+01-4.44574492E-02 1.94367746E-02-1.91028792E-05 3 + 1.11269376E-08-2.73735931E-12-7.91264761E+03-1.73363631E-01 4 + +! Thermo library: surfaceThermoPt111 +CHX(27) C 1H 1X 1 G 298.000 2000.000 1000.00 1 + 4.90429627E+00-2.63864718E-03 4.71728940E-06-2.51266853E-09 4.49659036E-13 2 +-3.74880735E+03-2.67107807E+01-2.66805407E+00 2.90693605E-02-4.82653639E-05 3 + 3.87589263E-08-1.19749398E-11-2.20255536E+03 9.72943273E+00 4 + +! Thermo library: surfaceThermoPt111 +CX(28) C 1X 1 G 298.000 2000.000 1000.00 1 + 2.81347906E+00-6.93962433E-04 1.30309030E-06-7.38705282E-10 1.38796644E-13 2 + 7.89572752E+03-1.55738741E+01-1.94351174E+00 1.97767481E-02-3.36336700E-05 3 + 2.69027206E-08-8.27958862E-12 8.83627043E+03 7.17471163E+00 4 + +! Thermo library: surfaceThermoPt111 +H2X(29) H 2X 1 G 298.000 2000.000 1000.00 1 + 4.06879706E+00-4.95807479E-04 6.59235100E-07-1.72598058E-10 7.62971064E-15 2 +-3.94091046E+03-9.71918064E+00 3.86406403E+00 7.53456762E-04-1.65571464E-06 3 + 1.55223218E-09-4.46781999E-13-3.92948485E+03-8.85806484E+00 4 + +! Thermo library: surfaceThermoPt111 +OHX(30) H 1O 1X 1 G 298.000 2000.000 1000.00 1 + 3.95939930E+00-1.65986776E-03 2.83126639E-06-1.40393699E-09 2.37010707E-13 2 +-1.88321114E+04-1.36888724E+01 6.89851980E-01 1.15607233E-02-1.81720747E-05 3 + 1.40194900E-08-4.13411896E-12-1.81533768E+04 2.12907995E+00 4 + +! Thermo library: surfaceThermoPt111 +H2OX(31) H 2O 1X 1 G 298.000 2000.000 1000.00 1 + 5.85496927E+00-3.28848314E-03 5.56991427E-06-2.73008501E-09 4.55898715E-13 2 +-3.21494868E+04-2.13518731E+01 2.72971274E+00 8.71052014E-03-1.29131852E-05 3 + 1.07295002E-08-3.39433374E-12-3.14575485E+04-6.04478964E+00 4 + +! Thermo library: surfaceThermoPt111 +CHOX(32) C 1H 1O 1X 1G 298.000 2000.000 1000.00 1 + 7.47249774E+00-4.25651788E-03 7.67239688E-06-4.15094029E-09 7.52056996E-13 2 +-2.54909110E+04-3.52777249E+01 1.33924811E+00 1.56187944E-02-1.78706100E-05 3 + 1.16103371E-08-3.20827612E-12-2.39292346E+04-4.27822204E+00 4 + +! Thermo library: surfaceThermoPt111 +XCH2CH3(54) C 2H 5X 1 G 298.000 2000.000 1000.00 1 + 1.50607594E+01-1.48576179E-02 2.64630594E-05-1.40881050E-08 2.51997765E-12 2 +-1.68078880E+04-7.82120078E+01 1.18931248E-01 2.54181066E-02-9.60813724E-06 3 +-4.29518492E-09 3.46435785E-12-1.26172959E+04-7.38043167E-01 4 + +! Thermo library: surfaceThermoPt111 +XCHCH3(64) C 2H 4X 1 G 298.000 2000.000 1000.00 1 + 1.32389476E+01-1.20662435E-02 2.15309277E-05-1.14893088E-08 2.05901969E-12 2 +-1.02396069E+04-7.02795488E+01-1.02965056E+00 3.05643884E-02-2.57333995E-05 3 + 1.12938146E-08-1.82181022E-12-6.45116380E+03 2.66180041E+00 4 + +! Thermo library: surfaceThermoPt111 +XCH2XCH2(66) C 2H 4X 2 G 298.000 2000.000 1000.00 1 + 1.32290080E+01-1.18706777E-02 2.11521841E-05-1.12641704E-08 2.01567079E-12 2 +-1.34206522E+04-7.01190966E+01-2.67192838E+00 3.80645354E-02-3.82436403E-05 3 + 2.04023331E-08-4.28928498E-12-9.34434900E+03 1.05041174E+01 4 + +! Thermo library: surfaceThermoPt111 +XCHCH2(67) C 2H 3X 1 G 298.000 2000.000 1000.00 1 + 1.13486303E+01-8.90556126E-03 1.58461703E-05-8.41756582E-09 1.50324480E-12 2 +-7.27897213E+01-5.79325824E+01-3.08863011E-01 2.83917093E-02-3.01517639E-05 3 + 1.77197663E-08-4.27593032E-12 2.89021507E+03 1.02857491E+00 4 + +! Thermo library: surfaceThermoPt111 +CH2CH2X(68) C 2H 4X 1 G 298.000 2000.000 1000.00 1 + 1.21842218E+01-1.15021169E-02 2.03950367E-05-1.07880351E-08 1.91997735E-12 2 +-4.38056356E+03-5.56581039E+01 1.30720366E+00 1.65960850E-02-1.65594391E-06 3 +-8.53643523E-09 4.49817426E-12-1.28085886E+03 1.00988157E+00 4 + +! Thermo library: surfaceThermoPt111 +XCHXO(70) C 1H 1O 1X 2G 298.000 2000.000 1000.00 1 + 7.63455293E+00-3.73565753E-03 6.72664791E-06-3.63437587E-09 6.57956543E-13 2 +-2.20908199E+04-3.67791152E+01 8.73094515E-01 1.93259165E-02-2.43372881E-05 3 + 1.61326695E-08-4.34526852E-12-2.04466195E+04-2.94043006E+00 4 + +! Thermo library: surfaceThermoPt111 +XCOH(80) C 1H 1O 1X 1G 298.000 2000.000 1000.00 1 + 7.57277695E+00-3.16578459E-03 5.61811927E-06-2.96831941E-09 5.28683983E-13 2 +-2.80009212E+04-3.88297161E+01 2.81389530E-01 2.36061086E-02-3.32958999E-05 3 + 2.35937587E-08-6.59988062E-12-2.63389472E+04-2.84936464E+00 4 + +! Thermo library: surfaceThermoPt111 +XCHOH(81) C 1H 2O 1X 1G 298.000 2000.000 1000.00 1 + 8.40355861E+00-6.56451865E-03 1.17183675E-05-6.25847190E-09 1.12274948E-12 2 +-2.56433538E+04-3.79681005E+01-5.00708880E-01 2.03875211E-02-1.83412432E-05 3 + 8.05213096E-09-1.17601493E-12-2.33131337E+04 7.42265604E+00 4 + +! Thermo library: surfaceThermoPt111 +XCCH3(96) C 2H 3X 1 G 298.000 2000.000 1000.00 1 + 1.13071046E+01-9.36625341E-03 1.67150071E-05-8.92182977E-09 1.59934040E-12 2 +-1.39652458E+04-5.79411715E+01 4.57234129E-01 2.22262410E-02-1.66721437E-05 3 + 5.72136061E-09-3.99323091E-13-1.10436372E+04-2.27323815E+00 4 + +! Thermo library: surfaceThermoPt111 +XCXCO(105) C 2O 1X 2 G 298.000 2000.000 1000.00 1 + 8.17818492E+00-2.74873032E-03 5.05297612E-06-2.80344988E-09 5.18026205E-13 2 +-1.39471063E+04-4.05107308E+01 8.97579990E-01 2.46743251E-02-3.70136273E-05 3 + 2.82073324E-08-8.56860314E-12-1.22911976E+04-4.67311751E+00 4 + +! Thermo library: surfaceThermoPt111 +XCCO(106) C 2O 1X 1 G 298.000 2000.000 1000.00 1 + 8.07082355E+00-3.00852262E-03 5.51540020E-06-3.04805867E-09 5.61469536E-13 2 +-1.47647441E+04-4.08626151E+01 4.82293028E-01 2.58715712E-02-3.93603948E-05 3 + 3.04629752E-08-9.36533266E-12-1.30500602E+04-3.57374374E+00 4 + +! Thermo library: surfaceThermoPt111 +XCHCO(111) C 2H 1O 1X 1G 298.000 2000.000 1000.00 1 + 9.11773351E+00-5.00205029E-03 8.99634100E-06-4.84654156E-09 8.75266156E-13 2 +-1.22073761E+04-4.09366092E+01 4.25493544E-02 2.79328238E-02-3.94277514E-05 3 + 2.93799163E-08-8.78678926E-12-1.00824682E+04 4.03640870E+00 4 + +! Thermo library: surfaceThermoPt111 +XCXCH2(118) C 2H 2X 2 G 298.000 2000.000 1000.00 1 + 9.43020620E+00-6.45954121E-03 1.15448642E-05-6.16904076E-09 1.10713347E-12 2 +-3.66518703E+03-5.01224037E+01-1.79816112E+00 3.26996512E-02-4.25662671E-05 3 + 2.91542684E-08-8.03586947E-12-9.81598852E+02 5.84809747E+00 4 + +! Thermo library: surfaceThermoPt111 +XCCH2(119) C 2H 2X 1 G 298.000 2000.000 1000.00 1 + 9.50738620E+00-5.96521486E-03 1.06150130E-05-5.63034335E-09 1.00413638E-12 2 + 1.18564295E+04-4.81889471E+01 3.53716832E-01 2.73804972E-02-3.86126354E-05 3 + 2.92701458E-08-8.86074702E-12 1.39943134E+04-2.85680258E+00 4 + +! Thermo library: surfaceThermoPt111 +XCH2XCH(122) C 2H 3X 2 G 298.000 2000.000 1000.00 1 + 1.14364322E+01-9.00409359E-03 1.60927793E-05-8.59946784E-09 1.54310878E-12 2 +-6.17387487E+03-6.22564594E+01-4.49842378E+00 4.74505594E-02-6.33178514E-05 3 + 4.41445523E-08-1.23100777E-11-2.41150295E+03 1.69502447E+01 4 + +! Thermo library: surfaceThermoPt111 +XCHXCH(123) C 2H 2X 2 G 298.000 2000.000 1000.00 1 + 9.50734251E+00-6.29447123E-03 1.12600099E-05-6.02345902E-09 1.08201061E-12 2 +-1.03888642E+03-5.12967728E+01-3.12099318E+00 3.94849238E-02-5.46713898E-05 3 + 3.87299963E-08-1.08911043E-11 1.88314416E+03 1.11984448E+01 4 + +! Thermo library: surfaceThermoPt111 +CHCHX(176) C 2H 2X 1 G 298.000 2000.000 1000.00 1 + 8.53228527E+00-4.93781311E-03 8.64081803E-06-4.46203770E-09 7.78651926E-13 2 + 2.02566911E+04-3.66656834E+01 4.72391006E-01 2.77615181E-02-4.48825413E-05 3 + 3.68137783E-08-1.16132417E-11 2.19674643E+04 2.41181029E+00 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #1 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: H2(6), HX(21); X(1), HX(21); X(1), HX(21); +X(1)+X(1)+H2(6)<=>HX(21)+HX(21) 4.600e-02 0.000 0.000 + STICK + +! Reaction index: Chemkin #2; RMG #2 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: O2(3), OX(24); X(1), OX(24); X(1), OX(24); +X(1)+X(1)+O2(3)<=>OX(24)+OX(24) 1.890000e+21 -0.500 0.000 + +! Reaction index: Chemkin #3; RMG #3 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CH4(2), CH3X(26); X(1), OHX(30); OX(24), OHX(30); +X(1)+OX(24)+CH4(2)<=>OHX(30)+CH3X(26) 5.000000e+18 0.700 10.038 + +! Reaction index: Chemkin #4; RMG #4 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CH4(2), CH3X(26); X(1), H2OX(31); OHX(30), H2OX(31); +X(1)+OHX(30)+CH4(2)<=>H2OX(31)+CH3X(26) 1.000e+00 0.000 2.390 + STICK + +! Reaction index: Chemkin #5; RMG #5 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: X(1), H2OX(31); H2O(5), H2OX(31); +X(1)+H2O(5)<=>H2OX(31) 7.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #6; RMG #6 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: X(1), CO2X(22); CO2(4), CO2X(22); +X(1)+CO2(4)<=>CO2X(22) 5.000e-03 0.000 0.000 + STICK + +! Reaction index: Chemkin #7; RMG #7 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: COX(23), X(1); COX(23), CO(7); +COX(23)<=>X(1)+CO(7) 1.000000e+11 0.000 40.511 + +! Reaction index: Chemkin #8; RMG #8 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: COX(23), CX(28); X(1), OX(24); +X(1)+COX(23)<=>OX(24)+CX(28) 3.700000e+19 0.000 56.525 + +! Reaction index: Chemkin #9; RMG #9 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: COX(23), CO2X(22); OX(24), X(1); +OX(24)+COX(23)<=>X(1)+CO2X(22) 3.700000e+21 0.000 28.107 + +! Reaction index: Chemkin #10; RMG #10 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: COX(23), CO2X(22); OHX(30), HX(21); +OHX(30)+COX(23)<=>HX(21)+CO2X(22) 1.000000e+19 0.000 9.250 + +! Reaction index: Chemkin #11; RMG #11 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CH2X(25), CH3X(26); HX(21), X(1); +HX(21)+CH2X(25)<=>X(1)+CH3X(26) 3.090000e+22 0.000 0.000 + +! Reaction index: Chemkin #12; RMG #12 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CH2X(25), CHX(27); X(1), HX(21); +X(1)+CH2X(25)<=>HX(21)+CHX(27) 7.310000e+22 0.000 14.077 + +! Reaction index: Chemkin #13; RMG #13 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CHX(27), CX(28); X(1), HX(21); +X(1)+CHX(27)<=>HX(21)+CX(28) 3.090000e+22 0.000 12.357 + +! Reaction index: Chemkin #14; RMG #14 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: OHX(30), OX(24); X(1), HX(21); +X(1)+OHX(30)<=>OX(24)+HX(21) 7.390000e+19 0.000 18.475 + +! Reaction index: Chemkin #15; RMG #15 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: H2OX(31), OHX(30); X(1), HX(21); +X(1)+H2OX(31)<=>HX(21)+OHX(30) 1.150000e+19 0.000 24.235 + +! Reaction index: Chemkin #16; RMG #16 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: H2OX(31), OHX(30); OX(24), OHX(30); +OX(24)+H2OX(31)<=>OHX(30)+OHX(30) 1.000000e+20 0.000 21.630 + +! Reaction index: Chemkin #17; RMG #17 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: H2(6), CH2X(25); CX(28), CH2X(25); +H2(6)+CX(28)<=>CH2X(25) 4.000e-02 0.000 7.098 + STICK + +! Reaction index: Chemkin #18; RMG #18 +! Library reaction: Surface/CPOX_Pt/Deutschmann2006_adjusted +! Flux pairs: CH3X(26), CH4(2); HX(21), X(1); HX(21), X(1); +HX(21)+CH3X(26)<=>X(1)+X(1)+CH4(2) 3.300000e+21 0.000 11.950 + +! Reaction index: Chemkin #19; RMG #49 +! Template reaction: Surface_Adsorption_Single +! Flux pairs: H(12), HX(21); X(1), HX(21); +! Estimated using template [Adsorbate;VacantSite] for rate rule [H;VacantSite] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Single +X(1)+H(12)<=>HX(21) 8.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #20; RMG #52 +! Template reaction: Surface_Adsorption_Single +! Flux pairs: OH(17), OHX(30); X(1), OHX(30); +! Estimated using template [Adsorbate;VacantSite] for rate rule [O-H;VacantSite] +! Euclidian distance = 2.0 +! family: Surface_Adsorption_Single +X(1)+OH(17)<=>OHX(30) 8.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #21; RMG #53 +! Template reaction: Surface_Adsorption_Single +! Flux pairs: CH3(10), CH3X(26); X(1), CH3X(26); +! Estimated using template [Adsorbate;VacantSite] for rate rule [CH2-H;VacantSite] +! Euclidian distance = 2.0 +! family: Surface_Adsorption_Single +X(1)+CH3(10)<=>CH3X(26) 8.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #22; RMG #87 +! Template reaction: Surface_Adsorption_vdW +! Flux pairs: H2(6), H2X(29); X(1), H2X(29); +! Estimated using template [Adsorbate;VacantSite] for rate rule [H2;VacantSite] +! Euclidian distance = 2.0 +! family: Surface_Adsorption_vdW +X(1)+H2(6)<=>H2X(29) 8.000e-03 0.000 0.000 + STICK + +! Reaction index: Chemkin #23; RMG #88 +! Template reaction: Surface_Adsorption_Single +! Flux pairs: HCO(15), CHOX(32); X(1), CHOX(32); +! Estimated using template [Adsorbate;VacantSite] for rate rule [CH=O;VacantSite] +! Euclidian distance = 2.0 +! family: Surface_Adsorption_Single +X(1)+HCO(15)<=>CHOX(32) 8.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #24; RMG #90 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: H2O(5), OHX(30); X(1), HX(21); X(1), HX(21); +! Estimated using template [O-H;VacantSite1;VacantSite2] for rate rule [H2O;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+H2O(5)<=>HX(21)+OHX(30) 2.000e-01 0.000 35.642 + STICK + +! Reaction index: Chemkin #25; RMG #92 +! Template reaction: Surface_Adsorption_Dissociative_Double +! Flux pairs: CO2(4), COX(23); X(1), OX(24); X(1), OX(24); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [CO2;VacantSite1;VacantSite2] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Adsorption_Dissociative_Double +! Ea raised from 50.8 to 51.6 kJ/mol to match endothermicity of reaction. +X(1)+X(1)+CO2(4)<=>OX(24)+COX(23) 2.000e-02 0.000 12.324 + STICK + +! Reaction index: Chemkin #26; RMG #95 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: C2H6(8), CH3X(26); X(1), CH3X(26); X(1), CH3X(26); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [C;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+C2H6(8)<=>CH3X(26)+CH3X(26) 1.500e-02 0.000 1.195 + STICK + +! Reaction index: Chemkin #27; RMG #99 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: CH2O(9), CHOX(32); X(1), HX(21); X(1), HX(21); +! Exact match found for rate rule [C-H;VacantSite1;VacantSite2] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+CH2O(9)<=>HX(21)+CHOX(32) 2.000e-01 0.000 6.499 + STICK + +! Reaction index: Chemkin #28; RMG #100 +! Template reaction: Surface_Adsorption_Dissociative_Double +! Flux pairs: CH2O(9), CH2X(25); X(1), OX(24); X(1), OX(24); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [OC;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Dissociative_Double +X(1)+X(1)+CH2O(9)<=>OX(24)+CH2X(25) 1.000e-02 0.000 10.000 + STICK + +! Reaction index: Chemkin #29; RMG #104 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: CH3OH(14), CH3X(26); X(1), OHX(30); X(1), OHX(30); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [O-C;VacantSite1;VacantSite2] +! Euclidian distance = 2.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+CH3OH(14)<=>OHX(30)+CH3X(26) 1.500e-02 0.000 1.195 + STICK + +! Reaction index: Chemkin #30; RMG #109 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: CH3CHO(16), CHOX(32); X(1), CH3X(26); X(1), CH3X(26); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [C;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+CH3CHO(16)<=>CHOX(32)+CH3X(26) 1.500e-02 0.000 1.195 + STICK + +! Reaction index: Chemkin #31; RMG #116 +! Template reaction: Surface_Adsorption_Dissociative_Double +! Flux pairs: C2H4(18), CH2X(25); X(1), CH2X(25); X(1), CH2X(25); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [CC;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Dissociative_Double +X(1)+X(1)+C2H4(18)<=>CH2X(25)+CH2X(25) 1.000e-02 0.000 10.000 + STICK + +! Reaction index: Chemkin #32; RMG #119 +! Template reaction: Surface_Dissociation +! Flux pairs: COX(23), CHOX(32); HX(21), CHOX(32); +! Matched reaction 26 OCX_3 + HX_5 <=> CXHO_1 + Ni_4 in Surface_Dissociation/training +! This reaction matched rate rule [C-H;VacantSite] +! family: Surface_Dissociation +! metal: None +HX(21)+COX(23)<=>X(1)+CHOX(32) 3.140000e+21 0.000 22.830 + +! Reaction index: Chemkin #33; RMG #120 +! Template reaction: Surface_Dissociation_Double +! Flux pairs: CHOX(32), CHX(27); CHOX(32), OX(24); +! Exact match found for rate rule [C=O;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Double +X(1)+CHOX(32)<=>OX(24)+CHX(27) 4.180000e+21 0.000 46.687 + +! Reaction index: Chemkin #34; RMG #137 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: OX(24), OHX(30); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=O] for rate rule [H-H;*=O] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +OX(24)+H2X(29)<=>HX(21)+OHX(30) 4.782614e+24 -0.188 37.177 + +! Reaction index: Chemkin #35; RMG #138 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2X(25), CH3X(26); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [H-H;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+CH2X(25)<=>HX(21)+CH3X(26) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #36; RMG #143 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CHX(27), CH2X(25); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [H-H;*#CH] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+CHX(27)<=>HX(21)+CH2X(25) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #37; RMG #144 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CX(28), CHX(27); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [H-H;*$C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+CX(28)<=>HX(21)+CHX(27) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #38; RMG #145 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: COX(23), CHOX(32); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [H-H;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+COX(23)<=>HX(21)+CHOX(32) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #39; RMG #170 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); OHX(30), OX(24); +! Matched reaction 24 CH2X_1 + HOX_3 <=> CH3X_4 + OX_5 in Surface_Abstraction/training +! This reaction matched rate rule [O;*-CH2-H] +! family: Surface_Abstraction +! metal: None +OHX(30)+CH2X(25)<=>OX(24)+CH3X(26) 1.390000e+21 0.101 4.541 + +! Reaction index: Chemkin #40; RMG #175 +! Template reaction: Surface_Abstraction +! Flux pairs: CHX(27), CH2X(25); OHX(30), OX(24); +! Matched reaction 26 CHX_1 + HOX_3 <=> CH2X_4 + OX_5 in Surface_Abstraction/training +! This reaction matched rate rule [O;*=CH-H] +! family: Surface_Abstraction +! metal: None +! Ea raised from 42.4 to 55.0 kJ/mol to match endothermicity of reaction. +OHX(30)+CHX(27)<=>OX(24)+CH2X(25) 4.400000e+22 0.101 13.148 + +! Reaction index: Chemkin #41; RMG #178 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), CHX(27); OHX(30), OX(24); +! Matched reaction 28 CX_1 + HOX_3 <=> CHX_4 + OX_5 in Surface_Abstraction/training +! This reaction matched rate rule [O;*#C-H] +! family: Surface_Abstraction +! metal: None +OHX(30)+CX(28)<=>OX(24)+CHX(27) 2.430000e+21 -0.312 28.418 + +! Reaction index: Chemkin #42; RMG #180 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); OX(24), OHX(30); +! Matched reaction 39 OX_1 + HCOX_3 <=> HOX_4 + COX_5 in Surface_Abstraction/training +! This reaction matched rate rule [O;*-C-H] +! family: Surface_Abstraction +! metal: None +OX(24)+CHOX(32)<=>OHX(30)+COX(23) 3.298000e+21 0.000 0.000 + +! Reaction index: Chemkin #43; RMG #199 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2X(25), CH3X(26); H2OX(31), OHX(30); +! Estimated using template [O-R;*=C] for rate rule [O-R;*=C-2R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+CH2X(25)<=>OHX(30)+CH3X(26) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #44; RMG #208 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CHX(27), CH2X(25); H2OX(31), OHX(30); +! Estimated using template [O-R;*C] for rate rule [O-R;*#CH] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +! Ea raised from 120.8 to 122.6 kJ/mol to match endothermicity of reaction. +H2OX(31)+CHX(27)<=>OHX(30)+CH2X(25) 1.534107e+22 -0.150 29.304 + +! Reaction index: Chemkin #45; RMG #210 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CX(28), CHX(27); H2OX(31), OHX(30); +! Estimated using template [O-R;*C] for rate rule [O-R;*$C] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+CX(28)<=>OHX(30)+CHX(27) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #46; RMG #213 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CHOX(32), COX(23); OHX(30), H2OX(31); +! Matched reaction 40 OH_2* + HCO* <=> H2O* + CO* in Surface_Abstraction_vdW/training +! This reaction matched rate rule [O-R;*=C=R] +! family: Surface_Abstraction_vdW +! metal: None +OHX(30)+CHOX(32)<=>H2OX(31)+COX(23) 3.261000e+21 0.000 6.918 + +! Reaction index: Chemkin #47; RMG #225 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); CHOX(32), COX(23); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+CH2X(25)<=>COX(23)+CH3X(26) 4.180000e+21 0.000 14.635 + +! Reaction index: Chemkin #48; RMG #229 +! Template reaction: Surface_Abstraction +! Flux pairs: CH3X(26), CH2X(25); CX(28), CHX(27); +! Estimated using template [Abstracting;*-C-H] for rate rule [C$*;*-CH2-H] +! Euclidian distance = 2.8284271247461903 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction +CX(28)+CH3X(26)<=>CHX(27)+CH2X(25) 9.894000e+21 0.000 0.000 + +! Reaction index: Chemkin #49; RMG #233 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); CH2X(25), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+CH2X(25)<=>CHX(27)+CH3X(26) 8.360000e+21 0.000 17.379 + +! Reaction index: Chemkin #50; RMG #304 +! Template reaction: Surface_Abstraction +! Flux pairs: CHX(27), CH2X(25); CHOX(32), COX(23); +! Estimated using template [C;*C-H] for rate rule [C#*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHX(27)+CHOX(32)<=>COX(23)+CH2X(25) 4.180000e+21 0.000 20.989 + +! Reaction index: Chemkin #51; RMG #309 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), CHX(27); CHOX(32), COX(23); +! Estimated using template [C;*C-H] for rate rule [C$*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CX(28)+CHOX(32)<=>COX(23)+CHX(27) 4.180000e+21 0.000 11.654 + +! Reaction index: Chemkin #52; RMG #338 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); CX(28), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C$*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CX(28)+CH2X(25)<=>CHX(27)+CHX(27) 8.360000e+21 0.000 14.398 + +! Reaction index: Chemkin #53; RMG #142 +! Template reaction: Surface_Dissociation_Beta +! Flux pairs: XCOH(80), HX(21); XCOH(80), COX(23); +! Exact match found for rate rule [O-H;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Beta +X(1)+XCOH(80)<=>HX(21)+COX(23) 4.180000e+21 0.000 13.735 + +! Reaction index: Chemkin #54; RMG #204 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), COX(23); OX(24), OHX(30); +! Exact match found for rate rule [O;R-O-H] +! Euclidian distance = 0 +! family: Surface_Abstraction_Beta +OX(24)+XCOH(80)<=>OHX(30)+COX(23) 4.180000e+21 0.000 0.000 + +! Reaction index: Chemkin #55; RMG #207 +! Template reaction: Surface_Dissociation +! Flux pairs: XCOH(80), OHX(30); XCOH(80), CX(28); +! Estimated using an average for rate rule [C-O;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +! Ea raised from 139.5 to 140.2 kJ/mol to match endothermicity of reaction. +X(1)+XCOH(80)<=>OHX(30)+CX(28) 1.460000e+24 -0.213 33.508 + +! Reaction index: Chemkin #56; RMG #226 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), COX(23); CH2X(25), CH3X(26); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+CH2X(25)<=>COX(23)+CH3X(26) 4.180000e+21 0.000 12.430 + +! Reaction index: Chemkin #57; RMG #244 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CX(28), XCOH(80); H2OX(31), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [AdsorbateVdW;*$C] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+CX(28)<=>HX(21)+XCOH(80) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #58; RMG #305 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), COX(23); CHX(27), CH2X(25); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +CHX(27)+XCOH(80)<=>COX(23)+CH2X(25) 4.180000e+21 0.000 28.573 + +! Reaction index: Chemkin #59; RMG #310 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), COX(23); CX(28), CHX(27); +! Estimated using template [Abstracting;Donating] for rate rule [C$*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +CX(28)+XCOH(80)<=>COX(23)+CHX(27) 4.180000e+21 0.000 4.857 + +! Reaction index: Chemkin #60; RMG #313 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), CHOX(32); COX(23), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +COX(23)+XCOH(80)<=>COX(23)+CHOX(32) 4.180000e+21 0.000 35.544 + +! Reaction index: Chemkin #61; RMG #146 +! Template reaction: Surface_Dissociation_Beta +! Flux pairs: XCHOH(81), HX(21); XCHOH(81), CHOX(32); +! Exact match found for rate rule [O-H;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Beta +X(1)+XCHOH(81)<=>HX(21)+CHOX(32) 4.180000e+21 0.000 15.143 + +! Reaction index: Chemkin #62; RMG #211 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHOH(81), OHX(30); XCHOH(81), CHX(27); +! Estimated using an average for rate rule [C-O;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +X(1)+XCHOH(81)<=>OHX(30)+CHX(27) 1.460000e+24 -0.213 12.978 + +! Reaction index: Chemkin #63; RMG #212 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), CHOX(32); OX(24), OHX(30); +! Exact match found for rate rule [O;R-O-H] +! Euclidian distance = 0 +! family: Surface_Abstraction_Beta +OX(24)+XCHOH(81)<=>OHX(30)+CHOX(32) 4.180000e+21 0.000 0.000 + +! Reaction index: Chemkin #64; RMG #236 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), CHOX(32); CH2X(25), CH3X(26); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +CH2X(25)+XCHOH(81)<=>CHOX(32)+CH3X(26) 4.180000e+21 0.000 17.520 + +! Reaction index: Chemkin #65; RMG #246 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CHX(27), XCHOH(81); H2OX(31), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [AdsorbateVdW;*#CH] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+CHX(27)<=>HX(21)+XCHOH(81) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #66; RMG #347 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), CHOX(32); CHX(27), CH2X(25); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +CHX(27)+XCHOH(81)<=>CHOX(32)+CH2X(25) 4.180000e+21 0.000 33.663 + +! Reaction index: Chemkin #67; RMG #351 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), CHOX(32); CX(28), CHX(27); +! Estimated using template [Abstracting;Donating] for rate rule [C$*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +CX(28)+XCHOH(81)<=>CHX(27)+CHOX(32) 4.180000e+21 0.000 9.947 + +! Reaction index: Chemkin #68; RMG #548 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), CHOX(32); COX(23), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +COX(23)+XCHOH(81)<=>CHOX(32)+CHOX(32) 4.180000e+21 0.000 40.634 + +! Reaction index: Chemkin #69; RMG #554 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHOH(81), HX(21); XCHOH(81), XCOH(80); +! Estimated using template [C-H;VacantSite] for rate rule [CHR;VacantSite] +! Euclidian distance = 1.0 +! family: Surface_Dissociation +X(1)+XCHOH(81)<=>HX(21)+XCOH(80) 3.710000e+21 0.000 0.000 + +! Reaction index: Chemkin #70; RMG #558 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCOH(80), XCHOH(81); +! From training reaction 26 used for C#*;*OH +! Exact match found for rate rule [C#*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +! Ea raised from 63.3 to 65.8 kJ/mol to match endothermicity of reaction. +OHX(30)+XCOH(80)<=>OX(24)+XCHOH(81) 4.400000e+22 0.101 15.732 + +! Reaction index: Chemkin #71; RMG #561 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); XCHOH(81), XCOH(80); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CH2X(25)+XCHOH(81)<=>XCOH(80)+CH3X(26) 4.180000e+21 0.000 16.639 + +! Reaction index: Chemkin #72; RMG #564 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCOH(80), XCHOH(81); H2OX(31), OHX(30); +! Estimated using template [O-R;*C] for rate rule [O-R;*#C] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +! Ea raised from 129.2 to 133.4 kJ/mol to match endothermicity of reaction. +H2OX(31)+XCOH(80)<=>OHX(30)+XCHOH(81) 1.534107e+22 -0.150 31.888 + +! Reaction index: Chemkin #73; RMG #572 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); XCOH(80), XCHOH(81); +! Estimated using template [C;*C-H] for rate rule [C#*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCOH(80)+CH2X(25)<=>CHX(27)+XCHOH(81) 8.360000e+21 0.000 24.474 + +! Reaction index: Chemkin #74; RMG #575 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), XCOH(80); XCHOH(81), CHX(27); +! Estimated using template [C$*;Donating] for rate rule [C$*;*=C-OH] +! Euclidian distance = 4.0 +! family: Surface_Abstraction +CX(28)+XCHOH(81)<=>CHX(27)+XCOH(80) 2.430000e+21 -0.312 28.418 +DUPLICATE + +! Reaction index: Chemkin #75; RMG #577 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCOH(80), XCHOH(81); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [H-H;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCOH(80)<=>HX(21)+XCHOH(81) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #76; RMG #578 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); XCOH(80), XCHOH(81); +! Estimated using template [C;*C-H] for rate rule [C#*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCOH(80)<=>COX(23)+XCHOH(81) 4.180000e+21 0.000 21.730 + +! Reaction index: Chemkin #77; RMG #583 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCOH(80), XCHOH(81); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCOH(80)<=>COX(23)+XCHOH(81) 4.180000e+21 0.000 30.454 + +! Reaction index: Chemkin #78; RMG #605 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHOH(81), XCOH(80); CX(28), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C$*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CX(28)+XCHOH(81)<=>CHX(27)+XCOH(80) 4.180000e+21 0.000 13.658 +DUPLICATE + +! Reaction index: Chemkin #79; RMG #619 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHOH(81), XCHOH(81); XCOH(80), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCHOH(81)<=>CHOX(32)+XCHOH(81) 4.180000e+21 0.000 35.544 + +! Reaction index: Chemkin #80; RMG #339 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: XCXCH2(118), CH2X(25); XCXCH2(118), CX(28); +! From training reaction 1 used for Combined +! Exact match found for rate rule [Combined] +! Euclidian distance = 0 +! family: Surface_Bidentate_Dissociation +XCXCH2(118)<=>CX(28)+CH2X(25) 4.220000e+12 0.000 24.857 + +! Reaction index: Chemkin #81; RMG #230 +! Template reaction: Surface_Dissociation +! Flux pairs: XCCH3(96), CH3X(26); XCCH3(96), CX(28); +! Exact match found for rate rule [C-C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +X(1)+XCCH3(96)<=>CX(28)+CH3X(26) 4.180000e+21 0.000 46.998 + +! Reaction index: Chemkin #82; RMG #638 +! Template reaction: Surface_Dissociation_to_Bidentate +! Flux pairs: XCXCH2(118), XCCH3(96); HX(21), X(1); HX(21), X(1); +! Matched reaction 4 XCXCH2 + H_X <=> XCCH3 + Pt_5 + Pt_6 in Surface_Dissociation_to_Bidentate/training +! This reaction matched rate rule [Combined;VacantSite1;VacantSite2] +! family: Surface_Dissociation_to_Bidentate +! metal: None +HX(21)+XCXCH2(118)<=>X(1)+X(1)+XCCH3(96) 1.070000e+22 0.000 17.208 + +! Reaction index: Chemkin #83; RMG #112 +! Template reaction: Surface_Adsorption_Dissociative_Double +! Flux pairs: CH3CHO(16), XCHCH3(64); X(1), OX(24); X(1), OX(24); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [OC;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Dissociative_Double +X(1)+X(1)+CH3CHO(16)<=>OX(24)+XCHCH3(64) 1.000e-02 0.000 10.000 + STICK + +! Reaction index: Chemkin #84; RMG #235 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHCH3(64), CH3X(26); XCHCH3(64), CHX(27); +! Exact match found for rate rule [C-C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +X(1)+XCHCH3(64)<=>CHX(27)+CH3X(26) 4.180000e+21 0.000 24.965 + +! Reaction index: Chemkin #85; RMG #671 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHCH3(64), HX(21); XCHCH3(64), XCCH3(96); +! Estimated using template [C-H;VacantSite] for rate rule [CHR;VacantSite] +! Euclidian distance = 1.0 +! family: Surface_Dissociation +X(1)+XCHCH3(64)<=>HX(21)+XCCH3(96) 3.710000e+21 0.000 0.000 + +! Reaction index: Chemkin #86; RMG #676 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCCH3(96), XCHCH3(64); +! From training reaction 26 used for C#*;*OH +! Exact match found for rate rule [C#*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +! Ea raised from 77.4 to 78.5 kJ/mol to match endothermicity of reaction. +OHX(30)+XCCH3(96)<=>OX(24)+XCHCH3(64) 4.400000e+22 0.101 18.769 + +! Reaction index: Chemkin #87; RMG #679 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CH2X(25)+XCHCH3(64)<=>CH3X(26)+XCCH3(96) 4.180000e+21 0.000 15.391 + +! Reaction index: Chemkin #88; RMG #681 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCH3(96), XCHCH3(64); H2OX(31), OHX(30); +! Estimated using template [O-R;*C] for rate rule [O-R;*#C] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +! Ea raised from 143.3 to 146.1 kJ/mol to match endothermicity of reaction. +H2OX(31)+XCCH3(96)<=>OHX(30)+XCHCH3(64) 1.534107e+22 -0.150 34.925 + +! Reaction index: Chemkin #89; RMG #688 +! Template reaction: Surface_Abstraction +! Flux pairs: CHX(27), CH2X(25); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C#*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHX(27)+XCHCH3(64)<=>CH2X(25)+XCCH3(96) 4.180000e+21 0.000 21.746 + +! Reaction index: Chemkin #90; RMG #690 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), XCCH3(96); XCHCH3(64), CHX(27); +! Estimated using template [C$*;Donating] for rate rule [C$*;*C-C] +! Euclidian distance = 2.0 +! family: Surface_Abstraction +CX(28)+XCHCH3(64)<=>CHX(27)+XCCH3(96) 2.430000e+21 -0.312 28.418 +DUPLICATE + +! Reaction index: Chemkin #91; RMG #692 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCH3(96), XCHCH3(64); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [H-H;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCCH3(96)<=>HX(21)+XCHCH3(64) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #92; RMG #693 +! Template reaction: Surface_Abstraction +! Flux pairs: COX(23), CHOX(32); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +COX(23)+XCHCH3(64)<=>CHOX(32)+XCCH3(96) 4.180000e+21 0.000 24.489 + +! Reaction index: Chemkin #93; RMG #697 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCHCH3(64); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCCH3(96)<=>COX(23)+XCHCH3(64) 4.180000e+21 0.000 33.623 + +! Reaction index: Chemkin #94; RMG #701 +! Template reaction: Surface_Abstraction +! Flux pairs: XCOH(80), XCHOH(81); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C#*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCOH(80)+XCHCH3(64)<=>XCHOH(81)+XCCH3(96) 4.180000e+21 0.000 22.486 + +! Reaction index: Chemkin #95; RMG #702 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCHCH3(64); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCCH3(96)<=>CHOX(32)+XCHCH3(64) 4.180000e+21 0.000 38.713 + +! Reaction index: Chemkin #96; RMG #726 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), XCCH3(96); CX(28), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C$*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CX(28)+XCHCH3(64)<=>CHX(27)+XCCH3(96) 4.180000e+21 0.000 12.410 +DUPLICATE + +! Reaction index: Chemkin #97; RMG #340 +! Template reaction: Surface_Dissociation_Double +! Flux pairs: XCCH2(119), CH2X(25); XCCH2(119), CX(28); +! Exact match found for rate rule [C=C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Double +X(1)+XCCH2(119)<=>CX(28)+CH2X(25) 4.180000e+21 0.000 20.973 + +! Reaction index: Chemkin #98; RMG #634 +! Template reaction: Surface_Monodentate_to_Bidentate +! Flux pairs: XCCH2(119), XCXCH2(118); X(1), XCXCH2(118); +! Matched reaction 1 XCCH2 + Pt_4 <=> XCXCH2 in Surface_Monodentate_to_Bidentate/training +! This reaction matched rate rule [Monodentate;VacantSite] +! family: Surface_Monodentate_to_Bidentate +! metal: None +X(1)+XCCH2(119)<=>XCXCH2(118) 1.000000e+21 0.000 0.000 + +! Reaction index: Chemkin #99; RMG #669 +! Template reaction: Surface_Dissociation_Beta +! Flux pairs: XCCH3(96), XCCH2(119); XCCH3(96), HX(21); +! Estimated using template [C-H;VacantSite] for rate rule [CH3;VacantSite] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Dissociation_Beta +X(1)+XCCH3(96)<=>HX(21)+XCCH2(119) 1.254000e+22 0.000 50.906 + +! Reaction index: Chemkin #100; RMG #673 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); OX(24), OHX(30); +! Estimated using template [O;R-C-H] for rate rule [O;R-CH3] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +OX(24)+XCCH3(96)<=>OHX(30)+XCCH2(119) 1.254000e+22 0.000 68.675 + +! Reaction index: Chemkin #101; RMG #684 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); COX(23), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +COX(23)+XCCH3(96)<=>CHOX(32)+XCCH2(119) 1.254000e+22 0.000 87.995 + +! Reaction index: Chemkin #102; RMG #686 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); CX(28), CHX(27); +! Estimated using template [Abstracting;Donating] for rate rule [C$*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CX(28)+XCCH3(96)<=>CHX(27)+XCCH2(119) 1.254000e+22 0.000 57.308 + +! Reaction index: Chemkin #103; RMG #689 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); CH2X(25), CH3X(26); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CH2X(25)+XCCH3(96)<=>CH3X(26)+XCCH2(119) 1.254000e+22 0.000 64.881 + +! Reaction index: Chemkin #104; RMG #691 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); CHX(27), CH2X(25); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CHX(27)+XCCH3(96)<=>CH2X(25)+XCCH2(119) 1.254000e+22 0.000 81.024 + +! Reaction index: Chemkin #105; RMG #698 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCCH2(119); XCOH(80), XCHOH(81); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCOH(80)+XCCH3(96)<=>XCHOH(81)+XCCH2(119) 1.254000e+22 0.000 82.905 + +! Reaction index: Chemkin #106; RMG #706 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCHCH3(64); XCCH3(96), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH3(96)+XCCH3(96)<=>XCCH2(119)+XCHCH3(64) 1.254000e+22 0.000 86.074 + +! Reaction index: Chemkin #107; RMG #345 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: XCH2XCH(122), CHX(27); XCH2XCH(122), CH2X(25); +! Matched reaction 4 HCCH2_2X <=> CHX_3 + CH2X_4 in Surface_Bidentate_Dissociation/training +! This reaction matched rate rule [Combined] +! family: Surface_Bidentate_Dissociation +! metal: None +XCH2XCH(122)<=>CHX(27)+CH2X(25) 2.740000e+13 0.000 33.461 + +! Reaction index: Chemkin #108; RMG #637 +! Template reaction: Surface_Dissociation +! Flux pairs: XCH2XCH(122), HX(21); XCH2XCH(122), XCXCH2(118); +! Matched reaction 65 XCHXCH2_1 + Ni_4 <=> XCXCH2_3 + HX_5 in Surface_Dissociation/training +! This reaction matched rate rule [C-H_Bidentate;VacantSite] +! family: Surface_Dissociation +! metal: None +X(1)+XCH2XCH(122)<=>HX(21)+XCXCH2(118) 9.690000e+21 0.000 11.472 + +! Reaction index: Chemkin #109; RMG #641 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCXCH2(118), XCH2XCH(122); +! From training reaction 26 used for C#*;*OH +! Exact match found for rate rule [C#*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +OHX(30)+XCXCH2(118)<=>OX(24)+XCH2XCH(122) 4.400000e+22 0.101 10.134 + +! Reaction index: Chemkin #110; RMG #644 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); XCH2XCH(122), XCXCH2(118); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CH2X(25)+XCH2XCH(122)<=>CH3X(26)+XCXCH2(118) 4.180000e+21 0.000 19.939 + +! Reaction index: Chemkin #111; RMG #646 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCXCH2(118), XCH2XCH(122); H2OX(31), OHX(30); +! Estimated using template [O-R;*C] for rate rule [O-R;*#C] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+XCXCH2(118)<=>OHX(30)+XCH2XCH(122) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #112; RMG #654 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); XCXCH2(118), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C#*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCXCH2(118)<=>CHX(27)+XCH2XCH(122) 8.360000e+21 0.000 21.173 + +! Reaction index: Chemkin #113; RMG #656 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), CHX(27); XCH2XCH(122), XCXCH2(118); +! Estimated using template [C;*C-H] for rate rule [C$*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CX(28)+XCH2XCH(122)<=>CHX(27)+XCXCH2(118) 4.180000e+21 0.000 16.958 + +! Reaction index: Chemkin #114; RMG #657 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCXCH2(118), XCH2XCH(122); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*C] for rate rule [H-H;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCXCH2(118)<=>HX(21)+XCH2XCH(122) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #115; RMG #658 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); XCXCH2(118), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C#*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCXCH2(118)<=>COX(23)+XCH2XCH(122) 4.180000e+21 0.000 18.429 + +! Reaction index: Chemkin #116; RMG #663 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCXCH2(118), XCH2XCH(122); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCXCH2(118)<=>COX(23)+XCH2XCH(122) 4.180000e+21 0.000 22.070 + +! Reaction index: Chemkin #117; RMG #666 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHOH(81), XCOH(80); XCXCH2(118), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C#*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHOH(81)+XCXCH2(118)<=>XCOH(80)+XCH2XCH(122) 4.180000e+21 0.000 20.433 + +! Reaction index: Chemkin #118; RMG #667 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCXCH2(118), XCH2XCH(122); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCXCH2(118)<=>CHOX(32)+XCH2XCH(122) 4.180000e+21 0.000 27.159 + +! Reaction index: Chemkin #119; RMG #705 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCH2XCH(122); XCXCH2(118), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCXCH2(118)+XCCH3(96)<=>XCCH2(119)+XCH2XCH(122) 1.254000e+22 0.000 74.520 + +! Reaction index: Chemkin #120; RMG #708 +! Template reaction: Surface_Dissociation_to_Bidentate +! Flux pairs: XCHCH3(64), XCH2XCH(122); X(1), HX(21); X(1), HX(21); +! Matched reaction 2 HCCH3_X + Pt_5 + Pt_6 <=> HCCH2_2X + H_X in Surface_Dissociation_to_Bidentate/training +! This reaction matched rate rule [Combined;VacantSite1;VacantSite2] +! family: Surface_Dissociation_to_Bidentate +! metal: None +X(1)+X(1)+XCHCH3(64)<=>HX(21)+XCH2XCH(122) 6.500000e+29 0.000 11.711 + +! Reaction index: Chemkin #121; RMG #748 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), XCCH3(96); XCXCH2(118), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C#*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCXCH2(118)+XCHCH3(64)<=>XCCH3(96)+XCH2XCH(122) 4.180000e+21 0.000 19.186 + +! Reaction index: Chemkin #122; RMG #115 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: C2H4(18), XCHCH2(67); X(1), HX(21); X(1), HX(21); +! Exact match found for rate rule [C2H4;VacantSite1;VacantSite2] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+C2H4(18)<=>HX(21)+XCHCH2(67) 1.000e-01 0.000 16.632 + STICK + +! Reaction index: Chemkin #123; RMG #346 +! Template reaction: Surface_Dissociation_Double +! Flux pairs: XCHCH2(67), CH2X(25); XCHCH2(67), CHX(27); +! Exact match found for rate rule [C=C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Double +X(1)+XCHCH2(67)<=>CHX(27)+CH2X(25) 4.180000e+21 0.000 21.335 + +! Reaction index: Chemkin #124; RMG #707 +! Template reaction: Surface_Dissociation_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); XCHCH3(64), HX(21); +! Estimated using template [C-H;VacantSite] for rate rule [CH3;VacantSite] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Dissociation_Beta +X(1)+XCHCH3(64)<=>HX(21)+XCHCH2(67) 1.254000e+22 0.000 32.865 + +! Reaction index: Chemkin #125; RMG #712 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); OX(24), OHX(30); +! Estimated using template [O;R-C-H] for rate rule [O;R-CH3] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +OX(24)+XCHCH3(64)<=>OHX(30)+XCHCH2(67) 1.254000e+22 0.000 39.436 + +! Reaction index: Chemkin #126; RMG #724 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); COX(23), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +COX(23)+XCHCH3(64)<=>CHOX(32)+XCHCH2(67) 1.254000e+22 0.000 58.756 + +! Reaction index: Chemkin #127; RMG #727 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); CX(28), CHX(27); +! Estimated using template [Abstracting;Donating] for rate rule [C$*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CX(28)+XCHCH3(64)<=>CHX(27)+XCHCH2(67) 1.254000e+22 0.000 28.069 + +! Reaction index: Chemkin #128; RMG #730 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); CH2X(25), CH3X(26); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CH2X(25)+XCHCH3(64)<=>CH3X(26)+XCHCH2(67) 1.254000e+22 0.000 35.642 + +! Reaction index: Chemkin #129; RMG #732 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); CHX(27), CH2X(25); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +CHX(27)+XCHCH3(64)<=>CH2X(25)+XCHCH2(67) 1.254000e+22 0.000 51.785 + +! Reaction index: Chemkin #130; RMG #741 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); XCOH(80), XCHOH(81); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCOH(80)+XCHCH3(64)<=>XCHOH(81)+XCHCH2(67) 1.254000e+22 0.000 53.666 + +! Reaction index: Chemkin #131; RMG #750 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2XCH(122); XCXCH2(118), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCXCH2(118)+XCHCH3(64)<=>XCHCH2(67)+XCH2XCH(122) 1.254000e+22 0.000 45.281 + +! Reaction index: Chemkin #132; RMG #752 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH3(64); XCCH3(96), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C#*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH3(96)+XCHCH3(64)<=>XCHCH2(67)+XCHCH3(64) 1.254000e+22 0.000 56.835 + +! Reaction index: Chemkin #133; RMG #757 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHCH2(67), HX(21); XCHCH2(67), XCCH2(119); +! From training reaction 48 used for C-H;VacantSite +! Exact match found for rate rule [C-H;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +! Ea raised from 0.0 to 55.4 kJ/mol to match endothermicity of reaction. +X(1)+XCHCH2(67)<=>HX(21)+XCCH2(119) 3.710000e+21 0.000 13.250 + +! Reaction index: Chemkin #134; RMG #761 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCCH2(119), XCHCH2(67); +! From training reaction 24 used for C=*;*OH +! Exact match found for rate rule [C=*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +OHX(30)+XCCH2(119)<=>OX(24)+XCHCH2(67) 1.390000e+21 0.101 4.541 + +! Reaction index: Chemkin #135; RMG #764 +! Template reaction: Surface_Abstraction +! Flux pairs: CH3X(26), CH2X(25); XCCH2(119), XCHCH2(67); +! Estimated using template [Abstracting;*-C-H] for rate rule [C=*;*-CH2-H] +! Euclidian distance = 2.8284271247461903 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction +CH3X(26)+XCCH2(119)<=>CH2X(25)+XCHCH2(67) 9.894000e+21 0.000 0.000 + +! Reaction index: Chemkin #136; RMG #765 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCH2(119), XCHCH2(67); H2OX(31), OHX(30); +! From training reaction 40 used for O-R;*=C=R +! Exact match found for rate rule [O-R;*=C=R] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+XCCH2(119)<=>OHX(30)+XCHCH2(67) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #137; RMG #767 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCCH2(119)<=>CHX(27)+XCHCH2(67) 8.360000e+21 0.000 14.212 + +! Reaction index: Chemkin #138; RMG #768 +! Template reaction: Surface_Abstraction +! Flux pairs: CHX(27), CX(28); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*#C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHX(27)+XCCH2(119)<=>CX(28)+XCHCH2(67) 4.180000e+21 0.000 23.547 + +! Reaction index: Chemkin #139; RMG #769 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCH2(119), XCHCH2(67); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [H-H;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCCH2(119)<=>HX(21)+XCHCH2(67) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #140; RMG #770 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCCH2(119)<=>COX(23)+XCHCH2(67) 4.180000e+21 0.000 11.468 + +! Reaction index: Chemkin #141; RMG #772 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH2(119), XCHCH2(67); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCCH2(119)<=>COX(23)+XCHCH2(67) 4.180000e+21 0.000 4.384 + +! Reaction index: Chemkin #142; RMG #775 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHOH(81), XCOH(80); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHOH(81)+XCCH2(119)<=>XCOH(80)+XCHCH2(67) 4.180000e+21 0.000 13.472 + +! Reaction index: Chemkin #143; RMG #776 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH2(119), XCHCH2(67); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCCH2(119)<=>CHOX(32)+XCHCH2(67) 4.180000e+21 0.000 9.474 + +! Reaction index: Chemkin #144; RMG #780 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCHCH2(67); XCCH2(119), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH2(119)+XCCH3(96)<=>XCCH2(119)+XCHCH2(67) 1.254000e+22 0.000 56.835 + +! Reaction index: Chemkin #145; RMG #781 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), XCCH3(96); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCCH2(119)+XCHCH3(64)<=>XCCH3(96)+XCHCH2(67) 4.180000e+21 0.000 12.224 + +! Reaction index: Chemkin #146; RMG #782 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCHCH2(67); XCCH2(119), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH2(119)+XCHCH3(64)<=>XCHCH2(67)+XCHCH2(67) 1.254000e+22 0.000 27.596 + +! Reaction index: Chemkin #147; RMG #783 +! Template reaction: Surface_Monodentate_to_Bidentate +! Flux pairs: XCHCH2(67), XCH2XCH(122); X(1), XCH2XCH(122); +! Matched reaction 2 XCHCH2 + Pt_4 <=> XCHXCH2 in Surface_Monodentate_to_Bidentate/training +! This reaction matched rate rule [Monodentate;VacantSite] +! family: Surface_Monodentate_to_Bidentate +! metal: None +X(1)+XCHCH2(67)<=>XCH2XCH(122) 7.150000e+20 0.000 0.717 + +! Reaction index: Chemkin #148; RMG #827 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCXCH2(118); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCCH2(119)+XCH2XCH(122)<=>XCXCH2(118)+XCHCH2(67) 4.180000e+21 0.000 16.772 + +! Reaction index: Chemkin #149; RMG #350 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: XCHXCH(123), CHX(27); XCHXCH(123), CHX(27); +! Matched reaction 3 HCCH_2X <=> CHX_3 + CHX_4 in Surface_Bidentate_Dissociation/training +! This reaction matched rate rule [Combined] +! family: Surface_Bidentate_Dissociation +! metal: None +XCHXCH(123)<=>CHX(27)+CHX(27) 7.930000e+12 0.000 21.511 + +! Reaction index: Chemkin #150; RMG #784 +! Template reaction: Surface_Dissociation +! Flux pairs: XCH2XCH(122), XCHXCH(123); XCH2XCH(122), HX(21); +! Matched reaction 60 HCCH2_2X + Ni_4 <=> HCCH_2X + HX_5 in Surface_Dissociation/training +! This reaction matched rate rule [C-H_Bidentate;VacantSite] +! family: Surface_Dissociation +! metal: None +X(1)+XCH2XCH(122)<=>HX(21)+XCHXCH(123) 4.750000e+21 0.000 17.208 + +! Reaction index: Chemkin #151; RMG #785 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCHXCH(123), XCH2XCH(122); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [H-H;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCHXCH(123)<=>HX(21)+XCH2XCH(122) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #152; RMG #787 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); OHX(30), OX(24); +! From training reaction 24 used for C=*;*OH +! Exact match found for rate rule [C=*;*OH] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +OHX(30)+XCHXCH(123)<=>OX(24)+XCH2XCH(122) 2.780000e+21 0.101 4.541 + +! Reaction index: Chemkin #153; RMG #789 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCHXCH(123), XCH2XCH(122); H2OX(31), OHX(30); +! Estimated using template [O-R;*=C] for rate rule [O-R;*=C-2R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +H2OX(31)+XCHXCH(123)<=>OHX(30)+XCH2XCH(122) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #154; RMG #798 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); CHOX(32), COX(23); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CHOX(32)+XCHXCH(123)<=>COX(23)+XCH2XCH(122) 8.360000e+21 0.000 16.457 + +! Reaction index: Chemkin #155; RMG #799 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHXCH(123), XCH2XCH(122); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_Beta +XCOH(80)+XCHXCH(123)<=>COX(23)+XCH2XCH(122) 8.360000e+21 0.000 17.059 + +! Reaction index: Chemkin #156; RMG #800 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCHXCH(123); CX(28), CHX(27); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C$*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CX(28)+XCH2XCH(122)<=>CHX(27)+XCHXCH(123) 7.425804e+21 0.000 9.465 + +! Reaction index: Chemkin #157; RMG #801 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCHXCH(123); CH2X(25), CH3X(26); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCH2XCH(122)<=>CH3X(26)+XCHXCH(123) 7.425804e+21 0.000 10.956 + +! Reaction index: Chemkin #158; RMG #803 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); CH2X(25), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction +CH2X(25)+XCHXCH(123)<=>CHX(27)+XCH2XCH(122) 1.672000e+22 0.000 19.201 + +! Reaction index: Chemkin #159; RMG #807 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHXCH(123), XCH2XCH(122); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCHXCH(123)<=>CHOX(32)+XCH2XCH(122) 8.360000e+21 0.000 22.148 + +! Reaction index: Chemkin #160; RMG #810 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); XCHOH(81), XCOH(80); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCHOH(81)+XCHXCH(123)<=>XCOH(80)+XCH2XCH(122) 8.360000e+21 0.000 18.460 + +! Reaction index: Chemkin #161; RMG #818 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); XCH2XCH(122), XCXCH2(118); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCHXCH(123)+XCH2XCH(122)<=>XCXCH2(118)+XCH2XCH(122) 8.360000e+21 0.000 21.761 + +! Reaction index: Chemkin #162; RMG #820 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHXCH(123), XCH2XCH(122); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCHXCH(123)+XCHCH3(64)<=>XCCH3(96)+XCH2XCH(122) 8.360000e+21 0.000 17.213 + +! Reaction index: Chemkin #163; RMG #826 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCHXCH(123); XCCH2(119), XCHCH2(67); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCCH2(119)+XCH2XCH(122)<=>XCHXCH(123)+XCHCH2(67) 7.425804e+21 0.000 9.372 + +! Reaction index: Chemkin #164; RMG #828 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCH3(96), XCH2XCH(122); XCHXCH(123), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 6.0 +! family: Surface_Abstraction_Beta +XCHXCH(123)+XCCH3(96)<=>XCCH2(119)+XCH2XCH(122) 2.508000e+22 0.000 69.509 + +! Reaction index: Chemkin #165; RMG #832 +! Template reaction: Surface_Dissociation_to_Bidentate +! Flux pairs: XCHCH2(67), XCHXCH(123); X(1), HX(21); X(1), HX(21); +! From training reaction 1 used for Combined;VacantSite1;VacantSite2 +! Exact match found for rate rule [Combined;VacantSite1;VacantSite2] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Dissociation_to_Bidentate +X(1)+X(1)+XCHCH2(67)<=>HX(21)+XCHXCH(123) 3.713333e+29 0.000 10.994 + +! Reaction index: Chemkin #166; RMG #862 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2XCH(122); XCHXCH(123), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 6.0 +! family: Surface_Abstraction_Beta +XCHXCH(123)+XCHCH3(64)<=>XCHCH2(67)+XCH2XCH(122) 2.508000e+22 0.000 40.270 + +! Reaction index: Chemkin #167; RMG #121 +! Template reaction: Surface_Monodentate_to_Bidentate +! Flux pairs: X(1), XCHXO(70); CHOX(32), XCHXO(70); +! Matched reaction 3 HXCO + Pt_4 <=> HXCXO in Surface_Monodentate_to_Bidentate/training +! This reaction matched rate rule [Monodentate;VacantSite] +! family: Surface_Monodentate_to_Bidentate +! metal: None +! Ea raised from 0.0 to 28.8 kJ/mol to match endothermicity of reaction. +X(1)+CHOX(32)<=>XCHXO(70) 1.000000e+21 0.000 6.888 + +! Reaction index: Chemkin #168; RMG #179 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: CHX(27), XCHXO(70); OX(24), XCHXO(70); +! Matched reaction 6 CHX_3 + OX_4 <=> HCO_2X in Surface_Bidentate_Dissociation/training +! This reaction matched rate rule [Combined] +! family: Surface_Bidentate_Dissociation +! metal: None +OX(24)+CHX(27)<=>XCHXO(70) 6.540000e+21 0.000 33.939 + +! Reaction index: Chemkin #169; RMG #585 +! Template reaction: Surface_Dissociation_to_Bidentate +! Flux pairs: XCHOH(81), XCHXO(70); X(1), HX(21); X(1), HX(21); +! From training reaction 1 used for Combined;VacantSite1;VacantSite2 +! Exact match found for rate rule [Combined;VacantSite1;VacantSite2] +! Euclidian distance = 0 +! family: Surface_Dissociation_to_Bidentate +X(1)+X(1)+XCHOH(81)<=>HX(21)+XCHXO(70) 1.856667e+29 0.000 10.994 + +! Reaction index: Chemkin #170; RMG #96 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: C2H6(8), XCH2CH3(54); X(1), HX(21); X(1), HX(21); +! Exact match found for rate rule [C2H6;VacantSite1;VacantSite2] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+C2H6(8)<=>HX(21)+XCH2CH3(54) 2.052e+00 0.000 10.206 + STICK + +! Reaction index: Chemkin #171; RMG #102 +! Template reaction: Surface_Adsorption_Dissociative +! Flux pairs: C3H8(11), XCH2CH3(54); X(1), CH3X(26); X(1), CH3X(26); +! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [C;VacantSite1;VacantSite2] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Adsorption_Dissociative +X(1)+X(1)+C3H8(11)<=>CH3X(26)+XCH2CH3(54) 3.000e-02 0.000 1.195 + STICK + +! Reaction index: Chemkin #172; RMG #103 +! Template reaction: Surface_Adsorption_Single +! Flux pairs: X(1), XCH2CH3(54); C2H5(13), XCH2CH3(54); +! Estimated using template [Adsorbate;VacantSite] for rate rule [C;VacantSite] +! Euclidian distance = 1.0 +! family: Surface_Adsorption_Single +X(1)+C2H5(13)<=>XCH2CH3(54) 8.500e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #173; RMG #232 +! Template reaction: Surface_Dissociation +! Flux pairs: XCH2CH3(54), CH3X(26); XCH2CH3(54), CH2X(25); +! Exact match found for rate rule [C-C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +X(1)+XCH2CH3(54)<=>CH2X(25)+CH3X(26) 4.180000e+21 0.000 35.960 + +! Reaction index: Chemkin #174; RMG #687 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), XCCH3(96); XCH2CH3(54), CH2X(25); +! Estimated using template [C$*;Donating] for rate rule [C$*;*C-C] +! Euclidian distance = 2.0 +! family: Surface_Abstraction +CX(28)+XCH2CH3(54)<=>CH2X(25)+XCCH3(96) 2.430000e+21 -0.312 28.418 + +! Reaction index: Chemkin #175; RMG #710 +! Template reaction: Surface_Dissociation +! Flux pairs: XCH2CH3(54), HX(21); XCH2CH3(54), XCHCH3(64); +! Estimated using template [C-H;VacantSite] for rate rule [CH2R;VacantSite] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Dissociation +! Ea raised from 0.0 to 13.0 kJ/mol to match endothermicity of reaction. +X(1)+XCH2CH3(54)<=>HX(21)+XCHCH3(64) 7.420000e+21 0.000 3.109 + +! Reaction index: Chemkin #176; RMG #715 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCHCH3(64), XCH2CH3(54); +! From training reaction 24 used for C=*;*OH +! Exact match found for rate rule [C=*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +OHX(30)+XCHCH3(64)<=>OX(24)+XCH2CH3(54) 1.390000e+21 0.101 4.541 + +! Reaction index: Chemkin #177; RMG #718 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); XCH2CH3(54), XCHCH3(64); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCH2CH3(54)<=>CH3X(26)+XCHCH3(64) 7.425804e+21 0.000 11.515 + +! Reaction index: Chemkin #178; RMG #721 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCHCH3(64), XCH2CH3(54); H2OX(31), OHX(30); +! Estimated using template [O-R;*=C] for rate rule [O-R;*=C-2R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+XCHCH3(64)<=>OHX(30)+XCH2CH3(54) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #179; RMG #728 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), CHX(27); CH2X(25), XCH2CH3(54); +! Estimated using template [C=*;Donating] for rate rule [C=*;*C-C] +! Euclidian distance = 2.0 +! family: Surface_Abstraction +CH2X(25)+XCHCH3(64)<=>CHX(27)+XCH2CH3(54) 1.390000e+21 0.101 4.541 +DUPLICATE + +! Reaction index: Chemkin #180; RMG #729 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCHCH3(64)<=>CHX(27)+XCH2CH3(54) 8.360000e+21 0.000 18.083 +DUPLICATE + +! Reaction index: Chemkin #181; RMG #731 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), CHX(27); XCH2CH3(54), XCHCH3(64); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C$*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CX(28)+XCH2CH3(54)<=>CHX(27)+XCHCH3(64) 7.425804e+21 0.000 10.024 + +! Reaction index: Chemkin #182; RMG #733 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCHCH3(64), XCH2CH3(54); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [H-H;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCHCH3(64)<=>HX(21)+XCH2CH3(54) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #183; RMG #734 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCHCH3(64)<=>COX(23)+XCH2CH3(54) 4.180000e+21 0.000 15.339 + +! Reaction index: Chemkin #184; RMG #740 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2CH3(54); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCHCH3(64)<=>COX(23)+XCH2CH3(54) 4.180000e+21 0.000 14.218 + +! Reaction index: Chemkin #185; RMG #745 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHOH(81), XCOH(80); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHOH(81)+XCHCH3(64)<=>XCOH(80)+XCH2CH3(54) 4.180000e+21 0.000 17.342 + +! Reaction index: Chemkin #186; RMG #746 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2CH3(54); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCHCH3(64)<=>CHOX(32)+XCH2CH3(54) 4.180000e+21 0.000 19.308 + +! Reaction index: Chemkin #187; RMG #751 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2CH3(54); XCCH3(96), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH3(96)+XCHCH3(64)<=>XCCH2(119)+XCH2CH3(54) 1.254000e+22 0.000 66.669 + +! Reaction index: Chemkin #188; RMG #753 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), XCCH3(96); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHCH3(64)+XCHCH3(64)<=>XCCH3(96)+XCH2CH3(54) 4.180000e+21 0.000 16.095 + +! Reaction index: Chemkin #189; RMG #754 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2CH3(54); XCHCH3(64), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCHCH3(64)+XCHCH3(64)<=>XCHCH2(67)+XCH2CH3(54) 1.254000e+22 0.000 37.430 + +! Reaction index: Chemkin #190; RMG #822 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCHXCH(123); XCHCH3(64), XCH2CH3(54); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCH2XCH(122)+XCHCH3(64)<=>XCHXCH(123)+XCH2CH3(54) 7.425804e+21 0.000 11.308 + +! Reaction index: Chemkin #191; RMG #823 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCXCH2(118); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCH2XCH(122)+XCHCH3(64)<=>XCXCH2(118)+XCH2CH3(54) 4.180000e+21 0.000 20.643 + +! Reaction index: Chemkin #192; RMG #859 +! Template reaction: Surface_Abstraction +! Flux pairs: XCCH2(119), XCHCH2(67); XCH2CH3(54), XCHCH3(64); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCCH2(119)+XCH2CH3(54)<=>XCHCH2(67)+XCHCH3(64) 7.425804e+21 0.000 9.931 + +! Reaction index: Chemkin #193; RMG #835 +! Template reaction: Surface_Abstraction_Beta_double_vdW +! Flux pairs: XCHCH2(67), CHCHX(176); OHX(30), H2OX(31); +! Exact match found for rate rule [OH;R-C-H] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_Beta_double_vdW +OHX(30)+XCHCH2(67)<=>H2OX(31)+CHCHX(176) 8.360000e+21 0.000 34.012 + +! Reaction index: Chemkin #194; RMG #868 +! Template reaction: Surface_vdW_to_Bidentate +! Flux pairs: CHCHX(176), XCHXCH(123); X(1), XCHXCH(123); +! Matched reaction 1 HCCHX_vdW + X <=> HCCH_2X in Surface_vdW_to_Bidentate/training +! This reaction matched rate rule [Combined;VacantSite] +! family: Surface_vdW_to_Bidentate +! metal: None +X(1)+CHCHX(176)<=>XCHXCH(123) 1.000000e+21 0.000 0.000 + +! Reaction index: Chemkin #195; RMG #312 +! Template reaction: Surface_Dissociation_Double +! Flux pairs: XCHCO(111), COX(23); XCHCO(111), CHX(27); +! Exact match found for rate rule [C=C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Double +X(1)+XCHCO(111)<=>COX(23)+CHX(27) 4.180000e+21 0.000 0.000 + +! Reaction index: Chemkin #196; RMG #303 +! Template reaction: Surface_Dissociation_Double +! Flux pairs: XCCO(106), COX(23); XCCO(106), CX(28); +! Exact match found for rate rule [C=C;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation_Double +X(1)+XCCO(106)<=>CX(28)+COX(23) 4.180000e+21 0.000 19.459 + +! Reaction index: Chemkin #197; RMG #1039 +! Template reaction: Surface_Dissociation +! Flux pairs: XCHCO(111), XCCO(106); XCHCO(111), HX(21); +! From training reaction 48 used for C-H;VacantSite +! Exact match found for rate rule [C-H;VacantSite] +! Euclidian distance = 0 +! family: Surface_Dissociation +X(1)+XCHCO(111)<=>HX(21)+XCCO(106) 3.710000e+21 0.000 0.000 + +! Reaction index: Chemkin #198; RMG #1041 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCO(106), XCHCO(111); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [H-H;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCCO(106)<=>HX(21)+XCHCO(111) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #199; RMG #1045 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); OX(24), OHX(30); +! From training reaction 39 used for O;*-C-H +! Exact match found for rate rule [O;*-C-H] +! Euclidian distance = 0 +! family: Surface_Abstraction +OX(24)+XCHCO(111)<=>OHX(30)+XCCO(106) 3.298000e+21 0.000 0.000 + +! Reaction index: Chemkin #200; RMG #1048 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCO(106), XCHCO(111); H2OX(31), OHX(30); +! From training reaction 40 used for O-R;*=C=R +! Exact match found for rate rule [O-R;*=C=R] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +! Ea raised from 130.6 to 133.4 kJ/mol to match endothermicity of reaction. +H2OX(31)+XCCO(106)<=>OHX(30)+XCHCO(111) 1.534107e+22 -0.150 31.891 + +! Reaction index: Chemkin #201; RMG #1059 +! Template reaction: Surface_Abstraction +! Flux pairs: XCCO(106), XCHCO(111); CHOX(32), COX(23); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCCO(106)<=>COX(23)+XCHCO(111) 4.180000e+21 0.000 21.856 + +! Reaction index: Chemkin #202; RMG #1060 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCO(106), XCHCO(111); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCCO(106)<=>COX(23)+XCHCO(111) 4.180000e+21 0.000 30.776 + +! Reaction index: Chemkin #203; RMG #1061 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); CX(28), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C$*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CX(28)+XCHCO(111)<=>CHX(27)+XCCO(106) 4.180000e+21 0.000 13.531 + +! Reaction index: Chemkin #204; RMG #1062 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); CH2X(25), CH3X(26); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CH2X(25)+XCHCO(111)<=>CH3X(26)+XCCO(106) 4.180000e+21 0.000 16.512 + +! Reaction index: Chemkin #205; RMG #1065 +! Template reaction: Surface_Abstraction +! Flux pairs: XCCO(106), XCHCO(111); CH2X(25), CHX(27); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCCO(106)<=>CHX(27)+XCHCO(111) 8.360000e+21 0.000 24.600 + +! Reaction index: Chemkin #206; RMG #1068 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCO(106), XCHCO(111); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCCO(106)<=>CHOX(32)+XCHCO(111) 4.180000e+21 0.000 35.865 + +! Reaction index: Chemkin #207; RMG #1072 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCOH(80), XCHOH(81); +! Estimated using template [C;*C-H] for rate rule [C#*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCOH(80)+XCHCO(111)<=>XCHOH(81)+XCCO(106) 4.180000e+21 0.000 23.607 + +! Reaction index: Chemkin #208; RMG #1080 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCXCH2(118), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C#*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHCO(111)+XCXCH2(118)<=>XCCO(106)+XCH2XCH(122) 4.180000e+21 0.000 20.306 + +! Reaction index: Chemkin #209; RMG #1083 +! Template reaction: Surface_Abstraction +! Flux pairs: XCCO(106), XCHCO(111); XCHCH3(64), XCCH3(96); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCCO(106)+XCHCH3(64)<=>XCHCO(111)+XCCH3(96) 4.180000e+21 0.000 22.612 + +! Reaction index: Chemkin #210; RMG #1084 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCHCH3(64), XCH2CH3(54); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHCO(111)+XCHCH3(64)<=>XCCO(106)+XCH2CH3(54) 4.180000e+21 0.000 17.216 + +! Reaction index: Chemkin #211; RMG #1087 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCCH2(119), XCHCH2(67); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHCO(111)+XCCH2(119)<=>XCCO(106)+XCHCH2(67) 4.180000e+21 0.000 13.345 + +! Reaction index: Chemkin #212; RMG #1088 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCO(106), XCHCO(111); XCCH3(96), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCO(106)+XCCH3(96)<=>XCHCO(111)+XCCH2(119) 1.254000e+22 0.000 83.226 + +! Reaction index: Chemkin #213; RMG #1094 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCCO(106), XCHCO(111); XCHCH3(64), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCO(106)+XCHCH3(64)<=>XCHCO(111)+XCHCH2(67) 1.254000e+22 0.000 53.988 + +! Reaction index: Chemkin #214; RMG #1099 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCHXCH(123), XCH2XCH(122); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCHCO(111)+XCHXCH(123)<=>XCCO(106)+XCH2XCH(122) 8.360000e+21 0.000 18.334 + +! Reaction index: Chemkin #215; RMG #302 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: XCXCO(105), CX(28); XCXCO(105), COX(23); +! From training reaction 1 used for Combined +! Exact match found for rate rule [Combined] +! Euclidian distance = 0 +! family: Surface_Bidentate_Dissociation +XCXCO(105)<=>CX(28)+COX(23) 4.220000e+12 0.000 24.857 + +! Reaction index: Chemkin #216; RMG #1112 +! Template reaction: Surface_Monodentate_to_Bidentate +! Flux pairs: X(1), XCXCO(105); XCCO(106), XCXCO(105); +! From training reaction 1 used for Monodentate;VacantSite +! Exact match found for rate rule [Monodentate;VacantSite] +! Euclidian distance = 0 +! family: Surface_Monodentate_to_Bidentate +! Ea raised from 0.0 to 6.7 kJ/mol to match endothermicity of reaction. +X(1)+XCCO(106)<=>XCXCO(105) 1.000000e+21 0.000 1.604 + +! Reaction index: Chemkin #217; RMG #117 +! Template reaction: Surface_Adsorption_vdW +! Flux pairs: X(1), CH2CH2X(68); C2H4(18), CH2CH2X(68); +! Estimated using template [C;VacantSite] for rate rule [C2H4;VacantSite] +! Euclidian distance = 3.0 +! family: Surface_Adsorption_vdW +X(1)+C2H4(18)<=>CH2CH2X(68) 7.000e-06 0.000 0.000 + STICK + +! Reaction index: Chemkin #218; RMG #344 +! Template reaction: Surface_Dissociation_Double_vdW +! Flux pairs: CH2CH2X(68), CH2X(25); CH2CH2X(68), CH2X(25); +! Estimated using an average for rate rule [AdsorbateVdW;VacantSite] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Dissociation_Double_vdW +X(1)+CH2CH2X(68)<=>CH2X(25)+CH2X(25) 3.282000e+20 0.000 57.651 + +! Reaction index: Chemkin #219; RMG #833 +! Template reaction: Surface_Dissociation_vdW +! Flux pairs: CH2CH2X(68), HX(21); CH2CH2X(68), XCHCH2(67); +! Estimated using template [CH2R;VacantSite] for rate rule [C2H4;VacantSite] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Dissociation_vdW +X(1)+CH2CH2X(68)<=>HX(21)+XCHCH2(67) 1.493995e+14 1.801 4.381 + +! Reaction index: Chemkin #220; RMG #836 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); OX(24), OHX(30); +! From training reaction 21 used for C-R;*=O +! Exact match found for rate rule [C-R;*=O] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +OX(24)+CH2CH2X(68)<=>OHX(30)+XCHCH2(67) 5.620000e+24 -0.101 22.156 + +! Reaction index: Chemkin #221; RMG #842 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); CH2X(25), CH3X(26); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [C-R;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +CH2X(25)+CH2CH2X(68)<=>CH3X(26)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #222; RMG #843 +! Template reaction: Surface_Abstraction_Single_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); OHX(30), H2OX(31); +! Estimated using template [Donating;Abstracting] for rate rule [C-R;*O-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_Single_vdW +OHX(30)+CH2CH2X(68)<=>H2OX(31)+XCHCH2(67) 1.672000e+22 0.000 14.516 + +! Reaction index: Chemkin #223; RMG #846 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); CHX(27), CH2X(25); +! Estimated using template [AdsorbateVdW;*C] for rate rule [C-R;*#CH] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +CHX(27)+CH2CH2X(68)<=>CH2X(25)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #224; RMG #847 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); CX(28), CHX(27); +! Estimated using template [AdsorbateVdW;*C] for rate rule [C-R;*$C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +CX(28)+CH2CH2X(68)<=>CHX(27)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #225; RMG #850 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); COX(23), CHOX(32); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [C-R;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +COX(23)+CH2CH2X(68)<=>CHOX(32)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #226; RMG #856 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); XCOH(80), XCHOH(81); +! Estimated using template [AdsorbateVdW;*C] for rate rule [C-R;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCOH(80)+CH2CH2X(68)<=>XCHOH(81)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #227; RMG #860 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH3(64); XCCH3(96), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*C] for rate rule [C-R;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCCH3(96)+CH2CH2X(68)<=>XCHCH2(67)+XCHCH3(64) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #228; RMG #863 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCH2XCH(122); XCHXCH(123), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [C-R;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 8.0 +! family: Surface_Abstraction_vdW +XCHXCH(123)+CH2CH2X(68)<=>XCHCH2(67)+XCH2XCH(122) 6.136428e+22 -0.150 26.653 + +! Reaction index: Chemkin #229; RMG #864 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCH2XCH(122); XCXCH2(118), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*C] for rate rule [C-R;*#C] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCXCH2(118)+CH2CH2X(68)<=>XCHCH2(67)+XCH2XCH(122) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #230; RMG #865 +! Template reaction: Surface_Abstraction_Beta_double_vdW +! Flux pairs: XCHCH2(67), CH2CH2X(68); XCHCH2(67), CHCHX(176); +! Estimated using template [Abstracting;Donating] for rate rule [Abstracting;R-C-H] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_Beta_double_vdW +XCHCH2(67)+XCHCH2(67)<=>CHCHX(176)+CH2CH2X(68) 8.360000e+21 0.000 45.867 + +! Reaction index: Chemkin #231; RMG #866 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCHCH2(67); XCCH2(119), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [C-R;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCCH2(119)+CH2CH2X(68)<=>XCHCH2(67)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #232; RMG #954 +! Template reaction: Surface_Dissociation_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); XCH2CH3(54), HX(21); +! From training reaction 24 used for CH3;VacantSite +! Exact match found for rate rule [CH3;VacantSite] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Dissociation_Beta_vdW +X(1)+XCH2CH3(54)<=>HX(21)+CH2CH2X(68) 5.547763e+19 0.946 13.973 + +! Reaction index: Chemkin #233; RMG #959 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); OX(24), OHX(30); +! Exact match found for rate rule [O;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +OX(24)+XCH2CH3(54)<=>OHX(30)+CH2CH2X(68) 4.179000e+21 0.000 43.039 + +! Reaction index: Chemkin #234; RMG #961 +! Template reaction: Surface_Abstraction_Beta_double_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); OHX(30), H2OX(31); +! Estimated using template [OH;R-C-H] for rate rule [OH;R-CH3] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_double_vdW +OHX(30)+XCH2CH3(54)<=>H2OX(31)+CH2CH2X(68) 1.254000e+22 0.000 23.438 + +! Reaction index: Chemkin #235; RMG #977 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); COX(23), CHOX(32); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +COX(23)+XCH2CH3(54)<=>CHOX(32)+CH2CH2X(68) 4.179000e+21 0.000 62.359 + +! Reaction index: Chemkin #236; RMG #978 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); CH2X(25), CH3X(26); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +CH2X(25)+XCH2CH3(54)<=>CH3X(26)+CH2CH2X(68) 4.179000e+21 0.000 39.245 + +! Reaction index: Chemkin #237; RMG #994 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), XCH2CH3(54); XCHCH3(64), CH2CH2X(68); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +XCHCH3(64)+XCH2CH3(54)<=>CH2CH2X(68)+XCH2CH3(54) 4.179000e+21 0.000 41.033 + +! Reaction index: Chemkin #238; RMG #996 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); XCCH2(119), XCHCH2(67); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +XCCH2(119)+XCH2CH3(54)<=>XCHCH2(67)+CH2CH2X(68) 4.179000e+21 0.000 31.199 + +! Reaction index: Chemkin #239; RMG #1001 +! Template reaction: Surface_Abstraction_Beta_double_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); XCHCH2(67), CH2CH2X(68); +! Estimated using template [Abstracting;Donating] for rate rule [Abstracting;R-CH3] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_double_vdW +XCHCH2(67)+XCH2CH3(54)<=>CH2CH2X(68)+CH2CH2X(68) 1.254000e+22 0.000 35.293 + +! Reaction index: Chemkin #240; RMG #1003 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCHCH3(64), XCH2CH3(54); CH2CH2X(68), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [C-R;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +CH2CH2X(68)+XCHCH3(64)<=>XCHCH2(67)+XCH2CH3(54) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #241; RMG #1005 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), CH2CH2X(68); XCHXCH(123), XCH2XCH(122); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Surface_Abstraction_Beta_vdW +XCHXCH(123)+XCH2CH3(54)<=>XCH2XCH(122)+CH2CH2X(68) 8.358000e+21 0.000 43.874 + +! Reaction index: Chemkin #242; RMG #1097 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCCO(106), XCHCO(111); CH2CH2X(68), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*=C=R] for rate rule [C-R;*=C=R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCCO(106)+CH2CH2X(68)<=>XCHCO(111)+XCHCH2(67) 3.068214e+22 -0.150 26.653 + +! Reaction index: Chemkin #243; RMG #1141 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCCO(106), XCHCO(111); XCH2CH3(54), CH2CH2X(68); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +XCCO(106)+XCH2CH3(54)<=>XCHCO(111)+CH2CH2X(68) 4.179000e+21 0.000 57.591 + +! Reaction index: Chemkin #244; RMG #114 +! Template reaction: Surface_Adsorption_Bidentate +! Flux pairs: X(1), XCH2XCH2(66); X(1), XCH2XCH2(66); C2H4(18), XCH2XCH2(66); +! Matched reaction 2 H2CCH2 + X_3 + X_4 <=> H2CCH2_2X in Surface_Adsorption_Bidentate/training +! This reaction matched rate rule [Adsorbate;VacantSite1;VacantSite2] +! family: Surface_Adsorption_Bidentate +! metal: None +X(1)+X(1)+C2H4(18)<=>XCH2XCH2(66) 6.900e-01 0.000 0.000 + STICK + +! Reaction index: Chemkin #245; RMG #343 +! Template reaction: Surface_Bidentate_Dissociation +! Flux pairs: CH2X(25), XCH2XCH2(66); CH2X(25), XCH2XCH2(66); +! Matched reaction 5 CH2X_3 + CH2X_4 <=> H2CCH2_2X in Surface_Bidentate_Dissociation/training +! This reaction matched rate rule [Combined] +! family: Surface_Bidentate_Dissociation +! metal: None +CH2X(25)+CH2X(25)<=>XCH2XCH2(66) 9.890000e+23 0.000 36.807 + +! Reaction index: Chemkin #246; RMG #786 +! Template reaction: Surface_Dissociation +! Flux pairs: XCH2XCH2(66), HX(21); XCH2XCH2(66), XCH2XCH(122); +! Matched reaction 61 H2CCH2_2X + Ni_4 <=> H2CCH_2X + HX_5 in Surface_Dissociation/training +! This reaction matched rate rule [C-H_Bidentate;VacantSite] +! family: Surface_Dissociation +! metal: None +X(1)+XCH2XCH2(66)<=>HX(21)+XCH2XCH(122) 2.225000e+21 0.000 14.101 + +! Reaction index: Chemkin #247; RMG #788 +! Template reaction: Surface_Abstraction +! Flux pairs: OHX(30), OX(24); XCH2XCH(122), XCH2XCH2(66); +! From training reaction 24 used for C=*;*OH +! Exact match found for rate rule [C=*;*OH] +! Euclidian distance = 0 +! family: Surface_Abstraction +OHX(30)+XCH2XCH(122)<=>OX(24)+XCH2XCH2(66) 1.390000e+21 0.101 4.541 + +! Reaction index: Chemkin #248; RMG #791 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CH3X(26); XCH2XCH2(66), XCH2XCH(122); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction +CH2X(25)+XCH2XCH2(66)<=>CH3X(26)+XCH2XCH(122) 1.485161e+22 0.000 11.768 + +! Reaction index: Chemkin #249; RMG #794 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCH2XCH(122), XCH2XCH2(66); H2OX(31), OHX(30); +! Estimated using template [O-R;*=C] for rate rule [O-R;*=C-2R] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2OX(31)+XCH2XCH(122)<=>OHX(30)+XCH2XCH2(66) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #250; RMG #802 +! Template reaction: Surface_Abstraction +! Flux pairs: CH2X(25), CHX(27); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*=CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +CH2X(25)+XCH2XCH(122)<=>CHX(27)+XCH2XCH2(66) 8.360000e+21 0.000 17.576 + +! Reaction index: Chemkin #251; RMG #804 +! Template reaction: Surface_Abstraction +! Flux pairs: CX(28), CHX(27); XCH2XCH2(66), XCH2XCH(122); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C$*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction +CX(28)+XCH2XCH2(66)<=>CHX(27)+XCH2XCH(122) 1.485161e+22 0.000 10.278 + +! Reaction index: Chemkin #252; RMG #805 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: XCH2XCH(122), XCH2XCH2(66); H2X(29), HX(21); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [H-H;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction_vdW +H2X(29)+XCH2XCH(122)<=>HX(21)+XCH2XCH2(66) 1.534107e+22 -0.150 26.653 + +! Reaction index: Chemkin #253; RMG #806 +! Template reaction: Surface_Abstraction +! Flux pairs: CHOX(32), COX(23); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +CHOX(32)+XCH2XCH(122)<=>COX(23)+XCH2XCH2(66) 4.180000e+21 0.000 14.832 + +! Reaction index: Chemkin #254; RMG #812 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCH2XCH(122), XCH2XCH2(66); XCOH(80), COX(23); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCOH(80)+XCH2XCH(122)<=>COX(23)+XCH2XCH2(66) 4.180000e+21 0.000 12.931 + +! Reaction index: Chemkin #255; RMG #816 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHOH(81), XCOH(80); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHOH(81)+XCH2XCH(122)<=>XCOH(80)+XCH2XCH2(66) 4.180000e+21 0.000 16.836 + +! Reaction index: Chemkin #256; RMG #817 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCH2XCH(122), XCH2XCH2(66); XCHOH(81), CHOX(32); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-O-H] +! Euclidian distance = 2.8284271247461903 +! family: Surface_Abstraction_Beta +XCHOH(81)+XCH2XCH(122)<=>CHOX(32)+XCH2XCH2(66) 4.180000e+21 0.000 18.021 + +! Reaction index: Chemkin #257; RMG #821 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCH2XCH(122), XCH2XCH2(66); XCCH3(96), XCCH2(119); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCCH3(96)+XCH2XCH(122)<=>XCCH2(119)+XCH2XCH2(66) 1.254000e+22 0.000 65.382 + +! Reaction index: Chemkin #258; RMG #824 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCH3(64), XCCH3(96); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCH2XCH(122)+XCHCH3(64)<=>XCCH3(96)+XCH2XCH2(66) 4.180000e+21 0.000 15.589 + +! Reaction index: Chemkin #259; RMG #825 +! Template reaction: Surface_Abstraction_Beta +! Flux pairs: XCHCH3(64), XCH2XCH2(66); XCH2XCH(122), XCHCH2(67); +! Estimated using template [Abstracting;Donating] for rate rule [C=*;R-CH3] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta +XCH2XCH(122)+XCHCH3(64)<=>XCHCH2(67)+XCH2XCH2(66) 1.254000e+22 0.000 36.143 + +! Reaction index: Chemkin #260; RMG #829 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCHXCH(123); XCH2XCH(122), XCH2XCH2(66); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCH2XCH(122)+XCH2XCH(122)<=>XCHXCH(123)+XCH2XCH2(66) 7.425804e+21 0.000 11.054 + +! Reaction index: Chemkin #261; RMG #830 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2XCH(122), XCXCH2(118); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*=C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCH2XCH(122)+XCH2XCH(122)<=>XCXCH2(118)+XCH2XCH2(66) 4.180000e+21 0.000 20.136 + +! Reaction index: Chemkin #262; RMG #861 +! Template reaction: Surface_Abstraction +! Flux pairs: XCCH2(119), XCHCH2(67); XCH2XCH2(66), XCH2XCH(122); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction +XCCH2(119)+XCH2XCH2(66)<=>XCHCH2(67)+XCH2XCH(122) 1.485161e+22 0.000 10.185 + +! Reaction index: Chemkin #263; RMG #955 +! Template reaction: Surface_Dissociation_to_Bidentate +! Flux pairs: XCH2CH3(54), XCH2XCH2(66); X(1), HX(21); X(1), HX(21); +! Matched reaction 1 H2CCH3_X + Pt_5 + Pt_6 <=> H2CCH2_2X + H_X in Surface_Dissociation_to_Bidentate/training +! This reaction matched rate rule [Combined;VacantSite1;VacantSite2] +! family: Surface_Dissociation_to_Bidentate +! metal: None +X(1)+X(1)+XCH2CH3(54)<=>HX(21)+XCH2XCH2(66) 5.570000e+29 0.000 10.994 + +! Reaction index: Chemkin #264; RMG #997 +! Template reaction: Surface_Abstraction +! Flux pairs: XCH2CH3(54), XCHCH3(64); XCH2XCH(122), XCH2XCH2(66); +! Estimated using average of templates [Abstracting;*-C-H] + [C;*C-H] for rate rule [C=*;*-CH-H] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Surface_Abstraction +XCH2XCH(122)+XCH2CH3(54)<=>XCHCH3(64)+XCH2XCH2(66) 7.425804e+21 0.000 11.613 + +! Reaction index: Chemkin #265; RMG #998 +! Template reaction: Surface_Abstraction_Beta_vdW +! Flux pairs: XCH2CH3(54), XCH2XCH2(66); XCH2XCH(122), CH2CH2X(68); +! Exact match found for rate rule [Abstracting;R-CH3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Surface_Abstraction_Beta_vdW +XCH2XCH(122)+XCH2CH3(54)<=>CH2CH2X(68)+XCH2XCH2(66) 4.179000e+21 0.000 39.746 + +! Reaction index: Chemkin #266; RMG #1089 +! Template reaction: Surface_Abstraction +! Flux pairs: XCHCO(111), XCCO(106); XCH2XCH(122), XCH2XCH2(66); +! Estimated using template [C;*C-H] for rate rule [C=*;*-C-H] +! Euclidian distance = 1.4142135623730951 +! family: Surface_Abstraction +XCHCO(111)+XCH2XCH(122)<=>XCCO(106)+XCH2XCH2(66) 4.180000e+21 0.000 16.709 + +! Reaction index: Chemkin #267; RMG #1193 +! Template reaction: Surface_vdW_to_Bidentate +! Flux pairs: X(1), XCH2XCH2(66); CH2CH2X(68), XCH2XCH2(66); +! Matched reaction 2 H2CCH2X_vdW + X <=> H2CCH2_2X in Surface_vdW_to_Bidentate/training +! This reaction matched rate rule [Combined;VacantSite] +! family: Surface_vdW_to_Bidentate +! metal: None +X(1)+CH2CH2X(68)<=>XCH2XCH2(66) 1.780000e+21 0.000 2.868 + +! Reaction index: Chemkin #268; RMG #1202 +! Template reaction: Surface_Abstraction_vdW +! Flux pairs: CH2CH2X(68), XCH2XCH2(66); XCH2XCH(122), XCHCH2(67); +! Estimated using template [AdsorbateVdW;*=C] for rate rule [C-R;*=C-2R] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 4.0 +! family: Surface_Abstraction_vdW +XCH2XCH(122)+CH2CH2X(68)<=>XCHCH2(67)+XCH2XCH2(66) 3.068214e+22 -0.150 26.653 + +END + diff --git a/ipython/data/cpox_methane/input.py b/ipython/data/cpox_methane/input.py new file mode 100644 index 0000000000..e25e7ac8e9 --- /dev/null +++ b/ipython/data/cpox_methane/input.py @@ -0,0 +1,341 @@ +# Data sources +database( + thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo'], + reactionLibraries = ['Surface/CPOX_Pt/Deutschmann2006_adjusted', 'BurkeH2O2inArHe'], + seedMechanisms = ['Surface/CPOX_Pt/Deutschmann2006_adjusted'], + kineticsDepositories = ['training'], + kineticsFamilies = ['default', 'surface'], + kineticsEstimator = 'rate rules', +) + +catalystProperties( + metal = 'Pt111' +) + +# List of species +species( + label='X', + reactive=True, + structure=adjacencyList("1 X u0"), +) + +species( + label='CH4', + reactive=True, + structure=SMILES("[CH4]"), +) +species( + label='O2', + reactive=True, + structure=adjacencyList( + """ + 1 O u1 p2 c0 {2,S} + 2 O u1 p2 c0 {1,S} + """), +) + +species( + label='Ar', + reactive=False, + structure=SMILES("[Ar]"), +) + +species( + label='CO2', + reactive=True, + structure=SMILES("O=C=O"), +) + +species( + label='H2O', + reactive=True, + structure=SMILES("O"), +) + +species( + label='H2', + reactive=True, + structure=SMILES("[H][H]"), +) + +species( + label='CO', + reactive=True, + structure=SMILES("[C-]#[O+]"), +) + +species( + label='C2H6', + reactive=True, + structure=SMILES("CC"), +) + +species( + label='CH2O', + reactive=True, + structure=SMILES("C=O"), +) + +species( + label='CH3', + reactive=True, + structure=SMILES("[CH3]"), +) + +species( + label='C3H8', + reactive=True, + structure=SMILES("CCC"), +) + +species( + label='H', + reactive=True, + structure=SMILES("[H]"), +) + +species( + label='C2H5', + reactive=True, + structure=SMILES("C[CH2]"), +) + +species( + label='CH3OH', + reactive=True, + structure=SMILES("CO"), +) + +species( + label='HCO', + reactive=True, + structure=SMILES("[CH]=O"), +) + +species( + label='CH3CHO', + reactive=True, + structure=SMILES("CC=O"), +) + +species( + label='OH', + reactive=True, + structure=SMILES("[OH]"), +) + +species( + label='C2H4', + reactive=True, + structure=SMILES("C=C"), +) + +species( + label='CH3CH', + reactive=True, + structure=SMILES("[CH]C"), +) + +species( + label='CH3OO', + reactive=True, + structure=SMILES("CO[O]"), +) + +species( + label='HX', + reactive=True, + structure=adjacencyList( + """ + 1 H u0 p0 c0 {2,S} + 2 X u0 p0 c0 {1,S} + """), +) + +species( + label='CO2X', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {3,D} + 2 O u0 p2 c0 {3,D} + 3 C u0 p0 c0 {1,D} {2,D} + 4 X u0 p0 c0 + """), +) + +species( + label='COX', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {2,D} + 2 C u0 p0 c0 {1,D} {3,D} + 3 X u0 p0 c0 {2,D} + """), +) + +forbidden( + label='CH4X', + structure=adjacencyList( + """ + 1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} + 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 H u0 p0 c0 {1,S} + 5 H u0 p0 c0 {1,S} + 6 X u0 p0 c0 + """), +) + +species( + label='OX', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {2,D} + 2 X u0 p0 c0 {1,D} + """), +) + +species( + label='CH2X', + reactive=True, + structure=adjacencyList( + """ + 1 C u0 p0 c0 {2,S} {3,S} {4,D} + 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 X u0 p0 c0 {1,D} + """), +) + +species( + label='CH3X', + reactive=True, + structure=adjacencyList( + """ + 1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} + 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 H u0 p0 c0 {1,S} + 5 X u0 p0 c0 {1,S} + """), +) + +species( + label='CHX', + reactive=True, + structure=adjacencyList( + """ + 1 C u0 p0 c0 {2,S} {3,T} + 2 H u0 p0 c0 {1,S} + 3 X u0 p0 c0 {1,T} + """), +) + +species( + label='CX', + reactive=True, + structure=adjacencyList( + """ + 1 C u0 p0 c0 {2,Q} + 2 X u0 p0 c0 {1,Q} + """), +) + +species( + label='H2X', + reactive=True, + structure=adjacencyList( + """ + 1 H u0 p0 c0 {2,S} + 2 H u0 p0 c0 {1,S} + 3 X u0 p0 c0 + """), +) + +species( + label='OHX', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {2,S} {3,S} + 2 H u0 p0 c0 {1,S} + 3 X u0 p0 c0 {1,S} + """), +) + +species( + label='H2OX', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {2,S} {3,S} + 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 X u0 p0 c0 + """), +) + +species( + label='CHOX', + reactive=True, + structure=adjacencyList( + """ + 1 O u0 p2 c0 {2,D} + 2 C u0 p0 c0 {1,D} {3,S} {4,S} + 3 H u0 p0 c0 {2,S} + 4 X u0 p0 c0 {2,S} + """), +) + +surfaceReactor( + temperature=(1000,'K'), + initialPressure=(1.0, 'bar'), + initialGasMoleFractions={ + "CH4": 0.108574, + "O2": 0.02088, + "Ar": 0.78547, + }, + initialSurfaceCoverages={ + "X": 1.0, + }, + surfaceVolumeRatio=(1.e5, 'm^-1'), + terminationConversion = { "CH4":0.95,}, + terminationTime=(10., 's'), +# terminationConversion={'O2': 0.99,}, + terminationRateRatio=0.01 +) + +simulator( + atol=1e-18, + rtol=1e-12, +) + +model( + toleranceKeepInEdge=0.0, + toleranceMoveToCore=0.1, + toleranceInterruptSimulation=0.1, + maximumEdgeSpecies=500000, + maxNumSpecies=70, # stop after 70 species +) + +options( + units='si', + saveRestartPeriod=None, + generateOutputHTML=False, + generatePlots=False, + saveEdgeSpecies=False, + saveSimulationProfiles=False, +) + +generatedSpeciesConstraints( + allowed=['input species', 'reaction libraries', 'seed mechanisms'], + maximumSurfaceSites=2, + maximumCarbonAtoms=2, + maximumOxygenAtoms=2, + maximumNitrogenAtoms=2, + maximumSurfaceBondOrder=4, +) + diff --git a/ipython/data/cpox_methane/species_dictionary.txt b/ipython/data/cpox_methane/species_dictionary.txt new file mode 100644 index 0000000000..74ad7c6034 --- /dev/null +++ b/ipython/data/cpox_methane/species_dictionary.txt @@ -0,0 +1,343 @@ +X(1) +1 X u0 p0 c0 + +H2(6) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +HX(21) +1 H u0 p0 c0 {2,S} +2 X u0 p0 c0 {1,S} + +O2(3) +multiplicity 3 +1 O u1 p2 c0 {2,S} +2 O u1 p2 c0 {1,S} + +OX(24) +1 O u0 p2 c0 {2,D} +2 X u0 p0 c0 {1,D} + +CH4(2) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} + +OHX(30) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 X u0 p0 c0 {1,S} + +CH3X(26) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {1,S} + +H2OX(31) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 + +H2O(5) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +CO2(4) +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,D} {2,D} + +CO2X(22) +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,D} {2,D} +4 X u0 p0 c0 + +COX(23) +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 X u0 p0 c0 {2,D} + +CO(7) +1 O u0 p1 c+1 {2,T} +2 C u0 p1 c-1 {1,T} + +CX(28) +1 C u0 p0 c0 {2,Q} +2 X u0 p0 c0 {1,Q} + +CH2X(25) +1 C u0 p0 c0 {2,S} {3,S} {4,D} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {1,D} + +CHX(27) +1 C u0 p0 c0 {2,S} {3,T} +2 H u0 p0 c0 {1,S} +3 X u0 p0 c0 {1,T} + +Ar +1 Ar u0 p4 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +C2H6(8) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} + +CH2O(9) +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} + +CH3(10) +multiplicity 2 +1 C u1 p0 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C3H8(11) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} +11 H u0 p0 c0 {3,S} + +H(12) +multiplicity 2 +1 H u1 p0 c0 + +C2H5(13) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u1 p0 c0 {1,S} {6,S} {7,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {2,S} + +CH3OH(14) +1 O u0 p2 c0 {2,S} {6,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {1,S} + +HCO(15) +multiplicity 2 +1 O u0 p2 c0 {2,D} +2 C u1 p0 c0 {1,D} {3,S} +3 H u0 p0 c0 {2,S} + +CH3CHO(16) +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {1,D} {2,S} {7,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} + +OH(17) +multiplicity 2 +1 O u1 p2 c0 {2,S} +2 H u0 p0 c0 {1,S} + +C2H4(18) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p0 c0 {1,D} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} + +CH3CH(19) +multiplicity 3 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u2 p0 c0 {1,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} + +CH3OO(20) +multiplicity 2 +1 O u0 p2 c0 {2,S} {3,S} +2 O u1 p2 c0 {1,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {3,S} + +H2X(29) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} +3 X u0 p0 c0 + +CHOX(32) +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 X u0 p0 c0 {2,S} + +XCOH(80) +1 O u0 p2 c0 {2,S} {3,S} +2 C u0 p0 c0 {1,S} {4,T} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {2,T} + +XCHOH(81) +1 O u0 p2 c0 {2,S} {4,S} +2 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {2,D} + +XCXCH2(118) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,T} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {1,S} +6 X u0 p0 c0 {2,T} + +XCCH3(96) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,T} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 X u0 p0 c0 {2,T} + +XCHCH3(64) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,S} {7,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 X u0 p0 c0 {2,D} + +XCCH2(119) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p0 c0 {1,D} {5,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {2,D} + +XCH2XCH(122) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {6,S} +2 C u0 p0 c0 {1,S} {5,S} {7,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 X u0 p0 c0 {1,S} +7 X u0 p0 c0 {2,D} + +XCHCH2(67) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p0 c0 {1,D} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 X u0 p0 c0 {2,S} + +XCHXCH(123) +1 C u0 p0 c0 {2,S} {3,S} {5,D} +2 C u0 p0 c0 {1,S} {4,S} {6,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} +5 X u0 p0 c0 {1,D} +6 X u0 p0 c0 {2,D} + +XCHXO(70) +1 O u0 p2 c0 {2,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {4,D} +3 H u0 p0 c0 {2,S} +4 X u0 p0 c0 {2,D} +5 X u0 p0 c0 {1,S} + +XCH2CH3(54) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {2,S} +8 X u0 p0 c0 {2,S} + +CHCHX(176) +1 C u0 p0 c0 {2,T} {3,S} +2 C u0 p0 c0 {1,T} {4,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} +5 X u0 p0 c0 + +XCHCO(111) +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,D} {4,S} {5,S} +3 C u0 p0 c0 {1,D} {2,D} +4 H u0 p0 c0 {2,S} +5 X u0 p0 c0 {2,S} + +XCCO(106) +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,D} {4,D} +3 C u0 p0 c0 {1,D} {2,D} +4 X u0 p0 c0 {2,D} + +XCXCO(105) +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 C u0 p0 c0 {2,S} {5,T} +4 X u0 p0 c0 {2,S} +5 X u0 p0 c0 {3,T} + +CH2CH2X(68) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p0 c0 {1,D} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 X u0 p0 c0 + +XCH2XCH2(66) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S} +2 C u0 p0 c0 {1,S} {5,S} {6,S} {8,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 X u0 p0 c0 {1,S} +8 X u0 p0 c0 {2,S} + diff --git a/ipython/surface_uncertainty.ipynb b/ipython/surface_uncertainty.ipynb new file mode 100644 index 0000000000..527bcdb801 --- /dev/null +++ b/ipython/surface_uncertainty.ipynb @@ -0,0 +1,1456 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "7d2bb3df-3278-4514-bee1-dd6eea5af95f", + "metadata": {}, + "source": [ + "# First-order local uncertainty for a surface mechanism\n", + "\n", + "## With and without correlations through BEEF-vdW DFT ensemble\n", + "\n", + "\n", + "**Uncorrelated Analysis:**\n", + "\n", + "The uncorrelated first-order local variance $(\\Delta \\ln c_i)^2$, for the concentration of species $i$ is:\n", + "\n", + "$$(\\Delta \\ln c_i)^2 = \\sum_{\\mathrm{reactions}\\; m} \\left(\\frac{\\partial\\ln c_i}{\\partial\\ln k_m}\\right)^2 (\\Delta \\ln k_m)^2 + \\sum_{\\mathrm{species}\\; n} \\left(\\frac{\\partial\\ln c_i}{\\partial G_n}\\right)^2(\\Delta G_n)^2$$\n", + "\n", + "We can get the derivatives $\\frac{\\partial\\ln c_i}{\\partial\\ln k_m}$ and $\\frac{\\partial\\ln c_i}{\\partial G_n}$ through sensitivity analysis.\n", + "\n", + "We compute the input uncertainties $\\Delta G_n$ and $\\Delta \\ln k_m$ by looking up the parameter source and adding the uncertainty that corresponds to that method. See the local_uncertainty.ipynb example or [Gao CW, Liu M, Green WH. Uncertainty analysis of correlated parameters in automated reaction mechanism generation. International journal of chemical kinetics. 2020;52(4):266-282. doi:10.1002/kin.21348](https://onlinelibrary.wiley.com/doi/10.1002/kin.21348) for more information.\n", + "\n", + "\n", + "**Correlated Analysis:**\n", + "\n", + "The correlated first-order local variance $(\\Delta \\ln c_i)^2$, for the concentration of species $i$ is:\n", + "\n", + "$$(\\Delta \\ln x)^2 = \\sum_w \\sum_{w'} \\left(\\sum_m \\frac{\\partial \\ln x}{\\partial \\ln k_m} \\frac{\\partial \\ln k_m}{\\partial q_w} + \\sum_n \\frac{\\partial \\ln x}{\\partial G_n} \\frac{\\partial G_n}{\\partial q_w}\\right) \\Sigma_{ww'} \\left(\\sum_{m'} \\frac{\\partial \\ln x}{\\partial \\ln k_{m'}} \\frac{\\partial \\ln k_{m'}}{\\partial q_{w'}} + \\sum_{n'} \\frac{\\partial \\ln x}{\\partial G_{n'}} \\frac{\\partial G_{n'}}{\\partial q_{w'}}\\right)$$\n", + "\n", + "Here, we utilize underlying input parameters $q_w$ which may be correlated to each other. For example, species thermo libraries computed using BEEF-vdW have known correlations through the DFT ensemble.\n", + "\n", + "These covariances are computed and saved in the covariance matrix $\\Sigma_{ww'}$.\n", + "\n", + "The derivatives $\\frac{\\partial\\ln c_i}{\\partial\\ln k_m}$ and $\\frac{\\partial\\ln c_i}{\\partial G_n}$ are computed through sensitivity analysis, same as the uncorrelated analysis. \n", + "\n", + "Finally, the derivatives $\\frac{\\partial\\ln k_m}{\\partial q_w}$ and $\\frac{\\partial\\ln G_n}{\\partial q_w}$ describe the weight of each underlying parameter's contribution to a particular species Gibbs energy or reaction rate, and these are tallied up by the uncertainty tool." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5b47ba72-0654-448b-9d96-c27548983e07", + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "\n", + "from IPython.display import display, Image\n", + "\n", + "import rmgpy\n", + "from rmgpy.tools.uncertainty import Uncertainty, process_local_results\n", + "from rmgpy.tools.canteramodel import get_rmg_species_from_user_species\n", + "from rmgpy.species import Species\n", + "\n", + "import logging\n", + "logging.basicConfig()\n", + "logging.getLogger().setLevel(logging.WARNING)\n", + "\n", + "import matplotlib.pyplot as plt\n", + "%matplotlib inline" + ] + }, + { + "cell_type": "markdown", + "id": "e08914e8-5036-4972-bd2d-7fdf17b7d95d", + "metadata": {}, + "source": [ + "## 1. Load the mechanism (CH4 + O2 over Pt111) and reactor settings" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "383d62bd-7926-4190-8968-bd25906c79fb", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:(The line it would be on is ' 300.000 1000.000 5000.000\\n' but that is not formatted as such)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:(It should have Tmin in columns 1-10, Tmid in columns 11-20, and Tmax in columns 21-30)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Ignoring short but non-empty line: ' 300.000 1000.000 5000.000\\n'\n" + ] + } + ], + "source": [ + "# This is a mechanism of methane partial oxidation over Pt111\n", + "\n", + "# Must use annotated chemkin file\n", + "chemkin_file = 'data/cpox_methane/chem_annotated-gas.inp'\n", + "surface_chemkin_file = 'data/cpox_methane/chem_annotated-surface.inp'\n", + "dict_file = 'data/cpox_methane/species_dictionary.txt'\n", + "\n", + "# Initialize the Uncertainty class instance and load the model\n", + "uncertainty = Uncertainty(output_directory='./temp/surface_uncertainty')\n", + "uncertainty.load_model(chemkin_file, dict_file, surface_path=surface_chemkin_file)\n", + "\n", + "# Map the species to the objects within the Uncertainty class\n", + "methane = Species().from_smiles('C')\n", + "X = Species().from_smiles('*') # surface site\n", + "Ar = Species().from_smiles('[Ar]')\n", + "O2 = Species().from_smiles('[O][O]')\n", + "H2O = Species().from_smiles('O')\n", + "CO2 = Species().from_smiles('O=C=O')\n", + "mapping = get_rmg_species_from_user_species([methane, O2, H2O, CO2, Ar, X], uncertainty.species_list)\n", + "\n", + "# Define the reaction conditions\n", + "initial_mole_fractions = {mapping[methane]: 0.1, mapping[Ar]: 0.8, mapping[O2]: 0.1}\n", + "initial_surface_coverage = {mapping[X]: 1.0}\n", + "T = (800, 'K')\n", + "P = (1, 'atm')\n", + "termination_time = (1.0, 's')\n", + "surface_volume_ratio = (1e5, 'm^-1')\n", + "surface_site_density = (2.4830E-09, 'mol/(cm^2)')\n", + "\n", + "# Pick the species to do sensitivity analysis for (which output concentrations to analyze)\n", + "sensitive_species=[mapping[methane], mapping[CO2]]" + ] + }, + { + "cell_type": "markdown", + "id": "357012e9-b724-4282-9d2f-4e5e91eccb30", + "metadata": {}, + "source": [ + "## 2. Run Sensitivity Analysis\n", + "This computes the derivatives $\\frac{\\partial \\ln c_i}{\\partial G_n}$ and $\\frac{\\partial \\ln c_i}{\\partial \\ln k_m}$ for every input species Gibbs energy $G_n$ and reaction rate $\\ln k_m$ in the mechanism with respect to each sensitive species concentration $c_i$\n", + "\n", + "These sensitivities will be used later to propagate the uncertain inputs through the model." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7af15bb1-17b6-4f8e-a779-a82647e25a4b", + "metadata": {}, + "outputs": [], + "source": [ + "# Perform the sensitivity analysis- this takes ~30 seconds\n", + "uncertainty.sensitivity_analysis(\n", + " initial_mole_fractions,\n", + " sensitive_species,\n", + " T,\n", + " P,\n", + " termination_time,\n", + " number=5,\n", + " fileformat='.png',\n", + " initial_surface_coverages=initial_surface_coverage,\n", + " surface_volume_ratio=surface_volume_ratio,\n", + " surface_site_density=surface_site_density,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e7cb29bd-95ba-441b-92b4-090625fb02fd", + "metadata": {}, + "outputs": [], + "source": [ + "# Show the sensitivity plots\n", + "for species in sensitive_species:\n", + " print('{}: Reaction Sensitivities'.format(species))\n", + " index = species.index\n", + " display(Image(filename=os.path.join(uncertainty.output_directory,'solver','sensitivity_1_SPC_{}_reactions.png'.format(index))))\n", + " \n", + " print('{}: Thermo Sensitivities'.format(species))\n", + " display(Image(filename=os.path.join(uncertainty.output_directory,'solver','sensitivity_1_SPC_{}_thermo.png'.format(index))))" + ] + }, + { + "cell_type": "markdown", + "id": "210a41fb-3c40-4b70-ac93-2ef3f66182e1", + "metadata": {}, + "source": [ + "## 3. Assign (Uncorrelated) Parameter Uncertainties\n", + "\n", + "Here we look up the sources used to compute each parameter and assign a value for $\\Delta G_n$ or $\\Delta \\ln k_m$" + ] + }, + { + "cell_type": "markdown", + "id": "5bb96967-24d9-4d6e-a190-500512edb1b0", + "metadata": {}, + "source": [ + "### Load the same database that's used in the RMG input file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "359ce9cc-9c60-49f0-9760-12a9da485acd", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading transport library from NOx2018.py in /home/moon/rmg/RMG-database/input/transport/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading transport library from GRI-Mech.py in /home/moon/rmg/RMG-database/input/transport/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading transport library from NIST_Fluorine.py in /home/moon/rmg/RMG-database/input/transport/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading transport group database from /home/moon/rmg/RMG-database/input/transport/groups...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading kinetics library Surface/CPOX_Pt/Deutschmann2006_adjusted from /home/moon/rmg/RMG-database/input/kinetics/libraries/Surface/CPOX_Pt/Deutschmann2006_adjusted/reactions.py...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading kinetics library BurkeH2O2inArHe from /home/moon/rmg/RMG-database/input/kinetics/libraries/BurkeH2O2inArHe/reactions.py...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading frequencies library from halogens_G4.py in /home/moon/rmg/RMG-database/input/statmech/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading frequencies group database from /home/moon/rmg/RMG-database/input/statmech/groups...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading solvation thermodynamics group database from /home/moon/rmg/RMG-database/input/solvation/groups...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics library from surfaceThermoPt111.py in /home/moon/rmg/RMG-database/input/thermo/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics library from primaryThermoLibrary.py in /home/moon/rmg/RMG-database/input/thermo/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics library from thermo_DFT_CCSDTF12_BAC.py in /home/moon/rmg/RMG-database/input/thermo/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics library from DFT_QCI_thermo.py in /home/moon/rmg/RMG-database/input/thermo/libraries...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics group database from /home/moon/rmg/RMG-database/input/thermo/groups...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Loading thermodynamics SIDTs from /home/moon/rmg/RMG-database/input/thermo/sidt...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Cphigh is above the theoretical CpInf value for ThermoData object\n", + "ThermoData(Tdata=([300,400,500,600,800,1000,1500],'K'), Cpdata=([60.2599,68.0494,74.7775,80.9311,90.8846,97.4337,105.393],'J/(mol*K)'), H298=(-477.191,'kJ/mol'), S298=(269.551,'J/(mol*K)'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(103.931,'J/(mol*K)'), comment=\"\"\"Thermo group additivity estimation: group(O2s-(Cds-Cd)(Cds-Cd)) + group(O2s-(Cds-O2d)H) + group(Cds-OdOsOs) + group(Li-OCOdO) + radical(OC=OOJ)\"\"\").\n", + "The thermo for this species is probably wrong! Setting CpInf = Cphigh for Entropy calculationat T = 2000.0 K...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Cphigh is above the theoretical CpInf value for ThermoData object\n", + "ThermoData(Tdata=([300,400,500,600,800,1000,1500],'K'), Cpdata=([60.2599,68.0494,74.7775,80.9311,90.8846,97.4337,105.393],'J/(mol*K)'), H298=(-477.191,'kJ/mol'), S298=(269.551,'J/(mol*K)'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(103.931,'J/(mol*K)'), comment=\"\"\"Thermo group additivity estimation: group(O2s-(Cds-Cd)(Cds-Cd)) + group(O2s-(Cds-O2d)H) + group(Cds-OdOsOs) + group(Li-OCOdO) + radical(OC=OOJ)\"\"\").\n", + "The thermo for this species is probably wrong! Setting CpInf = Cphigh for Entropy calculationat T = 1666.6666666666665 K...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Ni'. Using 'Ni111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Pt'. Using 'Pt111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Found multiple binding energies for 'Cu'. Using 'Cu111'.\n" + ] + } + ], + "source": [ + "uncertainty.load_database(\n", + " thermo_libraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo'],\n", + " kinetics_families=['default', 'surface'],\n", + " reaction_libraries=['Surface/CPOX_Pt/Deutschmann2006_adjusted', 'BurkeH2O2inArHe'],\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "142ce48b-80b6-4f02-b05b-956b32cd7bc7", + "metadata": {}, + "source": [ + "### Assign input parameter uncertainties according to their sources" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f639a69f-828d-499b-9047-041715a97060", + "metadata": {}, + "outputs": [], + "source": [ + "# reset the correlated libraries/groups back to the uncorrelated defaults in case someone runs the cells out of order\n", + "uncertainty.thermo_covariance_libraries = None # default is None\n", + "uncertainty.thermo_covariance_groups = None # these are the defaults\n", + "\n", + "uncertainty.extract_sources_from_model()\n", + "uncertainty.assign_intermediate_uncertainties(correlated=False)\n", + "\n", + "# Save the covariance matrix for later comparison\n", + "uncorrelated_thermo_cov = uncertainty.get_thermo_covariance_matrix()\n", + "uncorrelated_kinetics_cov = uncertainty.get_kinetic_covariance_matrix()\n" + ] + }, + { + "cell_type": "markdown", + "id": "667713de-0461-4c20-aaf8-ccd19a09d919", + "metadata": {}, + "source": [ + "# 4. Propagate the input uncertainties through the mechanism local analysis and show the resulting sensitivity index\n", + "\n", + "Use the first-order local uncertainty equation to get the overall variance in concentration:\n", + "$$(\\Delta \\ln c_i)^2 = \\sum_{\\mathrm{reactions}\\; m} \\left(\\frac{\\partial\\ln c_i}{\\partial\\ln k_m}\\right)^2 (\\Delta \\ln k_m)^2 + \\sum_{\\mathrm{species}\\; n} \\left(\\frac{\\partial\\ln c_i}{\\partial G_n}\\right)^2(\\Delta G_n)^2$$\n", + "\n", + "The Sensitivity Index shows the % an input parameter contributes to the overall variance of the output" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b5676863-89f9-48ca-9a45-04cd1aed9c2e", + "metadata": {}, + "outputs": [], + "source": [ + "result = uncertainty.local_analysis_intermediate(sensitive_species, correlated=False, number=10, fileformat='.png')\n", + "print(process_local_results(result, sensitive_species, number=5)[1])" + ] + }, + { + "cell_type": "markdown", + "id": "165c905f-2f26-4a12-a0b5-a854fe319a9d", + "metadata": {}, + "source": [ + "### Repeat for Correlated Uncertainties\n", + "\n", + "The next cell computes correlated uncertainties of the underlying parameters and saves them in $\\Sigma_{ww'}$\n", + "\n", + "It also computes the derivatives $\\frac{\\partial \\ln k_m}{\\partial q_w}$ and $\\frac{\\partial \\ln G_n}{\\partial q_w}$\n", + "\n", + "We use the same sensitivities computed in Step 2.\n", + "\n", + "Then the correlated first-order local variance $(\\Delta \\ln c_i)^2$, for the concentration of species $i$ is:\n", + "\n", + "$$(\\Delta \\ln c_i)^2 = \\sum_w \\sum_{w'} \\left(\\sum_m \\frac{\\partial \\ln c_i}{\\partial \\ln k_m} \\frac{\\partial \\ln k_m}{\\partial q_w} + \\sum_n \\frac{\\partial \\ln c_i}{\\partial G_n} \\frac{\\partial G_n}{\\partial q_w}\\right) \\Sigma_{ww'} \\left(\\sum_{m'} \\frac{\\partial \\ln c_i}{\\partial \\ln k_{m'}} \\frac{\\partial \\ln k_{m'}}{\\partial q_{w'}} + \\sum_{n'} \\frac{\\partial \\ln c_i}{\\partial G_{n'}} \\frac{\\partial G_{n'}}{\\partial q_{w'}}\\right)$$" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e024e373-73d7-4d3c-b025-53bf39ab6314", + "metadata": {}, + "outputs": [], + "source": [ + "uncertainty.thermo_covariance_libraries = [os.path.join(rmgpy.settings['database.directory'], 'thermo', 'uncertainty', 'surfaceThermoPt111')]\n", + "uncertainty.thermo_covariance_groups = [os.path.join(rmgpy.settings['database.directory'], 'thermo', 'uncertainty', 'adsorptionPt111')]\n", + "\n", + "uncertainty.extract_sources_from_model()\n", + "uncertainty.assign_intermediate_uncertainties(correlated=True)\n", + "\n", + "# Save the covariance matrix for later comparison\n", + "correlated_thermo_cov = uncertainty.get_thermo_covariance_matrix()\n", + "correlated_kinetics_cov = uncertainty.get_kinetic_covariance_matrix()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8df6b087-67ec-4f14-a2c6-7fa9686d6203", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "================================================================================\n", + "Total variance [(d ln(c))^2] for species CH4 is 3.248625\n", + "--------------------------------------------------------------------------------\n", + "Top 5 reaction rate contributors Sensitivity Index\n", + "--------------------------------------------------------------------------------\n", + "Surface Rate Rule Surface_Abstraction_vdW O-R;*=C=R 2.4434%\n", + "Surface_Library COX(23)<=>X(1)+CO(7) 1.0319%\n", + "Estimation Nonexact H2OX(31)+CHX(27)<=>HX(21)+XCHOH(81) 0.2719%\n", + "Estimation Family H2OX(31)+CHX(27)<=>HX(21)+XCHOH(81) 0.2450%\n", + "Surface_Library X(1)+H2OX(31)<=>HX(21)+OHX(30) 0.1869%\n", + "--------------------------------------------------------------------------------\n", + "Top 5 thermochemistry contributors Sensitivity Index\n", + "--------------------------------------------------------------------------------\n", + "Surface_Library X(1) 85.9865%\n", + "Surface_Library H2OX(31) 3.7244%\n", + "Library H2(6) 2.3298%\n", + "Surface_Library H2X(29) 1.1730%\n", + "Library CH4(2) 0.9880%\n", + "================================================================================\n", + "\n", + "================================================================================\n", + "Total variance [(d ln(c))^2] for species CO2 is 0.615255\n", + "--------------------------------------------------------------------------------\n", + "Top 5 reaction rate contributors Sensitivity Index\n", + "--------------------------------------------------------------------------------\n", + "Surface Rate Rule Surface_Abstraction_vdW O-R;*=C=R 8.8033%\n", + "Surface Training Surface_Abstraction OHX(30)+CHX(27)<=>OX(24)+CH2X(25) 2.5025%\n", + "Surface_Library COX(23)<=>X(1)+CO(7) 2.2631%\n", + "Estimation Nonexact H2OX(31)+CHX(27)<=>HX(21)+XCHOH(81) 0.9745%\n", + "Estimation Family H2OX(31)+CHX(27)<=>HX(21)+XCHOH(81) 0.8779%\n", + "--------------------------------------------------------------------------------\n", + "Top 5 thermochemistry contributors Sensitivity Index\n", + "--------------------------------------------------------------------------------\n", + "Surface_Library X(1) 62.0032%\n", + "Surface_Library H2OX(31) 14.0870%\n", + "Surface_Library OHX(30) 5.2360%\n", + "Library H2O(5) 2.2144%\n", + "Library CO2(4) 0.2343%\n", + "================================================================================\n", + "\n", + "\n" + ] + } + ], + "source": [ + "result = uncertainty.local_analysis_intermediate(sensitive_species, correlated=True, number=10, fileformat='.png')\n", + "print(process_local_results(result, sensitive_species, number=5)[1])" + ] + }, + { + "cell_type": "markdown", + "id": "55cf9bdd-e6e0-473e-a66b-b4ee173c2dec", + "metadata": {}, + "source": [ + "# 5. We can also export covariance matrices of the input parameter uncertainties\n", + "\n", + "Here we compute the species covariance matrix $\\Sigma_G$ and the reaction covariance matrix $\\Sigma_{\\ln k}$ - note this is different from the covariance matrix for the underlying parameters $\\Sigma_{ww'}$, which represents sources that might be reused across species/reactions like individual Benson groups or rate rules.\n", + "\n", + "The species Gibbs covariance matrix $\\Sigma_G$ and reaction rate covariance matrix $\\Sigma_{\\ln k}$ can be useful for uncertainty quantification performed outside of RMG. They can also be useful for optimization and parameter fitting, which can used correlated uncertainties to find the best fit to experimental data.\n", + "\n", + "\n", + "For the uncorrelated covariance matrices on the left, only the diagonal values are non-zero.\n", + "The correlated analysis for the thermo on the right includes correlations through the BEEF-vdW ensemble and the reference species that are used to compute each species.\n", + "\n", + "The gas-phase species are listed first in the mechanism, and these have much lower uncertainty values than the surface-phase species because the DFT is more accurate for gas-phase species than for adsorbates" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ff40668a-252f-446f-933f-10dac739a859", + "metadata": {}, + "outputs": [], + "source": [ + "fig, axs = plt.subplots(1, 2, figsize=(10, 6))\n", + "plt.subplots_adjust(wspace=0.3)\n", + "\n", + "# Uncorrelated Species Thermo Uncertainties\n", + "mat1 = axs[0].matshow(uncorrelated_thermo_cov)\n", + "axs[0].xaxis.set_ticks_position('bottom')\n", + "axs[0].xaxis.set_label_position('bottom')\n", + "cb1 = fig.colorbar(mat1, ax=axs[0], fraction=0.046, pad=0.04)\n", + "cb1.ax.set_title(' (kcal/mol)^2')\n", + "axs[0].set_title('Uncorrelated\\nThermo Covariance Matrix')\n", + "axs[0].set_xlabel('Species Index')\n", + "axs[0].set_ylabel('Species Index')\n", + "\n", + "# Correlated Species Thermo Uncertainties\n", + "mat2 = axs[1].matshow(correlated_thermo_cov)\n", + "axs[1].xaxis.set_ticks_position('bottom')\n", + "axs[1].xaxis.set_label_position('bottom')\n", + "cb2 = fig.colorbar(mat2, ax=axs[1], fraction=0.046, pad=0.04)\n", + "cb2.ax.set_title(' (kcal/mol)^2')\n", + "axs[1].set_title('Correlated\\nThermo Covariance Matrix')\n", + "axs[1].set_xlabel('Species Index')\n", + "axs[1].set_ylabel('Species Index')\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "904957bf-ab1a-401f-bedc-74ecf104c012", + "metadata": {}, + "outputs": [], + "source": [ + "fig, axs = plt.subplots(1, 2, figsize=(10, 6))\n", + "plt.subplots_adjust(wspace=0.3)\n", + "\n", + "# Uncorrelated Species Thermo Uncertainties\n", + "mat1 = axs[0].matshow(uncorrelated_kinetics_cov)\n", + "axs[0].xaxis.set_ticks_position('bottom')\n", + "axs[0].xaxis.set_label_position('bottom')\n", + "cb1 = fig.colorbar(mat1, ax=axs[0], fraction=0.046, pad=0.04)\n", + "cb1.ax.set_title(' (ln k)^2')\n", + "axs[0].set_title('Uncorrelated\\nKinetics Covariance Matrix')\n", + "axs[0].set_xlabel('Reaction Index')\n", + "axs[0].set_ylabel('Reaction Index')\n", + "\n", + "# Correlated Species Thermo Uncertainties\n", + "mat2 = axs[1].matshow(correlated_kinetics_cov)\n", + "axs[1].xaxis.set_ticks_position('bottom')\n", + "axs[1].xaxis.set_label_position('bottom')\n", + "cb2 = fig.colorbar(mat2, ax=axs[1], fraction=0.046, pad=0.04)\n", + "cb2.ax.set_title(' (ln k)^2')\n", + "axs[1].set_title('Correlated\\nKinetics Covariance Matrix')\n", + "axs[1].set_xlabel('Reaction Index')\n", + "axs[1].set_ylabel('Reaction Index')\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8cee9fe6-0b3f-45cd-993f-b24546c476d1", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.23" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/rmgpy/tools/uncertainty.py b/rmgpy/tools/uncertainty.py index 965df1db6d..1811a55458 100644 --- a/rmgpy/tools/uncertainty.py +++ b/rmgpy/tools/uncertainty.py @@ -708,9 +708,9 @@ def load_thermo_covariances_from_groups(self): # --------------------------------- add group-group correlations --------------------------------- # only consider groups actually in the model to keep this a reasonable size groups_in_model = [] - if cov_group_tree_name == 'adsorptionPt111' and 'ADS' in self.all_thermo_sources: + if cov_group_tree_name == 'adsorptionPt111' and 'ADS' in self.all_thermo_sources and cov_group_tree_name in self.all_thermo_sources['ADS']: groups_in_model = self.all_thermo_sources['ADS'][cov_group_tree_name] - else: + elif cov_group_tree_name in self.all_thermo_sources['GAV']: groups_in_model = self.all_thermo_sources['GAV'][cov_group_tree_name] group_items_in_model = [x.item for x in groups_in_model] group_labels_in_model = [x.label for x in groups_in_model]