From 35df3e1d80bc25656735653f3484099459a2d7e0 Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 12:57:41 -0500 Subject: [PATCH 1/7] delete the script and example files no longer use Reduction example folder is deleted because /rmgpy/reduction/main.py no longer exists. convertFAME.py is also deleted because it is no longer used --- examples/reduction/example.sh | 2 - examples/reduction/example_parallel.sh | 2 - .../minimal/chemkin/chem_annotated.inp | 372 ------------- .../minimal/chemkin/species_dictionary.txt | 155 ------ examples/reduction/minimal/input.py | 60 --- examples/reduction/minimal/reduction_input.py | 21 - scripts/convertFAME.py | 502 ------------------ 7 files changed, 1114 deletions(-) delete mode 100644 examples/reduction/example.sh delete mode 100644 examples/reduction/example_parallel.sh delete mode 100644 examples/reduction/minimal/chemkin/chem_annotated.inp delete mode 100644 examples/reduction/minimal/chemkin/species_dictionary.txt delete mode 100644 examples/reduction/minimal/input.py delete mode 100644 examples/reduction/minimal/reduction_input.py delete mode 100644 scripts/convertFAME.py diff --git a/examples/reduction/example.sh b/examples/reduction/example.sh deleted file mode 100644 index c5ca4aa6e9..0000000000 --- a/examples/reduction/example.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python ../../rmgpy/reduction/main.py minimal/input.py minimal/reduction_input.py minimal/chemkin/chem_annotated.inp minimal/chemkin/species_dictionary.txt \ No newline at end of file diff --git a/examples/reduction/example_parallel.sh b/examples/reduction/example_parallel.sh deleted file mode 100644 index 2258ab0b50..0000000000 --- a/examples/reduction/example_parallel.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python -m scoop ../../rmgpy/reduction/main.py minimal/input.py minimal/reduction_input.py minimal/chemkin/chem_annotated.inp minimal/chemkin/species_dictionary.txt \ No newline at end of file diff --git a/examples/reduction/minimal/chemkin/chem_annotated.inp b/examples/reduction/minimal/chemkin/chem_annotated.inp deleted file mode 100644 index 1ace47d026..0000000000 --- a/examples/reduction/minimal/chemkin/chem_annotated.inp +++ /dev/null @@ -1,372 +0,0 @@ -ELEMENTS H C O N Ne Ar He Si S Cl END - -SPECIES - Ar ! Ar - He ! He - Ne ! Ne - N2 ! N2 - ethane(1) ! ethane(1) - CH3(2) ! [CH3](2) - C2H5(3) ! C[CH2](3) - H(4) ! [H](4) - C(6) ! C(6) - C2H4(8) ! C=C(8) - H2(12) ! [H][H](12) - C2H3(13) ! [CH]=C(13) - C3H7(14) ! [CH2]CC(14) - C#C(25) ! C#C(25) - C4H7(28) ! [CH2]CC=C(28) - C4H6(30) ! C=CC=C(30) - C3H5(32) ! [CH]=CC(32) - C4H7(38) ! [CH2]C1CC1(38) - C4H7(42) ! C=C[CH]C(42) -END - - - -THERM ALL - 300.000 1000.000 5000.000 - -! Thermo library: primaryThermoLibrary -Ar Ar1 G200.000 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 -He He1 G200.000 6000.000 1000.00 1 - 2.50000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 --7.45375000E+02 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 - 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 4 - -! Thermo library: primaryThermoLibrary -Ne Ne1 G200.000 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 G200.000 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 group additivity estimation: group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) -ethane(1) C 2 H 6 G100.000 5000.000 954.53 1 - 4.58997390E+00 1.41505285E-02-4.75947845E-06 8.60260221E-10-6.21688243E-14 2 --1.27218243E+04-3.61819191E+00 3.78029291E+00-3.24211430E-03 5.52361704E-05 3 --6.38555558E-08 2.28625654E-11-1.16203391E+04 5.21048530E+00 4 - -! Thermo library: primaryThermoLibrary + radical(CH3) -CH3(2) C 1 H 3 G100.000 5000.000 1337.63 1 - 3.54146159E+00 4.76786209E-03-1.82148094E-06 3.28875850E-10-2.22545011E-14 2 - 1.62239559E+04 1.66032608E+00 3.91546733E+00 1.84154615E-03 3.48740903E-06 3 --3.32746709E-09 8.49953855E-13 1.62856394E+04 3.51742525E-01 4 - -! Thermo group additivity estimation: group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + radical(CCJ) -C2H5(3) C 2 H 5 G100.000 5000.000 900.30 1 - 5.15612067E+00 9.43138060E-03-1.81955154E-06 2.21217788E-10-1.43499804E-14 2 - 1.20641180E+04-2.91049373E+00 3.82186929E+00-3.43402417E-03 5.09273273E-05 3 --6.20234340E-08 2.37083980E-11 1.30660115E+04 7.61631583E+00 4 - -! Thermo library: primaryThermoLibrary -H(4) H 1 G100.000 5000.000 4570.96 1 - 2.49829732E+00 1.45963990E-06-4.69032548E-10 6.69551836E-14-3.58258629E-18 2 - 2.54758061E+04-4.34136157E-01 2.50000000E+00 1.77470207E-12-2.27500193E-15 3 - 9.48631670E-19-1.21629755E-22 2.54742178E+04-4.44972895E-01 4 - -! Thermo library: primaryThermoLibrary -C(6) C 1 H 4 G100.000 5000.000 1084.12 1 - 9.08278050E-01 1.14540655E-02-4.57172682E-06 8.29189010E-10-5.66312716E-14 2 --9.71997984E+03 1.39930246E+01 4.20541310E+00-5.35554899E-03 2.51122436E-05 3 --2.13761821E-08 5.97519843E-12-1.01619432E+04-9.21271573E-01 4 - -! Thermo group additivity estimation: group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) -C2H4(8) C 2 H 4 G100.000 5000.000 940.44 1 - 5.20294372E+00 7.82451164E-03-2.12688492E-06 3.79702680E-10-2.94680849E-14 2 - 3.93630185E+03-6.62382783E+00 3.97976020E+00-7.57579352E-03 5.52980432E-05 3 --6.36231570E-08 2.31771655E-11 5.07746019E+03 4.04617155E+00 4 - -! Thermo library: primaryThermoLibrary -H2(12) H 2 G100.000 5000.000 1959.07 1 - 2.78817485E+00 5.87629226E-04 1.59015901E-07-5.52750034E-11 4.34319008E-15 2 --5.96149590E+02 1.12679202E-01 3.43536403E+00 2.12711102E-04-2.78626742E-07 3 - 3.40268499E-10-7.76035298E-14-1.03135984E+03-3.90841699E+00 4 - -! Thermo group additivity estimation: group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + radical(Cds_P) -C2H3(13) C 2 H 3 G100.000 5000.000 931.97 1 - 5.44799578E+00 4.98350870E-03-1.08817688E-06 1.79829928E-10-1.45090109E-14 2 - 3.38297623E+04-4.87825197E+00 3.90669557E+00-4.06228810E-03 3.86775481E-05 3 --4.62970100E-08 1.72897519E-11 3.47971787E+04 6.09792480E+00 4 - -! Thermo group additivity estimation: group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group -! (Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + radical(RCCJ) -C3H7(14) C 3 H 7 G100.000 5000.000 995.41 1 - 5.69430152E+00 1.96033543E-02-7.42050458E-06 1.35883147E-09-9.56216475E-14 2 - 8.87585173E+03-4.32885235E+00 3.09191508E+00 1.32172227E-02 2.75848448E-05 3 --3.90849999E-08 1.43313800E-11 1.02284117E+04 1.24057799E+01 4 - -! Thermo group additivity estimation: group(Ct-CtH) + other(R) + group(Ct-CtH) + other(R) -C#C(25) C 2 H 2 G100.000 5000.000 888.64 1 - 5.76207781E+00 2.37152998E-03-1.49548398E-07-2.19237341E-11 2.21848824E-15 2 - 2.50944370E+04-9.82626759E+00 3.03573436E+00 7.71255481E-03 2.53429827E-06 3 --1.08124066E-08 5.50714193E-12 2.58526449E+04 4.54465886E+00 4 - -! Thermo group additivity estimation: group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cs-CsHHH) -! + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Cds)CsHH) + gauche(Cs(CsRRR)) + other(R) + radical(RCCJ) -C4H7(28) C 4 H 7 G100.000 5000.000 1000.95 1 - 7.59471914E+00 2.06425956E-02-7.89790375E-06 1.45966122E-09-1.03414888E-13 2 - 2.08073397E+04-1.19155141E+01 2.68061422E+00 2.10825717E-02 2.02123278E-05 3 --3.64243621E-08 1.41445056E-11 2.27528011E+04 1.66008558E+01 4 - -! Thermo group additivity estimation: group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-Cds -! (Cds-Cds)H) + gauche(CsOsCdSs) + other(R) + group(Cds-Cds(Cds-Cds)H) + gauche(CsOsCdSs) + other(R) -C4H6(30) C 4 H 6 G100.000 5000.000 940.94 1 - 1.10822419E+01 1.17737116E-02-3.11425072E-06 5.37771117E-10-4.10644270E-14 2 - 8.42132232E+03-3.51690176E+01 2.68208510E+00 1.69318777E-02 3.73663437E-05 3 --6.26500507E-08 2.59155776E-11 1.13546004E+04 1.20323036E+01 4 - -! Thermo group additivity estimation: group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cs-(Cds- -! Cds)HHH) + gauche(Cs(RRRR)) + other(R) + radical(Cds_P) -C3H5(32) C 3 H 5 G100.000 5000.000 997.88 1 - 5.66471792E+00 1.44325983E-02-5.46737286E-06 1.00157739E-09-7.04858445E-14 2 - 2.93870825E+04-4.48516098E+00 3.23407992E+00 1.18208487E-02 1.70305145E-05 3 --2.64365643E-08 9.91215619E-12 3.04873066E+04 1.03182841E+01 4 - -! Thermo group additivity estimation: group(Cs-CsHHH) + other(R) + group(Cs-CsCsHH) + other(R) + group(Cs-CsCsHH) + other(R) + group(Cs-CsCsCsH) + -! other(R) + ring(Cyclopropane) + radical(Isobutyl) -C4H7(38) C 4 H 7 G100.000 5000.000 926.06 1 - 1.02344188E+01 1.41135542E-02-2.99948260E-06 4.56675293E-10-3.49845534E-14 2 - 2.27934407E+04-2.92336660E+01 3.04744056E+00 5.45478227E-03 7.53343014E-05 3 --1.02231435E-07 4.01850124E-11 2.58269356E+04 1.40788412E+01 4 - -! Thermo group additivity estimation: group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cs-(Cds- -! Cds)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cs-(Cds-Cds)HHH) + gauche(Cs(RRRR)) + other(R) + radical(Allyl_P) -C4H7(42) C 4 H 7 G100.000 5000.000 998.56 1 - 7.82805776E+00 2.08400020E-02-7.96749567E-06 1.47336693E-09-1.04524685E-13 2 - 1.26472202E+04-1.65754633E+01 2.64213152E+00 2.15954070E-02 2.09683526E-05 3 --3.79209643E-08 1.47844796E-11 1.46809432E+04 1.34335096E+01 4 - -END - - - -REACTIONS KCAL/MOLE MOLES - -! Reaction index: Chemkin #1; RMG #1 -! Template reaction: R_Recombination -! Exact match found for rate rule (C_methyl;C_methyl) -CH3(2)+CH3(2)=ethane(1) 8.260e+17 -1.400 1.000 - -! Reaction index: Chemkin #2; RMG #4 -! Template reaction: H_Abstraction -! Estimated using template (C/H3/Cs;C_methyl) for rate rule (C/H3/Cs\H3;C_methyl) -! Multiplied by reaction path degeneracy 6 -ethane(1)+CH3(2)=C2H5(3)+C(6) 4.488e-05 4.990 8.000 - -! Reaction index: Chemkin #3; RMG #2 -! Template reaction: R_Recombination -! Exact match found for rate rule (C_rad/H2/Cs;H_rad) -C2H5(3)+H(4)=ethane(1) 1.000e+14 0.000 0.000 - -! Reaction index: Chemkin #4; RMG #13 -! Template reaction: R_Recombination -! Exact match found for rate rule (C_methyl;H_rad) -CH3(2)+H(4)=C(6) 1.930e+14 0.000 0.270 - -! Reaction index: Chemkin #5; RMG #6 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Cds-HH_Cds-HH;HJ) -! Multiplied by reaction path degeneracy 2 -C2H4(8)+H(4)=C2H5(3) 4.620e+08 1.640 1.010 - -! Reaction index: Chemkin #6; RMG #8 -! Template reaction: Disproportionation -! Exact match found for rate rule (C_methyl;Cmethyl_Csrad) -! Multiplied by reaction path degeneracy 3 -CH3(2)+C2H5(3)=C2H4(8)+C(6) 6.570e+14 -0.680 0.000 - -! Reaction index: Chemkin #7; RMG #11 -! Template reaction: Disproportionation -! Exact match found for rate rule (C_rad/H2/Cs;Cmethyl_Csrad) -! Multiplied by reaction path degeneracy 3 -C2H5(3)+C2H5(3)=ethane(1)+C2H4(8) 6.900e+13 -0.350 0.000 - -! Reaction index: Chemkin #8; RMG #15 -! Template reaction: H_Abstraction -! Estimated using template (C/H3/Cs;H_rad) for rate rule (C/H3/Cs\H3;H_rad) -! Multiplied by reaction path degeneracy 6 -ethane(1)+H(4)=H2(12)+C2H5(3) 6.180e+03 3.240 7.100 - -! Reaction index: Chemkin #9; RMG #17 -! Template reaction: Disproportionation -! Exact match found for rate rule (H_rad;Cmethyl_Csrad) -! Multiplied by reaction path degeneracy 6 -C2H5(3)+H(4)=C2H4(8)+H2(12) 2.166e+13 0.000 0.000 - -! Reaction index: Chemkin #10; RMG #18 -! Template reaction: H_Abstraction -! Exact match found for rate rule (C_methane;H_rad) -! Multiplied by reaction path degeneracy 4 -H(4)+C(6)=H2(12)+CH3(2) 8.760e-01 4.340 8.200 - -! Reaction index: Chemkin #11; RMG #19 -! Template reaction: R_Recombination -! Exact match found for rate rule (H_rad;H_rad) -H(4)+H(4)=H2(12) 1.090e+11 0.000 1.500 - -! Reaction index: Chemkin #12; RMG #23 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Cds-HH_Cds-HH;CsJ-HHH) -! Multiplied by reaction path degeneracy 2 -C2H4(8)+CH3(2)=C3H7(14) 4.180e+04 2.410 5.630 - -! Reaction index: Chemkin #13; RMG #20 -! Template reaction: R_Recombination -! Exact match found for rate rule (Cd_pri_rad;H_rad) -C2H3(13)+H(4)=C2H4(8) 1.210e+14 0.000 0.000 - -! Reaction index: Chemkin #14; RMG #24 -! Template reaction: H_Abstraction -! Estimated using template (C_methane;Cd_pri_rad) for rate rule (C_methane;Cd_Cd\H2_pri_rad) -! Multiplied by reaction path degeneracy 4 -C2H3(13)+C(6)=C2H4(8)+CH3(2) 2.236e-02 4.340 5.700 - -! Reaction index: Chemkin #15; RMG #27 -! Template reaction: H_Abstraction -! Estimated using template (C/H3/Cs;Cd_Cd\H2_pri_rad) for rate rule (C/H3/Cs\H3;Cd_Cd\H2_pri_rad) -! Multiplied by reaction path degeneracy 6 -ethane(1)+C2H3(13)=C2H4(8)+C2H5(3) 1.080e-03 4.550 3.500 - -! Reaction index: Chemkin #16; RMG #28 -! Template reaction: H_Abstraction -! Estimated using template (H2;Cd_pri_rad) for rate rule (H2;Cd_Cd\H2_pri_rad) -! Multiplied by reaction path degeneracy 2 -H2(12)+C2H3(13)=C2H4(8)+H(4) 9.460e+03 2.560 5.030 - -! Reaction index: Chemkin #17; RMG #29 -! Template reaction: Disproportionation -! Exact match found for rate rule (Cd_pri_rad;Cmethyl_Csrad) -! Multiplied by reaction path degeneracy 3 -C2H3(13)+C2H5(3)=C2H4(8)+C2H4(8) 4.560e+14 -0.700 0.000 - -! Reaction index: Chemkin #18; RMG #59 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Ct-H_Ct-H;HJ) -! Multiplied by reaction path degeneracy 2 -C#C(25)+H(4)=C2H3(13) 1.030e+09 1.640 2.110 - -! Reaction index: Chemkin #19; RMG #61 -! Template reaction: Disproportionation -! Estimated using template (C_methyl;CH_d_Rrad) for rate rule (C_methyl;Cd_Cdrad) -! Multiplied by reaction path degeneracy 2 -C2H3(13)+CH3(2)=C#C(25)+C(6) 2.277e+06 1.870 -1.110 - -! Reaction index: Chemkin #20; RMG #65 -! Template reaction: Disproportionation -! Estimated using template (Cs_rad;XH_d_Rrad) for rate rule (C_rad/H2/Cs;Cd_Cdrad) -! Multiplied by reaction path degeneracy 2 -C2H3(13)+C2H5(3)=ethane(1)+C#C(25) 1.932e+06 1.870 -1.110 - -! Reaction index: Chemkin #21; RMG #68 -! Template reaction: Disproportionation -! Estimated using template (H_rad;CH_d_Rrad) for rate rule (H_rad;Cd_Cdrad) -! Multiplied by reaction path degeneracy 4 -C2H3(13)+H(4)=H2(12)+C#C(25) 1.358e+09 1.500 -0.890 - -! Reaction index: Chemkin #22; RMG #77 -! Template reaction: Disproportionation -! Estimated using template (Y_rad;XH_Rrad) for rate rule (Cd_pri_rad;Cd_Cdrad) -! Multiplied by reaction path degeneracy 2 -C2H3(13)+C2H3(13)=C2H4(8)+C#C(25) 4.670e+09 0.969 -3.686 - -! Reaction index: Chemkin #23; RMG #71 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Cds-HH_Cds-HH;CdsJ-H) -! Multiplied by reaction path degeneracy 2 -C2H4(8)+C2H3(13)=C4H7(28) 2.860e+04 2.410 1.800 - -! Reaction index: Chemkin #24; RMG #97 -! Template reaction: Intra_R_Add_Exocyclic -! Exact match found for rate rule (R4_S_D;doublebond_intra_2H_pri;radadd_intra_cs2H) -C4H7(28)=C4H7(38) 3.840e+10 0.210 8.780 - -! Reaction index: Chemkin #25; RMG #82 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Ct-H_Ct-H;CsJ-HHH) -! Multiplied by reaction path degeneracy 2 -C#C(25)+CH3(2)=C3H5(32) 1.338e+05 2.410 6.770 - -! Reaction index: Chemkin #26; RMG #79 -! Template reaction: R_Recombination -! Exact match found for rate rule (Cd_pri_rad;Cd_pri_rad) -C2H3(13)+C2H3(13)=C4H6(30) 7.230e+13 0.000 0.000 - -! Reaction index: Chemkin #27; RMG #98 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Cds-CdH_Cds-HH;HJ) -! Multiplied by reaction path degeneracy 2 -C4H6(30)+H(4)=C4H7(28) 3.240e+08 1.640 2.400 - -! Reaction index: Chemkin #28; RMG #111 -! Template reaction: Disproportionation -! Estimated using template (C_methyl;Cpri_Rrad) for rate rule (C_methyl;C/H2/De_Csrad) -! Multiplied by reaction path degeneracy 2 -C4H7(28)+CH3(2)=C4H6(30)+C(6) 2.300e+13 -0.320 0.000 - -! Reaction index: Chemkin #29; RMG #121 -! Template reaction: Disproportionation -! Estimated using template (C_pri_rad;Cpri_Rrad) for rate rule (C_rad/H2/Cs;C/H2/De_Csrad) -! Multiplied by reaction path degeneracy 2 -C4H7(28)+C2H5(3)=ethane(1)+C4H6(30) 2.009e+12 0.000 -0.043 - -! Reaction index: Chemkin #30; RMG #132 -! Template reaction: Disproportionation -! Estimated using template (H_rad;Cpri_Rrad) for rate rule (H_rad;C/H2/De_Csrad) -! Multiplied by reaction path degeneracy 4 -C4H7(28)+H(4)=H2(12)+C4H6(30) 7.240e+12 0.000 0.000 - -! Reaction index: Chemkin #31; RMG #163 -! Template reaction: Disproportionation -! Estimated using template (Cd_pri_rad;Cpri_Rrad) for rate rule (Cd_pri_rad;C/H2/De_Csrad) -! Multiplied by reaction path degeneracy 2 -C2H3(13)+C4H7(28)=C2H4(8)+C4H6(30) 2.420e+12 0.000 0.000 - -! Reaction index: Chemkin #32; RMG #104 -! Template reaction: intra_H_migration -! Exact match found for rate rule (R2H_S;C_rad_out_H/OneDe;Cs_H_out_2H) -! Multiplied by reaction path degeneracy 3 -C4H7(42)=C4H7(28) 6.180e+09 1.220 47.800 - -! Reaction index: Chemkin #33; RMG #312 -! Template reaction: Disproportionation -! Estimated using template (C_rad/H2/Cs;Cmethyl_Csrad) for rate rule (C_rad/H2/Cs;Cmethyl_Csrad/H/Cd) -! Multiplied by reaction path degeneracy 3 -C4H7(42)+C2H5(3)=ethane(1)+C4H6(30) 6.900e+13 -0.350 0.000 - -! Reaction index: Chemkin #34; RMG #325 -! Template reaction: Disproportionation -! Estimated using template (C_methyl;Cmethyl_Csrad) for rate rule (C_methyl;Cmethyl_Csrad/H/Cd) -! Multiplied by reaction path degeneracy 3 -C4H7(42)+CH3(2)=C4H6(30)+C(6) 6.570e+14 -0.680 0.000 - -! Reaction index: Chemkin #35; RMG #326 -! Template reaction: R_Addition_MultipleBond -! Exact match found for rate rule (Cds-HH_Cds-CdH;HJ) -! Multiplied by reaction path degeneracy 2 -C4H6(30)+H(4)=C4H7(42) 4.620e+08 1.640 -0.470 - -! Reaction index: Chemkin #36; RMG #330 -! Template reaction: Disproportionation -! Estimated using template (Cd_pri_rad;Cmethyl_Csrad) for rate rule (Cd_pri_rad;Cmethyl_Csrad/H/Cd) -! Multiplied by reaction path degeneracy 3 -C2H3(13)+C4H7(42)=C2H4(8)+C4H6(30) 4.560e+14 -0.700 0.000 - -! Reaction index: Chemkin #37; RMG #335 -! Template reaction: Disproportionation -! Estimated using template (H_rad;Cmethyl_Csrad) for rate rule (H_rad;Cmethyl_Csrad/H/Cd) -! Multiplied by reaction path degeneracy 6 -C4H7(42)+H(4)=H2(12)+C4H6(30) 2.166e+13 0.000 0.000 - -END - diff --git a/examples/reduction/minimal/chemkin/species_dictionary.txt b/examples/reduction/minimal/chemkin/species_dictionary.txt deleted file mode 100644 index 2063369c1a..0000000000 --- a/examples/reduction/minimal/chemkin/species_dictionary.txt +++ /dev/null @@ -1,155 +0,0 @@ -Ar -1 Ar u0 p4 c0 - -He -1 He u0 p1 c0 - -Ne -1 Ne u0 p4 c0 - -N2 -1 N u0 p1 c0 {2,T} -2 N u0 p1 c0 {1,T} - -ethane(1) -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} - -CH3(2) -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} - -C2H5(3) -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} - -C(6) -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} - -H(4) -multiplicity 2 -1 H u1 p0 c0 - -C2H4(8) -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} - -H2(12) -1 H u0 p0 c0 {2,S} -2 H u0 p0 c0 {1,S} - -C3H7(14) -multiplicity 2 -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 u1 p0 c0 {1,S} {9,S} {10,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} - -C2H3(13) -multiplicity 2 -1 C u0 p0 c0 {2,D} {3,S} {4,S} -2 C u1 p0 c0 {1,D} {5,S} -3 H u0 p0 c0 {1,S} -4 H u0 p0 c0 {1,S} -5 H u0 p0 c0 {2,S} - -C#C(25) -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} - -C4H7(28) -multiplicity 2 -1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} -2 C u0 p0 c0 {1,S} {4,D} {7,S} -3 C u1 p0 c0 {1,S} {8,S} {9,S} -4 C u0 p0 c0 {2,D} {10,S} {11,S} -5 H u0 p0 c0 {1,S} -6 H u0 p0 c0 {1,S} -7 H u0 p0 c0 {2,S} -8 H u0 p0 c0 {3,S} -9 H u0 p0 c0 {3,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {4,S} - -C4H7(38) -multiplicity 2 -1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} -2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} -3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} -4 C u1 p0 c0 {1,S} {10,S} {11,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 {3,S} -9 H u0 p0 c0 {3,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {4,S} - -C3H5(32) -multiplicity 2 -1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} -2 C u0 p0 c0 {1,S} {3,D} {7,S} -3 C u1 p0 c0 {2,D} {8,S} -4 H u0 p0 c0 {1,S} -5 H u0 p0 c0 {1,S} -6 H u0 p0 c0 {1,S} -7 H u0 p0 c0 {2,S} -8 H u0 p0 c0 {3,S} - -C4H6(30) -1 C u0 p0 c0 {2,S} {3,D} {5,S} -2 C u0 p0 c0 {1,S} {4,D} {6,S} -3 C u0 p0 c0 {1,D} {7,S} {8,S} -4 C u0 p0 c0 {2,D} {9,S} {10,S} -5 H u0 p0 c0 {1,S} -6 H u0 p0 c0 {2,S} -7 H u0 p0 c0 {3,S} -8 H u0 p0 c0 {3,S} -9 H u0 p0 c0 {4,S} -10 H u0 p0 c0 {4,S} - -C4H7(42) -multiplicity 2 -1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} -2 C u0 p0 c0 {1,S} {3,D} {8,S} -3 C u0 p0 c0 {2,D} {4,S} {9,S} -4 C u1 p0 c0 {3,S} {10,S} {11,S} -5 H u0 p0 c0 {1,S} -6 H u0 p0 c0 {1,S} -7 H u0 p0 c0 {1,S} -8 H u0 p0 c0 {2,S} -9 H u0 p0 c0 {3,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {4,S} - diff --git a/examples/reduction/minimal/input.py b/examples/reduction/minimal/input.py deleted file mode 100644 index a0910211d3..0000000000 --- a/examples/reduction/minimal/input.py +++ /dev/null @@ -1,60 +0,0 @@ -# Data sources -database( - thermoLibraries = ['primaryThermoLibrary'], - reactionLibraries = [], - seedMechanisms = [], - kineticsDepositories = ['training'], - kineticsFamilies = 'default', - kineticsEstimator = 'rate rules', -) - -# List of species -species( - label='ethane', - reactive=True, - structure=SMILES("CC"), -) - -# Reaction systems -simpleReactor( - temperature=(1350,'K'), - pressure=(1.0,'bar'), - initialMoleFractions={ - "ethane": 1.0, - }, - # terminationConversion={ - # 'ethane': 0.9, - # }, - terminationTime=(1e-3,'s'), -) - -# simpleReactor( -# temperature=(1750,'K'), -# pressure=(10.0,'bar'), -# initialMoleFractions={ -# "ethane": 1.0, -# }, -# # terminationConversion={ -# # 'ethane': 0.9, -# # }, -# terminationTime=(1e-2,'s'), -# ) - -simulator( - atol=1e-16, - rtol=1e-8, -) - -model( - toleranceKeepInEdge=0.0, - toleranceMoveToCore=0.1, - toleranceInterruptSimulation=0.1, - maximumEdgeSpecies=100000 -) - -options( - units='si', - generatePlots=False, - saveEdgeSpecies=True, - saveSimulationProfiles=True, -) diff --git a/examples/reduction/minimal/reduction_input.py b/examples/reduction/minimal/reduction_input.py deleted file mode 100644 index 1702e776cb..0000000000 --- a/examples/reduction/minimal/reduction_input.py +++ /dev/null @@ -1,21 +0,0 @@ -""" -A list of the names of the species whose observables will be use to reduce the model. - -A species observable may be the mole fraction at the end time of the batch reactor simulation. - -The species name is the name of the species that can be found in the chemkin model or species -dictionary, MINUS the species index in parentheses. - -E.g.: ethane(1) --> ethane -""" - -targets = ['ethane'] - -""" -A value between 0 and 1 that indicates how much percent (1 = 100%) the species observables -may deviate from their original values. - -0.05 = 5% relative deviation -""" - -tolerance = .05 diff --git a/scripts/convertFAME.py b/scripts/convertFAME.py deleted file mode 100644 index b57160e49e..0000000000 --- a/scripts/convertFAME.py +++ /dev/null @@ -1,502 +0,0 @@ -#!/usr/bin/env python3 - -############################################################################### -# # -# RMG - Reaction Mechanism Generator # -# # -# Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu), # -# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # -# # -# Permission is hereby granted, free of charge, to any person obtaining a # -# copy of this software and associated documentation files (the 'Software'), # -# to deal in the Software without restriction, including without limitation # -# the rights to use, copy, modify, merge, publish, distribute, sublicense, # -# and/or sell copies of the Software, and to permit persons to whom the # -# Software is furnished to do so, subject to the following conditions: # -# # -# The above copyright notice and this permission notice shall be included in # -# all copies or substantial portions of the Software. # -# # -# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # -# DEALINGS IN THE SOFTWARE. # -# # -############################################################################### - -""" -Convert a FAME input file to a MEASURE input file. -MEASURE is the previous version of CanTherm. -CanTherm is the previous version of Arkane. -""" - -import argparse -import logging -import os.path - -import rmgpy.constants as constants -from arkane.pdep import PressureDependenceJob -from rmgpy.kinetics import Arrhenius -from rmgpy.molecule import Molecule -from rmgpy.pdep import Network, Configuration, SingleExponentialDown -from rmgpy.quantity import Quantity, Energy -from rmgpy.reaction import Reaction -from rmgpy.species import Species, TransitionState -from rmgpy.statmech import HarmonicOscillator, HinderedRotor, Conformer -from rmgpy.thermo import ThermoData -from rmgpy.transport import TransportData - - -################################################################################ - -def parse_command_line_arguments(): - """ - Parse the command-line arguments being passed to MEASURE. These are - described in the module docstring. - """ - - parser = argparse.ArgumentParser() - parser.add_argument('file', metavar='FILE', type=str, nargs='+', - help='a file to convert') - parser.add_argument('-d', '--dictionary', metavar='DICTFILE', type=str, nargs=1, - help='the RMG dictionary corresponding to these files') - parser.add_argument('-x', '--max-energy', metavar='VALUE UNITS', type=str, nargs=2, - help='A maximum energy to crop at') - - return parser.parse_args() - - -################################################################################ - -def loadFAMEInput(path, moleculeDict=None): - """ - Load the contents of a FAME input file into the MEASURE object. FAME - is an early version of MEASURE written in Fortran and used by RMG-Java. - This script enables importing FAME input files into MEASURE so we can - use the additional functionality that MEASURE provides. Note that it - is mostly designed to load the FAME input files generated automatically - by RMG-Java, and may not load hand-crafted FAME input files. If you - specify a `moleculeDict`, then this script will use it to associate - the species with their structures. - """ - - def readMeaningfulLine(f): - line = f.readline() - while line != '': - line = line.strip() - if len(line) > 0 and line[0] != '#': - return line - else: - line = f.readline() - return '' - - moleculeDict = moleculeDict or {} - - logging.info('Loading file "{0}"...'.format(path)) - f = open(path) - - job = PressureDependenceJob(network=None) - - # Read method - method = readMeaningfulLine(f).lower() - if method == 'modifiedstrongcollision': - job.method = 'modified strong collision' - elif method == 'reservoirstate': - job.method = 'reservoir state' - - # Read temperatures - Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split() - job.Tmin = Quantity(float(Tmin), Tunits) - job.Tmax = Quantity(float(Tmax), Tunits) - job.Tcount = int(Tcount) - Tlist = [] - for i in range(int(Tcount)): - Tlist.append(float(readMeaningfulLine(f))) - job.Tlist = Quantity(Tlist, Tunits) - - # Read pressures - Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split() - job.Pmin = Quantity(float(Pmin), Punits) - job.Pmax = Quantity(float(Pmax), Punits) - job.Pcount = int(Pcount) - Plist = [] - for i in range(int(Pcount)): - Plist.append(float(readMeaningfulLine(f))) - job.Plist = Quantity(Plist, Punits) - - # Read interpolation model - model = readMeaningfulLine(f).split() - if model[0].lower() == 'chebyshev': - job.interpolation_model = ('chebyshev', int(model[1]), int(model[2])) - elif model[0].lower() == 'pdeparrhenius': - job.interpolation_model = ('pdeparrhenius',) - - # Read grain size or number of grains - job.minimum_grain_count = 0 - job.maximum_grain_size = None - for i in range(2): - data = readMeaningfulLine(f).split() - if data[0].lower() == 'numgrains': - job.minimum_grain_count = int(data[1]) - elif data[0].lower() == 'grainsize': - job.maximum_grain_size = (float(data[2]), data[1]) - - # A FAME file is almost certainly created during an RMG job, so use RMG mode - job.rmgmode = True - - # Create the Network - job.network = Network() - - # Read collision model - data = readMeaningfulLine(f) - assert data.lower() == 'singleexpdown' - alpha0units, alpha0 = readMeaningfulLine(f).split() - T0units, T0 = readMeaningfulLine(f).split() - n = readMeaningfulLine(f) - energy_transfer_model = SingleExponentialDown( - alpha0=Quantity(float(alpha0), alpha0units), - T0=Quantity(float(T0), T0units), - n=float(n), - ) - - species_dict = {} - - # Read bath gas parameters - bath_gas = Species(label='bath_gas', energy_transfer_model=energy_transfer_model) - mol_wt_units, mol_wt = readMeaningfulLine(f).split() - if mol_wt_units == 'u': mol_wt_units = 'amu' - bath_gas.molecular_weight = Quantity(float(mol_wt), mol_wt_units) - sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split() - epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split() - assert epsilonLJunits == 'J' - bath_gas.transport_data = TransportData( - sigma=Quantity(float(sigmaLJ), sigmaLJunits), - epsilon=Quantity(float(epsilonLJ) / constants.kB, 'K'), - ) - job.network.bath_gas = {bath_gas: 1.0} - - # Read species data - n_spec = int(readMeaningfulLine(f)) - for i in range(n_spec): - species = Species() - species.conformer = Conformer() - species.energy_transfer_model = energy_transfer_model - - # Read species label - species.label = readMeaningfulLine(f) - species_dict[species.label] = species - if species.label in moleculeDict: - species.molecule = [moleculeDict[species.label]] - - # Read species E0 - E0units, E0 = readMeaningfulLine(f).split() - species.conformer.e0 = Quantity(float(E0), E0units) - species.conformer.e0.units = 'kJ/mol' - - # Read species thermo data - H298units, H298 = readMeaningfulLine(f).split() - S298units, S298 = readMeaningfulLine(f).split() - Cpcount, Cpunits = readMeaningfulLine(f).split() - Cpdata = [] - for i in range(int(Cpcount)): - Cpdata.append(float(readMeaningfulLine(f))) - if S298units == 'J/mol*K': S298units = 'J/(mol*K)' - if Cpunits == 'J/mol*K': Cpunits = 'J/(mol*K)' - species.thermo = ThermoData( - H298=Quantity(float(H298), H298units), - S298=Quantity(float(S298), S298units), - Tdata=Quantity([300, 400, 500, 600, 800, 1000, 1500], "K"), - Cpdata=Quantity(Cpdata, Cpunits), - Cp0=(Cpdata[0], Cpunits), - CpInf=(Cpdata[-1], Cpunits), - ) - - # Read species collision parameters - mol_wt_units, mol_wt = readMeaningfulLine(f).split() - if mol_wt_units == 'u': mol_wt_units = 'amu' - species.molecular_weight = Quantity(float(mol_wt), mol_wt_units) - sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split() - epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split() - assert epsilonLJunits == 'J' - species.transport_data = TransportData( - sigma=Quantity(float(sigmaLJ), sigmaLJunits), - epsilon=Quantity(float(epsilonLJ) / constants.kB, 'K'), - ) - - # Read species vibrational frequencies - freq_count, freq_units = readMeaningfulLine(f).split() - frequencies = [] - for j in range(int(freq_count)): - frequencies.append(float(readMeaningfulLine(f))) - species.conformer.modes.append(HarmonicOscillator( - frequencies=Quantity(frequencies, freq_units), - )) - - # Read species external rotors - rotCount, rotUnits = readMeaningfulLine(f).split() - if int(rotCount) > 0: - raise NotImplementedError('Cannot handle external rotational modes in FAME input.') - - # Read species internal rotors - freq_count, freq_units = readMeaningfulLine(f).split() - frequencies = [] - for j in range(int(freq_count)): - frequencies.append(float(readMeaningfulLine(f))) - barr_count, barr_units = readMeaningfulLine(f).split() - barriers = [] - for j in range(int(barr_count)): - barriers.append(float(readMeaningfulLine(f))) - if barr_units == 'cm^-1': - barr_units = 'J/mol' - barriers = [barr * constants.h * constants.c * constants.Na * 100. for barr in barriers] - elif barr_units in ['Hz', 's^-1']: - barr_units = 'J/mol' - barriers = [barr * constants.h * constants.Na for barr in barriers] - elif barr_units != 'J/mol': - raise Exception('Unexpected units "{0}" for hindered rotor barrier height.'.format(barr_units)) - inertia = [V0 / 2.0 / (nu * constants.c * 100.) ** 2 / constants.Na for nu, V0 in zip(frequencies, barriers)] - for I, V0 in zip(inertia, barriers): - species.conformer.modes.append(HinderedRotor( - inertia=Quantity(I, "kg*m^2"), - barrier=Quantity(V0, barr_units), - symmetry=1, - semiclassical=False, - )) - - # Read overall symmetry number - species.conformer.spin_multiplicity = int(readMeaningfulLine(f)) - - # Read isomer, reactant channel, and product channel data - n_isom = int(readMeaningfulLine(f)) - n_reac = int(readMeaningfulLine(f)) - n_prod = int(readMeaningfulLine(f)) - for i in range(n_isom): - data = readMeaningfulLine(f).split() - assert data[0] == '1' - job.network.isomers.append(species_dict[data[1]]) - for i in range(n_reac): - data = readMeaningfulLine(f).split() - assert data[0] == '2' - job.network.reactants.append([species_dict[data[1]], species_dict[data[2]]]) - for i in range(n_prod): - data = readMeaningfulLine(f).split() - if data[0] == '1': - job.network.products.append([species_dict[data[1]]]) - elif data[0] == '2': - job.network.products.append([species_dict[data[1]], species_dict[data[2]]]) - - # Read path reactions - n_rxn = int(readMeaningfulLine(f)) - for i in range(n_rxn): - - # Read and ignore reaction equation - equation = readMeaningfulLine(f) - reaction = Reaction(transition_state=TransitionState(), reversible=True) - job.network.path_reactions.append(reaction) - reaction.transition_state.conformer = Conformer() - - # Read reactant and product indices - data = readMeaningfulLine(f).split() - reac = int(data[0]) - 1 - prod = int(data[1]) - 1 - if reac < n_isom: - reaction.reactants = [job.network.isomers[reac]] - elif reac < n_isom + n_reac: - reaction.reactants = job.network.reactants[reac - n_isom] - else: - reaction.reactants = job.network.products[reac - n_isom - n_reac] - if prod < n_isom: - reaction.products = [job.network.isomers[prod]] - elif prod < n_isom + n_reac: - reaction.products = job.network.reactants[prod - n_isom] - else: - reaction.products = job.network.products[prod - n_isom - n_reac] - - # Read reaction E0 - E0units, E0 = readMeaningfulLine(f).split() - reaction.transition_state.conformer.e0 = Quantity(float(E0), E0units) - reaction.transition_state.conformer.e0.units = 'kJ/mol' - - # Read high-pressure limit kinetics - data = readMeaningfulLine(f) - assert data.lower() == 'arrhenius' - A_units, A = readMeaningfulLine(f).split() - if '/' in A_units: - index = A_units.find('/') - A_units = '{0}/({1})'.format(A_units[0:index], A_units[index + 1:]) - Ea_units, Ea = readMeaningfulLine(f).split() - n = readMeaningfulLine(f) - reaction.kinetics = Arrhenius( - A=Quantity(float(A), A_units), - Ea=Quantity(float(Ea), Ea_units), - n=Quantity(float(n)), - ) - reaction.kinetics.Ea.units = 'kJ/mol' - - f.close() - - job.network.isomers = [Configuration(isomer) for isomer in job.network.isomers] - job.network.reactants = [Configuration(*reactants) for reactants in job.network.reactants] - job.network.products = [Configuration(*products) for products in job.network.products] - - return job - - -def pruneNetwork(network, Emax): - """ - Prune the network by removing any configurations with ground-state energy - above `Emax` in J/mol and any reactions with transition state energy above - `Emax` from the network. All reactions involving removed configurations - are also removed. Any configurations that have zero reactions as a result - of this process are also removed. - """ - - # Remove configurations with ground-state energies above the given Emax - isomers_to_remove = [] - for isomer in network.isomers: - if isomer.E0 > Emax: - isomers_to_remove.append(isomer) - for isomer in isomers_to_remove: - network.isomers.remove(isomer) - - reactants_to_remove = [] - for reactant in network.reactants: - if reactant.E0 > Emax: - reactants_to_remove.append(reactant) - for reactant in reactants_to_remove: - network.reactants.remove(reactant) - - products_to_remove = [] - for product in network.products: - if product.E0 > Emax: - products_to_remove.append(product) - for product in products_to_remove: - network.products.remove(product) - - # Remove path reactions involving the removed configurations - removed_configurations = [] - removed_configurations.extend([isomer.species for isomer in isomers_to_remove]) - removed_configurations.extend([reactant.species for reactant in reactants_to_remove]) - removed_configurations.extend([product.species for product in products_to_remove]) - reactions_to_remove = [] - for rxn in network.path_reactions: - if rxn.reactants in removed_configurations or rxn.products in removed_configurations: - reactions_to_remove.append(rxn) - for rxn in reactions_to_remove: - network.path_reactions.remove(rxn) - - # Remove path reactions with barrier heights above the given Emax - reactions_to_remove = [] - for rxn in network.path_reactions: - if rxn.transition_state.conformer.E0.value_si > Emax: - reactions_to_remove.append(rxn) - for rxn in reactions_to_remove: - network.path_reactions.remove(rxn) - - def ismatch(speciesList1, speciesList2): - if len(speciesList1) == len(speciesList2) == 1: - return (speciesList1[0] is speciesList2[0]) - elif len(speciesList1) == len(speciesList2) == 2: - return ((speciesList1[0] is speciesList2[0] and speciesList1[1] is speciesList2[1]) or - (speciesList1[0] is speciesList2[1] and speciesList1[1] is speciesList2[0])) - elif len(speciesList1) == len(speciesList2) == 3: - return ((speciesList1[0] is speciesList2[0] and speciesList1[1] is speciesList2[1] and speciesList1[2] is - speciesList2[2]) or - (speciesList1[0] is speciesList2[0] and speciesList1[1] is speciesList2[2] and speciesList1[2] is - speciesList2[1]) or - (speciesList1[0] is speciesList2[1] and speciesList1[1] is speciesList2[0] and speciesList1[2] is - speciesList2[2]) or - (speciesList1[0] is speciesList2[1] and speciesList1[1] is speciesList2[2] and speciesList1[2] is - speciesList2[0]) or - (speciesList1[0] is speciesList2[2] and speciesList1[1] is speciesList2[0] and speciesList1[2] is - speciesList2[1]) or - (speciesList1[0] is speciesList2[2] and speciesList1[1] is speciesList2[1] and speciesList1[2] is - speciesList2[0])) - else: - return False - - # Remove orphaned configurations (those with zero path reactions involving them) - isomers_to_remove = [] - for isomer in network.isomers: - for rxn in network.path_reactions: - if ismatch(rxn.reactants, isomer.species) or ismatch(rxn.products, isomer.species): - break - else: - isomers_to_remove.append(isomer) - for isomer in isomers_to_remove: - network.isomers.remove(isomer) - - reactants_to_remove = [] - for reactant in network.reactants: - for rxn in network.path_reactions: - if ismatch(rxn.reactants, reactant.species) or ismatch(rxn.products, reactant.species): - break - else: - reactants_to_remove.append(reactant) - for reactant in reactants_to_remove: - network.reactants.remove(reactant) - - products_to_remove = [] - for product in network.products: - for rxn in network.path_reactions: - if ismatch(rxn.reactants, product.species) or ismatch(rxn.products, product.species): - break - else: - products_to_remove.append(product) - for product in products_to_remove: - network.products.remove(product) - - -################################################################################ - -if __name__ == '__main__': - - # Parse the command-line arguments - args = parse_command_line_arguments() - - if args.max_energy: - Emax = float(args.max_energy[0]) - Eunits = str(args.max_energy[1]) - Emax = Energy(Emax, Eunits).value_si - else: - Emax = None - - # Load RMG dictionary if specified - moleculeDict = {} - if args.dictionary is not None: - f = open(args.dictionary[0]) - adjlist = '' - label = '' - for line in f: - if len(line.strip()) == 0: - if len(adjlist.strip()) > 0: - molecule = Molecule() - molecule.from_adjacency_list(adjlist) - moleculeDict[label] = molecule - adjlist = '' - label = '' - else: - if len(adjlist.strip()) == 0: - label = line.strip() - adjlist += line - - f.close() - - method = None - - for fstr in args.file: - - # Construct Arkane job from FAME input - job = loadFAMEInput(fstr, moleculeDict) - - if Emax is not None: - pruneNetwork(job.network, Emax) - - # Save MEASURE input file based on the above - dirname, basename = os.path.split(os.path.abspath(fstr)) - basename, ext = os.path.splitext(basename) - path = os.path.join(dirname, basename + '.py') - job.save_input_file(path) From a1d842c3ab9c1799e5feb0ecc115b44b6185e98f Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 13:33:01 -0500 Subject: [PATCH 2/7] moved all the script example under example/scripts All the examples related to scripts are moved under a new folder example/scripts. Each bash scripts are changed appropriately to have correct relative paths for each script file. Also, for the examples file that were throwing error, I made somes changes to make them work: 1. generateReactions - This example was origianlly throwing error because surface chemistry was included in the kinetic_family in the input file. The kinetic family is changed to 'default', so it no longer throws error 2. simulate/withoutSensitivity - This example had minor error with default temperature range in chem.inp file. The temperature range in chem.inp file is changed appropriately. 3. thermoEstimator - input.py (run.sh) example had QM on in input file when it was not supposed to. The QM thermoEstimator has its own example (input_QM.py). The quantumMechanics portion in the input.py is deleted. --- examples/diffModels/example.sh | 10 ---------- examples/{ => scripts}/diffModels/Models/DFT_chem.inp | 0 .../diffModels/Models/DFT_species_dictionary.txt | 0 .../{ => scripts}/diffModels/Models/Primary_chem.inp | 0 .../diffModels/Models/Primary_species_dictionary.txt | 0 examples/scripts/diffModels/example.sh | 10 ++++++++++ examples/{ => scripts}/generateReactions/input.py | 4 ++-- examples/{ => scripts}/generateReactions/run.sh | 2 +- examples/{ => scripts/simulate}/sensitivity/chem.inp | 0 examples/{ => scripts/simulate}/sensitivity/input.py | 0 examples/{ => scripts/simulate}/sensitivity/run.sh | 2 +- .../simulate}/sensitivity/species_dictionary.txt | 0 .../simulate/withoutSensitivity}/chem.inp | 2 +- .../simulate/withoutSensitivity}/input.py | 0 examples/scripts/simulate/withoutSensitivity/run.sh | 4 ++++ .../withoutSensitivity}/species_dictionary.txt | 0 examples/{ => scripts}/thermoEstimator/input.py | 6 ------ examples/{ => scripts}/thermoEstimator/input_QM.py | 0 examples/{ => scripts}/thermoEstimator/input_ml.py | 0 examples/{ => scripts}/thermoEstimator/run.sh | 2 +- examples/{ => scripts}/thermoEstimator/run_QM.sh | 2 +- examples/{ => scripts}/thermoEstimator/run_ml.sh | 2 +- examples/simulate/run.sh | 4 ---- 23 files changed, 22 insertions(+), 28 deletions(-) delete mode 100755 examples/diffModels/example.sh rename examples/{ => scripts}/diffModels/Models/DFT_chem.inp (100%) rename examples/{ => scripts}/diffModels/Models/DFT_species_dictionary.txt (100%) rename examples/{ => scripts}/diffModels/Models/Primary_chem.inp (100%) rename examples/{ => scripts}/diffModels/Models/Primary_species_dictionary.txt (100%) create mode 100755 examples/scripts/diffModels/example.sh rename examples/{ => scripts}/generateReactions/input.py (95%) rename examples/{ => scripts}/generateReactions/run.sh (78%) rename examples/{ => scripts/simulate}/sensitivity/chem.inp (100%) rename examples/{ => scripts/simulate}/sensitivity/input.py (100%) rename examples/{ => scripts/simulate}/sensitivity/run.sh (54%) rename examples/{ => scripts/simulate}/sensitivity/species_dictionary.txt (100%) rename examples/{simulate => scripts/simulate/withoutSensitivity}/chem.inp (99%) rename examples/{simulate => scripts/simulate/withoutSensitivity}/input.py (100%) create mode 100755 examples/scripts/simulate/withoutSensitivity/run.sh rename examples/{simulate => scripts/simulate/withoutSensitivity}/species_dictionary.txt (100%) rename examples/{ => scripts}/thermoEstimator/input.py (79%) rename examples/{ => scripts}/thermoEstimator/input_QM.py (100%) rename examples/{ => scripts}/thermoEstimator/input_ml.py (100%) rename examples/{ => scripts}/thermoEstimator/run.sh (57%) rename examples/{ => scripts}/thermoEstimator/run_QM.sh (53%) rename examples/{ => scripts}/thermoEstimator/run_ml.sh (56%) delete mode 100755 examples/simulate/run.sh diff --git a/examples/diffModels/example.sh b/examples/diffModels/example.sh deleted file mode 100755 index b2a6e94760..0000000000 --- a/examples/diffModels/example.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -# Normal Output -python ../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt - -# Do no show identical species or reactions -#python ../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt --diffOnly - -# Only show species or reactions that are present in both models but have different values -#python ../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt --commonDiffOnly diff --git a/examples/diffModels/Models/DFT_chem.inp b/examples/scripts/diffModels/Models/DFT_chem.inp similarity index 100% rename from examples/diffModels/Models/DFT_chem.inp rename to examples/scripts/diffModels/Models/DFT_chem.inp diff --git a/examples/diffModels/Models/DFT_species_dictionary.txt b/examples/scripts/diffModels/Models/DFT_species_dictionary.txt similarity index 100% rename from examples/diffModels/Models/DFT_species_dictionary.txt rename to examples/scripts/diffModels/Models/DFT_species_dictionary.txt diff --git a/examples/diffModels/Models/Primary_chem.inp b/examples/scripts/diffModels/Models/Primary_chem.inp similarity index 100% rename from examples/diffModels/Models/Primary_chem.inp rename to examples/scripts/diffModels/Models/Primary_chem.inp diff --git a/examples/diffModels/Models/Primary_species_dictionary.txt b/examples/scripts/diffModels/Models/Primary_species_dictionary.txt similarity index 100% rename from examples/diffModels/Models/Primary_species_dictionary.txt rename to examples/scripts/diffModels/Models/Primary_species_dictionary.txt diff --git a/examples/scripts/diffModels/example.sh b/examples/scripts/diffModels/example.sh new file mode 100755 index 0000000000..2e6865c62d --- /dev/null +++ b/examples/scripts/diffModels/example.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +# Normal Output +python ../../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt + +# Do not show identical species or reactions +#python ../../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt --diffOnly + +# Only show species or reactions that are present in both models but have different values +#python ../../../scripts/diffModels.py Models/DFT_chem.inp Models/DFT_species_dictionary.txt Models/Primary_chem.inp Models/Primary_species_dictionary.txt --commonDiffOnly diff --git a/examples/generateReactions/input.py b/examples/scripts/generateReactions/input.py similarity index 95% rename from examples/generateReactions/input.py rename to examples/scripts/generateReactions/input.py index 5ea6991183..12676aca4e 100644 --- a/examples/generateReactions/input.py +++ b/examples/scripts/generateReactions/input.py @@ -5,7 +5,7 @@ seedMechanisms = [], kineticsDepositories = 'default', #this section lists possible reaction families to find reactioons with - kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'], + kineticsFamilies = ['default'], kineticsEstimator = 'rate rules', ) @@ -65,4 +65,4 @@ # maximumSulfurAtoms=0, # maximumHeavyAtoms=20, # maximumRadicalElectrons=1, -#) \ No newline at end of file +#) diff --git a/examples/generateReactions/run.sh b/examples/scripts/generateReactions/run.sh similarity index 78% rename from examples/generateReactions/run.sh rename to examples/scripts/generateReactions/run.sh index 09c5ba9dbc..51b4090b1c 100755 --- a/examples/generateReactions/run.sh +++ b/examples/scripts/generateReactions/run.sh @@ -5,4 +5,4 @@ # listed in the input file. # Run generateReactions on the given rmg input file -python ../../scripts/generateReactions.py input.py +python ../../../scripts/generateReactions.py input.py diff --git a/examples/sensitivity/chem.inp b/examples/scripts/simulate/sensitivity/chem.inp similarity index 100% rename from examples/sensitivity/chem.inp rename to examples/scripts/simulate/sensitivity/chem.inp diff --git a/examples/sensitivity/input.py b/examples/scripts/simulate/sensitivity/input.py similarity index 100% rename from examples/sensitivity/input.py rename to examples/scripts/simulate/sensitivity/input.py diff --git a/examples/sensitivity/run.sh b/examples/scripts/simulate/sensitivity/run.sh similarity index 54% rename from examples/sensitivity/run.sh rename to examples/scripts/simulate/sensitivity/run.sh index a0ec3759b6..2a41558269 100755 --- a/examples/sensitivity/run.sh +++ b/examples/scripts/simulate/sensitivity/run.sh @@ -1,4 +1,4 @@ #!/bin/bash # Run the stand-alone sensitivity analysis via simulate.py on a kinetic mechanism -python ../../scripts/simulate.py input.py chem.inp species_dictionary.txt +python ../../../../scripts/simulate.py input.py chem.inp species_dictionary.txt diff --git a/examples/sensitivity/species_dictionary.txt b/examples/scripts/simulate/sensitivity/species_dictionary.txt similarity index 100% rename from examples/sensitivity/species_dictionary.txt rename to examples/scripts/simulate/sensitivity/species_dictionary.txt diff --git a/examples/simulate/chem.inp b/examples/scripts/simulate/withoutSensitivity/chem.inp similarity index 99% rename from examples/simulate/chem.inp rename to examples/scripts/simulate/withoutSensitivity/chem.inp index 7fc3771f7d..35fcd82510 100644 --- a/examples/simulate/chem.inp +++ b/examples/scripts/simulate/withoutSensitivity/chem.inp @@ -19,7 +19,7 @@ END THERM ALL - 300.000 1000.000 5000.000 + 300.000 1000.000 5000.000 ethane(1) C 2 H 6 G100.000 5000.000 954.52 1 4.58991157E+00 1.41506360E-02-4.75954111E-06 8.60275134E-10-6.21700682E-14 2 diff --git a/examples/simulate/input.py b/examples/scripts/simulate/withoutSensitivity/input.py similarity index 100% rename from examples/simulate/input.py rename to examples/scripts/simulate/withoutSensitivity/input.py diff --git a/examples/scripts/simulate/withoutSensitivity/run.sh b/examples/scripts/simulate/withoutSensitivity/run.sh new file mode 100755 index 0000000000..3e7281d0c9 --- /dev/null +++ b/examples/scripts/simulate/withoutSensitivity/run.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Run the stand-alone simulation on a kinetic mechanism +python ../../../../scripts/simulate.py input.py chem.inp species_dictionary.txt diff --git a/examples/simulate/species_dictionary.txt b/examples/scripts/simulate/withoutSensitivity/species_dictionary.txt similarity index 100% rename from examples/simulate/species_dictionary.txt rename to examples/scripts/simulate/withoutSensitivity/species_dictionary.txt diff --git a/examples/thermoEstimator/input.py b/examples/scripts/thermoEstimator/input.py similarity index 79% rename from examples/thermoEstimator/input.py rename to examples/scripts/thermoEstimator/input.py index f642e06719..875771203a 100644 --- a/examples/thermoEstimator/input.py +++ b/examples/scripts/thermoEstimator/input.py @@ -23,9 +23,3 @@ structure=SMILES('CC12CCC(CC1)C(C)(C)O2'), ) -quantumMechanics( - software='mopac', - method='pm3', - onlyCyclics = True, - maxRadicalNumber = 0, -) diff --git a/examples/thermoEstimator/input_QM.py b/examples/scripts/thermoEstimator/input_QM.py similarity index 100% rename from examples/thermoEstimator/input_QM.py rename to examples/scripts/thermoEstimator/input_QM.py diff --git a/examples/thermoEstimator/input_ml.py b/examples/scripts/thermoEstimator/input_ml.py similarity index 100% rename from examples/thermoEstimator/input_ml.py rename to examples/scripts/thermoEstimator/input_ml.py diff --git a/examples/thermoEstimator/run.sh b/examples/scripts/thermoEstimator/run.sh similarity index 57% rename from examples/thermoEstimator/run.sh rename to examples/scripts/thermoEstimator/run.sh index 37bb17e782..4c3dcbb099 100755 --- a/examples/thermoEstimator/run.sh +++ b/examples/scripts/thermoEstimator/run.sh @@ -1,4 +1,4 @@ #!/bin/bash # Run the thermo estimator on the given thermo input file -python ../../scripts/thermoEstimator.py input.py +python ../../../scripts/thermoEstimator.py input.py diff --git a/examples/thermoEstimator/run_QM.sh b/examples/scripts/thermoEstimator/run_QM.sh similarity index 53% rename from examples/thermoEstimator/run_QM.sh rename to examples/scripts/thermoEstimator/run_QM.sh index 0542d54a6b..fb02d7b652 100644 --- a/examples/thermoEstimator/run_QM.sh +++ b/examples/scripts/thermoEstimator/run_QM.sh @@ -1,4 +1,4 @@ #!/bin/bash # Run the thermo estimator on the given thermo input file -python -m scoop ../../scripts/thermoEstimator.py input_QM.py +python ../../../scripts/thermoEstimator.py input_QM.py diff --git a/examples/thermoEstimator/run_ml.sh b/examples/scripts/thermoEstimator/run_ml.sh similarity index 56% rename from examples/thermoEstimator/run_ml.sh rename to examples/scripts/thermoEstimator/run_ml.sh index bc20f75f1c..bf95161c0d 100755 --- a/examples/thermoEstimator/run_ml.sh +++ b/examples/scripts/thermoEstimator/run_ml.sh @@ -1,4 +1,4 @@ #!/bin/bash # Run the thermo estimator on the given thermo input file -python ../../scripts/thermoEstimator.py input_ml.py +python ../../../scripts/thermoEstimator.py input_ml.py diff --git a/examples/simulate/run.sh b/examples/simulate/run.sh deleted file mode 100755 index e08bf1dabf..0000000000 --- a/examples/simulate/run.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -# Run the stand-alone simulation on a kinetic mechanism -python ../../scripts/simulate.py input.py chem.inp species_dictionary.txt From fbf0807c55c4a0c8412c71ee1f6d1750ac47c810 Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 14:30:32 -0500 Subject: [PATCH 3/7] added example for generateChemkimHTML.py An example for scripts/generateChemkimHTML.py is added --- .../generateChemkimHTML/chem_annotated.inp | 1118 +++++++++++++++++ examples/scripts/generateChemkimHTML/run.sh | 4 + .../species_dictionary.txt | 302 +++++ 3 files changed, 1424 insertions(+) create mode 100644 examples/scripts/generateChemkimHTML/chem_annotated.inp create mode 100755 examples/scripts/generateChemkimHTML/run.sh create mode 100644 examples/scripts/generateChemkimHTML/species_dictionary.txt diff --git a/examples/scripts/generateChemkimHTML/chem_annotated.inp b/examples/scripts/generateChemkimHTML/chem_annotated.inp new file mode 100644 index 0000000000..8bf029ae53 --- /dev/null +++ b/examples/scripts/generateChemkimHTML/chem_annotated.inp @@ -0,0 +1,1118 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + ethane(1) ! ethane(1) + CH4(3) ! CH4(3) + CH3(4) ! [CH3](4) + C2H5(5) ! C[CH2](5) + H(6) ! H(6) + C2H4(9) ! C=C(9) + H2(13) ! H2(13) + C2H3(14) ! [CH]=C(14) + C2H4(15) ! [CH]C(15) + C3H7(16) ! [CH2]CC(16) + C#C(30) ! C#C(30) + C4H7(33) ! [CH2]CC=C(33) + C4H6(35) ! C=CC=C(35) + C2H2(37) ! [C]=C(37) + C3H5(38) ! [CH]=CC(38) + C4H7(39) ! [CH]=CCC(39) + C4H5(43) ! [CH]=CC=C(43) + C4H7(49) ! [CH2]C1CC1(49) + C4H6(50) ! [CH2][CH]C=C(50) + C4H7(52) ! C=C[CH]C(52) + C4H6(118) ! C=C=CC(118) + C4H6(204) ! C1=CCC1(204) + C4H6(206) ! C=C[C]C(206) + C4H6(262) ! [C]1CCC1(262) + C4H5(302) ! C=C=[C]C(302) + C4H5(611) ! [CH2]C1C=C1(611) + C4H5(731) ! C[C]1C=C1(731) + C4H4(812) ! CC1=C=C1(812) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) +ethane(1) C 2H 6 G 100.000 5000.000 954.51 1 + 4.58979444E+00 1.41508381E-02-4.75965886E-06 8.60303158E-10-6.21724057E-14 2 +-1.27217503E+04-3.61718429E+00 3.78034607E+00-3.24276485E-03 5.52385525E-05 3 +-6.38587905E-08 2.28640069E-11-1.16203414E+04 5.21029625E+00 4 + +! Thermo library: primaryThermoLibrary +CH4(3) C 1H 4 G 100.000 5000.000 1084.12 1 + 9.08265721E-01 1.14540858E-02-4.57173828E-06 8.29191671E-10-5.66314895E-14 2 +-9.71997444E+03 1.39930944E+01 4.20541524E+00-5.35557362E-03 2.51123265E-05 3 +-2.13762843E-08 5.97523937E-12-1.01619433E+04-9.21279283E-01 4 + +! Thermo library: primaryThermoLibrary + radical(CH3) +CH3(4) C 1H 3 G 100.000 5000.000 1337.63 1 + 3.54145749E+00 4.76786834E-03-1.82148425E-06 3.28876586E-10-2.22545593E-14 2 + 1.62239579E+04 1.66034967E+00 3.91546761E+00 1.84154323E-03 3.48741760E-06 3 +-3.32747607E-09 8.49956882E-13 1.62856394E+04 3.51741490E-01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) + radical(CCJ) +C2H5(5) C 2H 5 G 100.000 5000.000 900.31 1 + 5.15621623E+00 9.43121232E-03-1.81945206E-06 2.21193866E-10-1.43479695E-14 2 + 1.20640796E+04-2.91102815E+00 3.82183329E+00-3.43357093E-03 5.09256026E-05 3 +-6.20209847E-08 2.37072520E-11 1.30660130E+04 7.61644314E+00 4 + +! Thermo library: primaryThermoLibrary +H(6) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) +C2H4(9) C 2H 4 G 100.000 5000.000 940.45 1 + 5.20299386E+00 7.82442468E-03-2.12683407E-06 3.79690544E-10-2.94670706E-14 2 + 3.93628131E+03-6.62410904E+00 3.97974441E+00-7.57559895E-03 5.52973238E-05 3 +-6.36221688E-08 2.31767197E-11 5.07746086E+03 4.04622760E+00 4 + +! Thermo library: primaryThermoLibrary +H2(13) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C2H3(14) C 2H 3 G 100.000 5000.000 931.96 1 + 5.44796550E+00 4.98356138E-03-1.08820775E-06 1.79837309E-10-1.45096285E-14 2 + 3.38297746E+04-4.87808224E+00 3.90670547E+00-4.06241062E-03 3.86780039E-05 3 +-4.62976404E-08 1.72900384E-11 3.47971783E+04 6.09788968E+00 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(CsJ2_singlet-CsH) +C2H4(15) C 2H 4 G 100.000 5000.000 1066.91 1 + 3.48115209E+00 1.16883236E-02-4.78434464E-06 8.90802946E-10-6.22433678E-14 2 + 4.22812570E+04 5.54898688E+00 3.71555285E+00 3.77628865E-03 1.62276340E-05 3 +-1.84174082E-08 5.90989211E-12 4.26315359E+04 6.27891490E+00 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsHHH) + group(Cs-CsHHH) + radical(RCCJ) +C3H7(16) C 3H 7 G 100.000 5000.000 995.41 1 + 5.69430979E+00 1.96033402E-02-7.42049648E-06 1.35882956E-09-9.56214889E-14 2 + 8.87584826E+03-4.32889887E+00 3.09191302E+00 1.32172474E-02 2.75847569E-05 3 +-3.90848844E-08 1.43313303E-11 1.02284118E+04 1.24057873E+01 4 + +! Thermo group additivity estimation: group(Ct-CtH) + group(Ct-CtH) +C#C(30) C 2H 2 G 100.000 5000.000 888.63 1 + 5.76204511E+00 2.37158782E-03-1.49582699E-07-2.19154662E-11 2.21779207E-15 2 + 2.50944501E+04-9.82608488E+00 3.03574736E+00 7.71239020E-03 2.53493006E-06 3 +-1.08133128E-08 5.50757058E-12 2.58526443E+04 4.54461297E+00 4 + +! ML Estimation + radical(RCCJ) +C4H7(33) C 4H 7 G 100.000 5000.000 1078.87 1 + 6.92232595E+00 2.17046609E-02-8.80220064E-06 1.64803378E-09-1.15890851E-13 2 + 2.06387442E+04-8.11802065E+00 2.65124021E+00 2.36511400E-02 7.80192789E-06 3 +-2.05446655E-08 7.79173851E-12 2.23686405E+04 1.65578190E+01 4 + +! ML Estimation +C4H6(35) C 4H 6 G 100.000 5000.000 954.15 1 + 1.03676849E+01 1.45821037E-02-4.67321619E-06 8.49490466E-10-6.30414970E-14 2 + 9.49991045E+03-3.15226171E+01 2.66951022E+00 1.75997221E-02 3.65733116E-05 3 +-6.01029274E-08 2.43266090E-11 1.23006441E+04 1.22337040E+01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(CdJ2_singlet-Cds) +C2H2(37) C 2H 2 G 100.000 5000.000 1423.26 1 + 4.43041986E+00 4.87757420E-03-1.79374459E-06 3.04085410E-10-1.96652162E-14 2 + 4.78744103E+04-1.67075241E-01 3.69251650E+00 6.06584723E-03-2.11277596E-06 3 + 1.63533182E-11 1.07665581E-13 4.81741496E+04 3.96842354E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C3H5(38) C 3H 5 G 100.000 5000.000 997.87 1 + 5.66465812E+00 1.44326998E-02-5.46743137E-06 1.00159120E-09-7.04869894E-14 2 + 2.93871077E+04-4.48482420E+00 3.23409465E+00 1.18206723E-02 1.70311418E-05 3 +-2.64373876E-08 9.91250979E-12 3.04873059E+04 1.03182315E+01 4 + +! ML Estimation + radical(Cds_P) +C4H7(39) C 4H 7 G 100.000 5000.000 1088.26 1 + 7.43030619E+00 2.10639706E-02-8.47867811E-06 1.57836912E-09-1.10522887E-13 2 + 2.55981431E+04-1.18519505E+01 2.53129347E+00 2.65456472E-02 1.22972909E-06 3 +-1.49450091E-08 6.11489161E-12 2.74060971E+04 1.56049405E+01 4 + +! ML Estimation + radical(Cds_P) +C4H5(43) C 4H 5 G 100.000 5000.000 955.64 1 + 1.06970014E+01 1.16010512E-02-3.57840830E-06 6.50033015E-10-4.86684885E-14 2 + 3.93608497E+04-3.09400155E+01 2.59081659E+00 2.12230334E-02 1.94729288E-05 3 +-4.20477294E-08 1.80843530E-11 4.20201271E+04 1.36072333E+01 4 + +! ML Estimation + radical(Isobutyl) +C4H7(49) C 4H 7 G 100.000 5000.000 950.84 1 + 8.61925602E+00 1.82848485E-02-5.82529494E-06 1.02602280E-09-7.35115648E-14 2 + 2.35749926E+04-1.93423218E+01 2.79233123E+00 1.58871755E-02 4.04099284E-05 3 +-6.11563015E-08 2.41018651E-11 2.58995634E+04 1.48723527E+01 4 + +! ML Estimation + radical(Allyl_P) + radical(Allyl_P) +C4H6(50) C 4H 6 G 100.000 5000.000 969.78 1 + 1.06933497E+01 1.31713172E-02-4.38797708E-06 8.51730358E-10-6.56940995E-14 2 + 3.03684785E+04-3.12144405E+01 2.72144234E+00 1.61881624E-02 3.71381701E-05 3 +-5.94494929E-08 2.36653401E-11 3.33190199E+04 1.42412818E+01 4 + +! ML Estimation + radical(Allyl_S) +C4H7(52) C 4H 7 G 100.000 5000.000 1024.08 1 + 6.98983798E+00 2.18068950E-02-8.71735467E-06 1.65319806E-09-1.18476776E-13 2 + 1.27222580E+04-1.24039020E+01 2.82652717E+00 1.75496097E-02 2.75728801E-05 3 +-4.15364349E-08 1.52012493E-11 1.46509312E+04 1.30340126E+01 4 + +! ML Estimation +C4H6(118) C 4H 6 G 100.000 5000.000 1050.31 1 + 6.91247067E+00 1.99659125E-02-8.06240299E-06 1.50325964E-09-1.05713842E-13 2 + 1.64740179E+04-1.08687975E+01 2.73020124E+00 2.18889508E-02 9.19221257E-06 3 +-2.21442289E-08 8.54482949E-12 1.81250129E+04 1.31908301E+01 4 + +! ML Estimation +C4H6(204) C 4H 6 G 100.000 5000.000 947.33 1 + 1.05003503E+01 1.34263547E-02-3.60393361E-06 6.93428896E-10-5.78005007E-14 2 + 1.41891065E+04-3.45159152E+01 3.39236739E+00-5.91857845E-03 1.05179439E-04 3 +-1.30859407E-07 4.91729935E-11 1.77505918E+04 1.10808957E+01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + group(CsJ2_singlet-CsH) +C4H6(206) C 4H 6 G 100.000 5000.000 2271.47 1 + 1.33033726E+01 1.41297275E-02-5.59015002E-06 9.21036568E-10-5.59628753E-14 2 + 4.39060412E+04-3.81544793E+01 2.68371413E+00 2.99287729E-02-1.41069865E-05 3 + 2.85826650E-09-2.07275399E-13 4.94791199E+04 2.34397882E+01 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(CsJ2_singlet-CsH) + ring(Cyclobutane) +C4H6(262) C 4H 6 G 100.000 5000.000 980.35 1 + 7.14704703E+00 2.10751316E-02-8.03260328E-06 1.52842626E-09-1.12007748E-13 2 + 5.09852626E+04-5.31313006E+00 3.16723720E+00 6.09463614E-03 6.26555185E-05 3 +-7.90245960E-08 2.87134488E-11 5.32657784E+04 2.14595013E+01 4 + +! ML Estimation + radical(Propargyl) +C4H5(302) C 4H 5 G 100.000 5000.000 1315.39 1 + 6.41498474E+00 1.79030746E-02-7.80803478E-06 1.46794405E-09-1.01382140E-13 2 + 3.28267991E+04-7.49357269E+00 2.93432630E+00 2.04689916E-02-1.59024215E-06 3 +-6.31762105E-09 2.25909769E-12 3.44361872E+04 1.28896247E+01 4 + +! ML Estimation + radical(Isobutyl) +C4H5(611) C 4H 5 G 100.000 5000.000 950.98 1 + 8.82100219E+00 1.64207490E-02-5.37530809E-06 9.43871506E-10-6.70140255E-14 2 + 4.09646430E+04-1.89209939E+01 2.71545999E+00 1.90191720E-02 2.69349209E-05 3 +-4.72303461E-08 1.93072123E-11 4.31696444E+04 1.57156143E+01 4 + +! ML Estimation + radical(Allyl_T) +C4H5(731) C 4H 5 G 100.000 5000.000 973.27 1 + 7.85854152E+00 1.86771894E-02-6.82738449E-06 1.27242853E-09-9.24592617E-14 2 + 3.21495813E+04-1.86936558E+01 2.97128106E+00 1.19781979E-02 4.47781461E-05 3 +-6.23528344E-08 2.35140773E-11 3.43695061E+04 1.12693601E+01 4 + +! ML Estimation +C4H4(812) C 4H 4 G 100.000 5000.000 1014.00 1 + 7.80825107E+00 2.01036086E-02-8.15845347E-06 1.52095603E-09-1.07480874E-13 2 + 3.32703654E+04-1.48110962E+01 2.62421107E+00 2.26939729E-02 1.44287845E-05 3 +-3.06987273E-08 1.21185930E-11 3.52398502E+04 1.47983764E+01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #2 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), ethane(1); CH3(4), ethane(1); +! Matched reaction 9 CH3 + CH3 <=> C2H6 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing] +! family: R_Recombination +CH3(4)+CH3(4)=ethane(1) 9.450000e+14 -0.538 0.135 + +! Reaction index: Chemkin #2; RMG #5 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); ethane(1), C2H5(5); +! Matched reaction 215 C2H6 + CH3_r3 <=> C2H5b + CH4 in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;C_methyl] +! family: H_Abstraction +CH3(4)+ethane(1)=CH4(3)+C2H5(5) 3.500000e+01 3.440 10.384 + +! Reaction index: Chemkin #3; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: C2H5(5), ethane(1); H(6), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #4; RMG #19 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), CH4(3); H(6), CH4(3); +! Matched reaction 57 H + CH3 <=> CH4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C] +! family: R_Recombination +H(6)+CH3(4)=CH4(3) 1.930000e+14 0.000 0.270 + +! Reaction index: Chemkin #5; RMG #24 +! Template reaction: R_Recombination +! Flux pairs: H(6), ethane(1); C2H5(5), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #6; RMG #9 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H4(9), C2H5(5); H(6), C2H5(5); +! 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(6)+C2H4(9)=C2H5(5) 4.620000e+08 1.640 1.010 + +! Reaction index: Chemkin #7; RMG #11 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); CH3(4), CH4(3); +! Matched reaction 5 CH3 + C2H5 <=> CH4 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_methyl;Cmethyl_Csrad] +! family: Disproportionation +CH3(4)+C2H5(5)=CH4(3)+C2H4(9) 6.570000e+14 -0.680 0.000 + +! Reaction index: Chemkin #8; RMG #15 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); C2H5(5), ethane(1); +! Matched reaction 6 C2H5 + C2H5-2 <=> C2H6 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_rad/H2/Cs;Cmethyl_Csrad] +! family: Disproportionation +C2H5(5)+C2H5(5)=C2H4(9)+ethane(1) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #9; RMG #20 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); ethane(1), C2H5(5); +! Matched reaction 210 C2H6 + H <=> C2H5b + H2_p in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;H_rad] +! family: H_Abstraction +H(6)+ethane(1)=H2(13)+C2H5(5) 1.150000e+08 1.900 7.530 + +! Reaction index: Chemkin #10; RMG #22 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); H(6), H2(13); +! Matched reaction 4 H + C2H5 <=> H2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [H_rad;Cmethyl_Csrad] +! family: Disproportionation +H(6)+C2H5(5)=H2(13)+C2H4(9) 1.083000e+13 0.000 0.000 + +! Reaction index: Chemkin #11; RMG #25 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); CH4(3), CH3(4); +! Matched reaction 186 CH4b + H <=> CH3_p1 + H2_p in H_Abstraction/training +! This reaction matched rate rule [C_methane;H_rad] +! family: H_Abstraction +H(6)+CH4(3)=H2(13)+CH3(4) 4.100000e+03 3.156 8.755 + +! Reaction index: Chemkin #12; RMG #26 +! Template reaction: R_Recombination +! Flux pairs: H(6), H2(13); H(6), H2(13); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(6)+H(6)=H2(13) 5.450000e+10 0.000 1.500 + +! Reaction index: Chemkin #13; RMG #28 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H4(15), C2H4(9); +! Estimated using template [CsJ2-C;singletcarbene;CH] for rate rule [CsJ2-C;CsJ2H;CH3] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 3.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H4(15)=C2H4(9) 1.582654e+14 -0.573 -7.598 + +! Reaction index: Chemkin #14; RMG #31 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H7(16); C2H4(9), C3H7(16); +! Matched reaction 219 CH3 + C2H4 <=> C3H7 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C2H4(9)=C3H7(16) 4.180000e+04 2.410 5.630 + +! Reaction index: Chemkin #15; RMG #27 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C2H4(9); H(6), C2H4(9); +! Matched reaction 60 H + C2H3 <=> C2H4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! family: R_Recombination +H(6)+C2H3(14)=C2H4(9) 1.210000e+14 0.000 0.000 + +! Reaction index: Chemkin #16; RMG #30 +! Template reaction: H_Abstraction +! Flux pairs: CH4(3), CH3(4); C2H3(14), C2H4(9); +! Matched reaction 843 C2H3 + CH4b <=> C2H4 + CH3_p23 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_methyl] +! family: H_Abstraction +CH4(3)+C2H3(14)=CH3(4)+C2H4(9) 2.236000e-02 4.340 5.700 + +! Reaction index: Chemkin #17; RMG #34 +! Template reaction: H_Abstraction +! Flux pairs: ethane(1), C2H5(5); C2H3(14), C2H4(9); +! Matched reaction 775 C2H3 + C2H6 <=> C2H4 + C2H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! family: H_Abstraction +C2H3(14)+ethane(1)=C2H4(9)+C2H5(5) 1.080000e-03 4.550 3.500 + +! Reaction index: Chemkin #18; RMG #36 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C2H4(9), C2H3(14); +! Matched reaction 217 C2H4 + H <=> C2H3_p + H2_p in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;H_rad] +! family: H_Abstraction +H(6)+C2H4(9)=H2(13)+C2H3(14) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #19; RMG #39 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C2H4(9); C2H5(5), C2H4(9); +! Matched reaction 11 C2H3-2 + C2H5 <=> C2H4-2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Cd_pri_rad;Cmethyl_Csrad] +! family: Disproportionation +C2H3(14)+C2H5(5)=C2H4(9)+C2H4(9) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #20; RMG #77 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C#C(30), C2H3(14); H(6), C2H3(14); +! Matched reaction 2697 H + C2H2 <=> C2H3-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;HJ] +! family: R_Addition_MultipleBond +H(6)+C#C(30)=C2H3(14) 1.030000e+09 1.640 2.110 + +! Reaction index: Chemkin #21; RMG #80 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); CH3(4), CH4(3); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_methyl;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C2H3(14)=CH4(3)+C#C(30) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #22; RMG #85 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); C2H5(5), ethane(1); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cs;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H5(5)=C#C(30)+ethane(1) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #23; RMG #92 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); H(6), H2(13); +! Estimated using template [H_rad;Cds/H2_d_Rrad] for rate rule [H_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C2H3(14)=H2(13)+C#C(30) 6.788225e+08 1.500 -0.890 + +! Reaction index: Chemkin #24; RMG #108 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); C2H3(14), C2H4(9); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H3(14)=C#C(30)+C2H4(9) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #25; RMG #114 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H2(37), C#C(30); +! Estimated using template [singletcarbene_CH;singletcarbene;CH] for rate rule [CdJ2=C;CdJ2;CdH2] +! Euclidian distance = 1.7320508075688772 +! Multiplied by reaction path degeneracy 2.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H2(37)=C#C(30) 5.784457e+12 0.007 -0.632 + +! Reaction index: Chemkin #26; RMG #97 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H7(33); C2H4(9), C4H7(33); +! Matched reaction 234 C2H3 + C2H4 <=> C4H7-3 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CdsJ-H] +! family: R_Addition_MultipleBond +C2H3(14)+C2H4(9)=C4H7(33) 2.860000e+04 2.410 1.800 + +! Reaction index: Chemkin #27; RMG #142 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H7(33), C4H7(49); +! Matched reaction 335 C4H7 <=> C4H7-2 in Intra_R_Add_Exocyclic/training +! This reaction matched rate rule [R4_S_D;doublebond_intra_2H_pri;radadd_intra_cs2H] +! family: Intra_R_Add_Exocyclic +C4H7(33)=C4H7(49) 6.320000e+08 0.970 8.900 + +! Reaction index: Chemkin #28; RMG #121 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H5(5), C4H7(39); C#C(30), C4H7(39); +! Matched reaction 2254 C2H2 + C2H5 <=> C4H7-6 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-CsHH] +! family: R_Addition_MultipleBond +C#C(30)+C2H5(5)=C4H7(39) 1.360000e+04 2.410 6.200 + +! Reaction index: Chemkin #29; RMG #150 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(39), C4H7(33); +! Estimated using template [R4H_DSS;Cd_rad_out_singleH;Cs_H_out] for rate rule [R4H_DSS;Cd_rad_out_singleH;Cs_H_out_2H] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: intra_H_migration +C4H7(39)=C4H7(33) 1.113000e+05 2.230 10.590 + +! Reaction index: Chemkin #30; RMG #148 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(52); +! Matched reaction 84 C:CC[CH2] <=> C:C[CH]C in intra_H_migration/training +! This reaction matched rate rule [R2H_S;C_rad_out_2H;Cs_H_out_H/Cd] +! family: intra_H_migration +C4H7(33)=C4H7(52) 1.720000e+06 1.990 27.200 + +! Reaction index: Chemkin #31; RMG #351 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(39), C4H7(52); +! Matched reaction 194 C4H7-4 <=> C4H7-5 in intra_H_migration/training +! This reaction matched rate rule [R3H_DS;Cd_rad_out_singleH;Cs_H_out_H/NonDeC] +! family: intra_H_migration +C4H7(39)=C4H7(52) 1.846000e+10 0.740 34.700 + +! Reaction index: Chemkin #32; RMG #112 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C4H6(35); C2H3(14), C4H6(35); +! Matched reaction 89 C2H3 + C2H3 <=> C4H6-4 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_N-Sp-3R!H-2R_N-3R!H->O_N-Sp-3CCSS#2R_Ext-1C-R] +! family: R_Recombination +C2H3(14)+C2H3(14)=C4H6(35) 3.615000e+13 0.000 0.000 + +! Reaction index: Chemkin #33; RMG #143 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(35), C4H7(33); H(6), C4H7(33); +! Matched reaction 2580 H + C4H6-2 <=> C4H7-11 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-CdH_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(35)=C4H7(33) 3.240000e+08 1.640 2.400 + +! Reaction index: Chemkin #34; RMG #154 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); CH3(4), CH4(3); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [C_methyl;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H7(33)=CH4(3)+C4H6(35) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #35; RMG #164 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); C2H5(5), ethane(1); +! Estimated using template [C_rad/H2/Cs;Cpri_Rrad] for rate rule [C_rad/H2/Cs;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H7(33)=ethane(1)+C4H6(35) 2.900000e+12 0.000 0.000 + +! Reaction index: Chemkin #36; RMG #180 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); H(6), H2(13); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [H_rad;C/H2/Cd_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H7(33)=H2(13)+C4H6(35) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #37; RMG #219 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); C2H3(14), C2H4(9); +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H7(33)=C2H4(9)+C4H6(35) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #38; RMG #464 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(35), C4H7(52); H(6), C4H7(52); +! Matched reaction 2544 H + C4H6 <=> C4H7-9 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-CdH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(35)=C4H7(52) 4.620000e+08 1.640 -0.470 + +! Reaction index: Chemkin #39; RMG #480 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cmethyl_Csrad/H/Cd] for rate rule [C_methyl;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +CH3(4)+C4H7(52)=CH4(3)+C4H6(35) 1.500000e+11 0.000 0.000 + +! Reaction index: Chemkin #40; RMG #494 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); C2H5(5), ethane(1); +! Estimated using template [C_rad/H2/Cs;Cmethyl_Csrad] for rate rule [C_rad/H2/Cs;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H7(52)=ethane(1)+C4H6(35) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #41; RMG #518 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); H(6), H2(13); +! Estimated using average of templates [Y_rad;Cmethyl_Csrad/H/Cd] + [H_rad;Cmethyl_Csrad] for rate rule [H_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +H(6)+C4H7(52)=H2(13)+C4H6(35) 1.274559e+12 0.000 0.000 + +! Reaction index: Chemkin #42; RMG #576 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); C2H3(14), C2H4(9); +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H3(14)+C4H7(52)=C2H4(9)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #43; RMG #759 +! Template reaction: Intra_2+2_cycloaddition_Cd +! Flux pairs: C4H6(35), C4H6(204); +! Estimated using template [1,3-butadiene_backbone;C=C_1;C=C_2] for rate rule [1,3-butadiene_backbone;CdH2_1;CdH2_2] +! Euclidian distance = 1.4142135623730951 +! family: Intra_2+2_cycloaddition_Cd +C4H6(35)=C4H6(204) 4.999980e+11 0.056 29.257 + +! Reaction index: Chemkin #44; RMG #765 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(206), C4H6(35); +! Estimated using template [CsJ2-C;CsJ2(C=C);CH] for rate rule [CsJ2-C;CsJ2(C=C);CH3] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(206)=C4H6(35) 6.011024e+12 -0.766 -14.909 + +! Reaction index: Chemkin #45; RMG #465 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(118), C4H7(52); H(6), C4H7(52); +! Matched reaction 2714 H + C4H6-4 <=> C4H7-13 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ca_Cds-CsH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(118)=C4H7(52) 5.460000e+08 1.640 3.780 + +! Reaction index: Chemkin #46; RMG #481 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +CH3(4)+C4H7(52)=CH4(3)+C4H6(118) 3.354068e+12 0.000 6.000 + +! Reaction index: Chemkin #47; RMG #495 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); C2H5(5), ethane(1); +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H5(5)+C4H7(52)=ethane(1)+C4H6(118) 9.640000e+11 0.000 6.000 + +! Reaction index: Chemkin #48; RMG #519 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); H(6), H2(13); +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +H(6)+C4H7(52)=H2(13)+C4H6(118) 3.010000e+12 0.000 6.000 + +! Reaction index: Chemkin #49; RMG #577 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); C2H3(14), C2H4(9); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H3(14)+C4H7(52)=C2H4(9)+C4H6(118) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #50; RMG #1019 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(206), C4H6(118); +! Estimated using an average for rate rule [CsJ2-C;CsJ2C;CH=C] +! Euclidian distance = 0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(206)=C4H6(118) 5.275512e+13 -0.573 -7.598 + +! Reaction index: Chemkin #51; RMG #1041 +! Template reaction: R_Recombination +! Flux pairs: C4H5(302), C4H6(118); H(6), C4H6(118); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(302)=C4H6(118) 1.554090e+97 -24.703 0.000 + +! Reaction index: Chemkin #52; RMG #1050 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;C_methyl] +! Euclidian distance = 0 +! family: H_Abstraction +CH3(4)+C4H6(118)=CH4(3)+C4H5(302) 7.130000e+00 3.317 6.610 + +! Reaction index: Chemkin #53; RMG #1062 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! family: H_Abstraction +C2H5(5)+C4H6(118)=ethane(1)+C4H5(302) 5.450000e-03 4.340 5.900 + +! Reaction index: Chemkin #54; RMG #1070 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;H_rad] +! Euclidian distance = 0 +! family: H_Abstraction +H(6)+C4H6(118)=H2(13)+C4H5(302) 3.532500e+00 3.852 3.502 + +! Reaction index: Chemkin #55; RMG #1080 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(302)=C2H4(9)+C4H6(118) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #56; RMG #1111 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;Cd_Cd\H2_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C2H3(14)+C4H6(118)=C2H4(9)+C4H5(302) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #57; RMG #1123 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_rad/NonDeC;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(302)=C#C(30)+C4H6(118) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #58; RMG #1248 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cpri_Rrad] for rate rule [Cd_rad/NonDeC;C/H2/Cd_Csrad] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(302)+C4H7(33)=C4H6(118)+C4H6(35) 2.420000e+12 0.000 0.000 + +! Reaction index: Chemkin #59; RMG #1251 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(302)+C4H7(52)=C4H6(118)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #60; RMG #1276 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cdpri_Csrad] for rate rule [Cd_rad/NonDeC;Cdpri_Csrad] +! Euclidian distance = 2.0 +! family: Disproportionation +C4H5(302)+C4H7(52)=C4H6(118)+C4H6(118) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #61; RMG #916 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(262), C4H6(204); +! Estimated using template [CsJ2-C;CsJ2(CsC);CH] for rate rule [CsJ2-C;CsJ2(CsC);CH2(C)] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(262)=C4H6(204) 5.555998e+15 -0.380 -0.286 + +! Reaction index: Chemkin #62; RMG #145 +! Template reaction: R_Recombination +! Flux pairs: C4H6(50), C4H7(33); H(6), C4H7(33); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(50)=C4H7(33) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #63; RMG #194 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(50)=C2H4(9)+C4H7(33) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #64; RMG #241 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(50)=C#C(30)+C4H7(33) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #65; RMG #466 +! Template reaction: R_Recombination +! Flux pairs: C4H6(50), C4H7(52); H(6), C4H7(52); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(50)=C4H7(52) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #66; RMG #534 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(50)=C2H4(9)+C4H7(52) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #67; RMG #604 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(50)=C#C(30)+C4H7(52) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #68; RMG #827 +! Template reaction: Disproportionation +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [Y_rad;C/H2/Cd_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(50)+C4H7(33)=C4H6(35)+C4H7(33) 4.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #69; RMG #828 +! Template reaction: Disproportionation +! Estimated using an average for rate rule [Y_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(35)+C4H7(33) 3.000000e+11 0.000 0.000 + +! Reaction index: Chemkin #70; RMG #874 +! Template reaction: Disproportionation +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [Y_rad;C/H2/Cd_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(50)+C4H7(33)=C4H6(35)+C4H7(52) 4.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #71; RMG #875 +! Template reaction: Disproportionation +! Estimated using an average for rate rule [Y_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(35)+C4H7(52) 3.000000e+11 0.000 0.000 + +! Reaction index: Chemkin #72; RMG #911 +! Template reaction: Birad_recombination +! Flux pairs: C4H6(50), C4H6(204); +! Estimated using template [R4;C_rad_out_2H;Cpri_rad_out_2H] for rate rule [R4_SDS;C_rad_out_2H;Cpri_rad_out_2H] +! Euclidian distance = 1.0 +! family: Birad_recombination +C4H6(50)=C4H6(204) 1.620000e+12 -0.305 1.980 + +! Reaction index: Chemkin #73; RMG #1037 +! Template reaction: Intra_Disproportionation +! Flux pairs: C4H6(50), C4H6(118); +! Estimated using an average for rate rule [R3radExo;Y_rad;XH_Rrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Intra_Disproportionation +C4H6(50)=C4H6(118) 1.487400e+09 1.045 15.153 + +! Reaction index: Chemkin #74; RMG #1136 +! Template reaction: Disproportionation +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(118)+C4H7(33) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #75; RMG #1202 +! Template reaction: Disproportionation +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(118)+C4H7(52) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #76; RMG #1649 +! Template reaction: 1,2-Birad_to_alkene +! Flux pairs: C4H6(50), C4H6(35); +! Matched reaction 5 C4H6 => C4H6-2 in 1,2-Birad_to_alkene/training +! This reaction matched rate rule [Y_12_01] +! family: 1,2-Birad_to_alkene +C4H6(50)=>C4H6(35) 5.010000e+07 0.000 0.000 + +! Reaction index: Chemkin #77; RMG #117 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H5(38); C#C(30), C3H5(38); +! Matched reaction 2253 C2H2 + CH3 <=> C3H5-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C#C(30)=C3H5(38) 1.338000e+05 2.410 6.770 + +! Reaction index: Chemkin #78; RMG #135 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H5(43); C#C(30), C4H5(43); +! Matched reaction 196 C2H2 + C2H3 <=> C4H5-8 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CdsJ-H] +! family: R_Addition_MultipleBond +C#C(30)+C2H3(14)=C4H5(43) 1.168000e+07 1.997 5.452 + +! Reaction index: Chemkin #79; RMG #764 +! Template reaction: R_Recombination +! Flux pairs: C4H5(43), C4H6(35); H(6), C4H6(35); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C +! Total Standard Deviation in ln(k): 6.83519320067 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(43)=C4H6(35) 9.988280e+13 0.006 0.000 + +! Reaction index: Chemkin #80; RMG #770 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(35), C4H5(43); +! From training reaction 1567 used for Cd/H2/NonDeC;C_methyl +! Exact match found for rate rule [Cd/H2/NonDeC;C_methyl] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +CH3(4)+C4H6(35)=CH4(3)+C4H5(43) 3.432000e-02 4.340 20.710 + +! Reaction index: Chemkin #81; RMG #778 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(35), C4H5(43); +! From training reaction 344 used for Cd/H2/NonDeC;C_rad/H2/Cs\H3 +! Exact match found for rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +C2H5(5)+C4H6(35)=ethane(1)+C4H5(43) 6.320000e+02 3.130 18.000 + +! Reaction index: Chemkin #82; RMG #782 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C4H6(35), C4H5(43); +! From training reaction 217 used for Cd/H2/NonDeC;H_rad +! Exact match found for rate rule [Cd/H2/NonDeC;H_rad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +H(6)+C4H6(35)=H2(13)+C4H5(43) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #83; RMG #789 +! Template reaction: Disproportionation +! From training reaction 11 used for Cd_pri_rad;Cmethyl_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(43)=C2H4(9)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #84; RMG #808 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(35), C4H5(43); +! Matched reaction 177 C4H6-3 + C2H3 <=> C2H4 + C4H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;Cd_Cd\H2_pri_rad] +! family: H_Abstraction +C2H3(14)+C4H6(35)=C2H4(9)+C4H5(43) 3.437000e-04 4.732 6.579 + +! Reaction index: Chemkin #85; RMG #817 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(43)=C#C(30)+C4H6(35) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #86; RMG #908 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(43)+C4H7(33)=C4H6(35)+C4H6(35) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #87; RMG #909 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(43)+C4H7(52)=C4H6(35)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #88; RMG #1246 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C4H5(43)+C4H7(52)=C4H6(118)+C4H6(35) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #89; RMG #1563 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(118), C4H5(302); C4H5(43), C4H6(35); +! Estimated using an average for rate rule [Cd_allenic;Cd_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C4H5(43)+C4H6(118)=C4H5(302)+C4H6(35) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #90; RMG #2163 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H5(43), C4H5(611); +! From training reaction 14 used for R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH +! Exact match found for rate rule [R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH] +! Euclidian distance = 0 +! family: Intra_R_Add_Exocyclic +C4H5(43)=C4H5(611) 2.540000e+10 0.690 20.376 + +! Reaction index: Chemkin #91; RMG #2615 +! Template reaction: intra_H_migration +! Flux pairs: C4H5(611), C4H5(731); +! Estimated using an average for rate rule [R2H_S;C_rad_out_2H;Cs_H_out_noH] +! Euclidian distance = 0 +! family: intra_H_migration +C4H5(611)=C4H5(731) 5.846148e+01 3.158 23.534 + +! Reaction index: Chemkin #92; RMG #2917 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H4(812), C4H5(731); H(6), C4H5(731); +! Estimated using an average for rate rule [Cdd_Cds;HJ] +! Euclidian distance = 0 +! family: R_Addition_MultipleBond +H(6)+C4H4(812)=C4H5(731) 7.956368e+08 1.576 4.912 + +! Reaction index: Chemkin #93; RMG #2932 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H5(731)=CH4(3)+C4H4(812) 6.708136e+12 0.000 6.000 + +! Reaction index: Chemkin #94; RMG #2943 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C2H5(5), ethane(1); +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H5(731)=ethane(1)+C4H4(812) 1.928000e+12 0.000 6.000 + +! Reaction index: Chemkin #95; RMG #2962 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); H(6), H2(13); +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H5(731)=H2(13)+C4H4(812) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #96; RMG #3006 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C2H3(14), C2H4(9); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(731)=C2H4(9)+C4H4(812) 4.820000e+12 0.000 6.000 + +! Reaction index: Chemkin #97; RMG #3259 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H5(302), C4H6(118); +! Estimated using template [Cd_rad;Cdpri_Csrad] for rate rule [Cd_rad/NonDeC;Cdpri_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(302)+C4H5(731)=C4H4(812)+C4H6(118) 4.820000e+12 0.000 6.000 + +! Reaction index: Chemkin #98; RMG #3270 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H6(50), C4H7(52); +! From training reaction 48 used for C_rad/H2/Cd;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cd;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H5(731)+C4H6(50)=C4H4(812)+C4H7(52) 3.372000e+11 0.000 6.000 + +! Reaction index: Chemkin #99; RMG #3291 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H6(50), C4H7(33); +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H5(731)+C4H6(50)=C4H4(812)+C4H7(33) 1.204000e+13 0.000 6.000 + +! Reaction index: Chemkin #100; RMG #3324 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H5(43), C4H6(35); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(731)+C4H5(43)=C4H4(812)+C4H6(35) 4.820000e+12 0.000 6.000 + +END + diff --git a/examples/scripts/generateChemkimHTML/run.sh b/examples/scripts/generateChemkimHTML/run.sh new file mode 100755 index 0000000000..0563dc5f38 --- /dev/null +++ b/examples/scripts/generateChemkimHTML/run.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Run generateChemkinHTML.py on a Chemkin input file and a RMG species dictionary file +python ../../../scripts/generateChemkinHTML.py chem_annotated.inp species_dictionary.txt diff --git a/examples/scripts/generateChemkimHTML/species_dictionary.txt b/examples/scripts/generateChemkimHTML/species_dictionary.txt new file mode 100644 index 0000000000..4e197877c3 --- /dev/null +++ b/examples/scripts/generateChemkimHTML/species_dictionary.txt @@ -0,0 +1,302 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +ethane(1) +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} + +CH3(4) +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} + +C2H5(5) +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} + +CH4(3) +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} + +H(6) +multiplicity 2 +1 H u1 p0 c0 + +C2H4(9) +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} + +H2(13) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +C2H4(15) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p1 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} + +C3H7(16) +multiplicity 2 +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 u1 p0 c0 {1,S} {9,S} {10,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} + +C2H3(14) +multiplicity 2 +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u1 p0 c0 {1,D} {5,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} + +C#C(30) +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} + +C2H2(37) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p1 c0 {1,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C4H7(33) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,D} {7,S} +3 C u1 p0 c0 {1,S} {8,S} {9,S} +4 C u0 p0 c0 {2,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(49) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} +3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} +4 C u1 p0 c0 {1,S} {10,S} {11,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 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(39) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {7,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,D} {10,S} +4 C u1 p0 c0 {3,D} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} +10 H u0 p0 c0 {3,S} +11 H u0 p0 c0 {4,S} + +C4H7(52) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {1,S} {3,S} {8,S} +3 C u0 p0 c0 {2,S} {4,D} {9,S} +4 C u0 p0 c0 {3,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H6(35) +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u0 p0 c0 {2,D} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(204) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {9,S} +4 C u0 p0 c0 {2,S} {3,D} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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 {4,S} + +C4H6(206) +1 C u0 p0 c0 {4,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {3,D} {4,S} {8,S} +3 C u0 p0 c0 {2,D} {9,S} {10,S} +4 C u0 p1 c0 {1,S} {2,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H6(118) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {4,D} {8,S} +3 C u0 p0 c0 {4,D} {9,S} {10,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H5(302) +multiplicity 2 +1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {4,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,T} +4 C u0 p0 c0 {2,S} {3,T} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} + +C4H6(262) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S} +4 C u0 p1 c0 {2,S} {3,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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} + +C4H6(50) +multiplicity 3 +1 C u0 p0 c0 {2,D} {3,S} {5,S} +2 C u0 p0 c0 {1,D} {4,S} {6,S} +3 C u1 p0 c0 {1,S} {7,S} {8,S} +4 C u1 p0 c0 {2,S} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C3H5(38) +multiplicity 2 +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 C u1 p0 c0 {2,D} {8,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} + +C4H5(43) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u1 p0 c0 {2,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H5(611) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,D} {6,S} +3 C u0 p0 c0 {1,S} {2,D} {7,S} +4 C u1 p0 c0 {1,S} {8,S} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {4,S} +9 H u0 p0 c0 {4,S} + +C4H5(731) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {1,S} {3,S} {4,S} +3 C u0 p0 c0 {2,S} {4,D} {8,S} +4 C u0 p0 c0 {2,S} {3,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H4(812) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {3,S} {4,D} +3 C u0 p0 c0 {2,S} {4,D} {8,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {3,S} + From a8bfe6df27cd565ff01b0fbee381b40da8364b66 Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 14:43:16 -0500 Subject: [PATCH 4/7] added an example for mergeModels.py An example for scripts/mergeModels.py is added. The run.sh file contains two examples: merging 2 models and merging 3 models. --- .../mergeModels/Models/minimal_chem.inp | 892 +++++++++++++ .../mergeModels/Models/minimal_ml_chem.inp | 1118 +++++++++++++++++ .../Models/minimal_ml_species_dictionary.txt | 302 +++++ .../Models/minimal_species_dictionary.txt | 248 ++++ .../mergeModels/Models/superminimal_chem.inp | 279 ++++ .../superminimal_species_dictionary.txt | 52 + examples/scripts/mergeModels/run.sh | 7 + 7 files changed, 2898 insertions(+) create mode 100644 examples/scripts/mergeModels/Models/minimal_chem.inp create mode 100644 examples/scripts/mergeModels/Models/minimal_ml_chem.inp create mode 100644 examples/scripts/mergeModels/Models/minimal_ml_species_dictionary.txt create mode 100644 examples/scripts/mergeModels/Models/minimal_species_dictionary.txt create mode 100644 examples/scripts/mergeModels/Models/superminimal_chem.inp create mode 100644 examples/scripts/mergeModels/Models/superminimal_species_dictionary.txt create mode 100644 examples/scripts/mergeModels/run.sh diff --git a/examples/scripts/mergeModels/Models/minimal_chem.inp b/examples/scripts/mergeModels/Models/minimal_chem.inp new file mode 100644 index 0000000000..32e0e375ca --- /dev/null +++ b/examples/scripts/mergeModels/Models/minimal_chem.inp @@ -0,0 +1,892 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + ethane(1) ! ethane(1) + CH4(3) ! CH4(3) + CH3(4) ! [CH3](4) + C2H5(5) ! C[CH2](5) + H(6) ! H(6) + C2H4(9) ! C=C(9) + H2(11) ! H2(11) + C2H3(14) ! [CH]=C(14) + C3H7(16) ! [CH2]CC(16) + C#C(27) ! C#C(27) + C4H7(29) ! [CH2]CC=C(29) + C2H2(31) ! [C]=C(31) + C3H5(32) ! [CH]=CC(32) + C4H7(33) ! [CH]=CCC(33) + C4H5(35) ! [CH]=CC=C(35) + C4H7(41) ! [CH2]C1CC1(41) + C4H6(42) ! C=CC=C(42) + C4H6(43) ! [CH2][CH]C=C(43) + C4H7(45) ! C=C[CH]C(45) + C4H6(69) ! C=C=CC(69) + C4H6(88) ! C1=CCC1(88) + C4H5(144) ! C=C=[C]C(144) + C4H5(185) ! [CH2]C1C=C1(185) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) +ethane(1) C 2H 6 G 100.000 5000.000 954.51 1 + 4.58979444E+00 1.41508381E-02-4.75965886E-06 8.60303158E-10-6.21724057E-14 2 +-1.27217503E+04-3.61718429E+00 3.78034607E+00-3.24276485E-03 5.52385525E-05 3 +-6.38587905E-08 2.28640069E-11-1.16203414E+04 5.21029625E+00 4 + +! Thermo library: primaryThermoLibrary +CH4(3) C 1H 4 G 100.000 5000.000 1084.12 1 + 9.08265721E-01 1.14540858E-02-4.57173828E-06 8.29191671E-10-5.66314895E-14 2 +-9.71997444E+03 1.39930944E+01 4.20541524E+00-5.35557362E-03 2.51123265E-05 3 +-2.13762843E-08 5.97523937E-12-1.01619433E+04-9.21279283E-01 4 + +! Thermo library: primaryThermoLibrary + radical(CH3) +CH3(4) C 1H 3 G 100.000 5000.000 1337.63 1 + 3.54145749E+00 4.76786834E-03-1.82148425E-06 3.28876586E-10-2.22545593E-14 2 + 1.62239579E+04 1.66034967E+00 3.91546761E+00 1.84154323E-03 3.48741760E-06 3 +-3.32747607E-09 8.49956882E-13 1.62856394E+04 3.51741490E-01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) + radical(CCJ) +C2H5(5) C 2H 5 G 100.000 5000.000 900.31 1 + 5.15621623E+00 9.43121232E-03-1.81945206E-06 2.21193866E-10-1.43479695E-14 2 + 1.20640796E+04-2.91102815E+00 3.82183329E+00-3.43357093E-03 5.09256026E-05 3 +-6.20209847E-08 2.37072520E-11 1.30660130E+04 7.61644314E+00 4 + +! Thermo library: primaryThermoLibrary +H(6) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) +C2H4(9) C 2H 4 G 100.000 5000.000 940.45 1 + 5.20299386E+00 7.82442468E-03-2.12683407E-06 3.79690544E-10-2.94670706E-14 2 + 3.93628131E+03-6.62410904E+00 3.97974441E+00-7.57559895E-03 5.52973238E-05 3 +-6.36221688E-08 2.31767197E-11 5.07746086E+03 4.04622760E+00 4 + +! Thermo library: primaryThermoLibrary +H2(11) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C2H3(14) C 2H 3 G 100.000 5000.000 931.96 1 + 5.44796550E+00 4.98356138E-03-1.08820775E-06 1.79837309E-10-1.45096285E-14 2 + 3.38297746E+04-4.87808224E+00 3.90670547E+00-4.06241062E-03 3.86780039E-05 3 +-4.62976404E-08 1.72900384E-11 3.47971783E+04 6.09788968E+00 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsHHH) + group(Cs-CsHHH) + radical(RCCJ) +C3H7(16) C 3H 7 G 100.000 5000.000 995.41 1 + 5.69430979E+00 1.96033402E-02-7.42049648E-06 1.35882956E-09-9.56214889E-14 2 + 8.87584826E+03-4.32889887E+00 3.09191302E+00 1.32172474E-02 2.75847569E-05 3 +-3.90848844E-08 1.43313303E-11 1.02284118E+04 1.24057873E+01 4 + +! Thermo group additivity estimation: group(Ct-CtH) + group(Ct-CtH) +C#C(27) C 2H 2 G 100.000 5000.000 888.63 1 + 5.76204511E+00 2.37158782E-03-1.49582699E-07-2.19154662E-11 2.21779207E-15 2 + 2.50944501E+04-9.82608488E+00 3.03574736E+00 7.71239020E-03 2.53493006E-06 3 +-1.08133128E-08 5.50757058E-12 2.58526443E+04 4.54461297E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(RCCJ) +C4H7(29) C 4H 7 G 100.000 5000.000 1000.95 1 + 7.59479951E+00 2.06424593E-02-7.89782526E-06 1.45964270E-09-1.03413353E-13 2 + 2.08073058E+04-1.19159668E+01 2.68059468E+00 2.10828055E-02 2.02114983E-05 3 +-3.64232761E-08 1.41440404E-11 2.27528020E+04 1.66009256E+01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(CdJ2_singlet-Cds) +C2H2(31) C 2H 2 G 100.000 5000.000 1423.26 1 + 4.43041986E+00 4.87757420E-03-1.79374459E-06 3.04085410E-10-1.96652162E-14 2 + 4.78744103E+04-1.67075241E-01 3.69251650E+00 6.06584723E-03-2.11277596E-06 3 + 1.63533182E-11 1.07665581E-13 4.81741496E+04 3.96842354E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C3H5(32) C 3H 5 G 100.000 5000.000 997.87 1 + 5.66465812E+00 1.44326998E-02-5.46743137E-06 1.00159120E-09-7.04869894E-14 2 + 2.93871077E+04-4.48482420E+00 3.23409465E+00 1.18206723E-02 1.70311418E-05 3 +-2.64373876E-08 9.91250979E-12 3.04873059E+04 1.03182315E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C4H7(33) C 4H 7 G 100.000 5000.000 999.92 1 + 8.06557472E+00 2.00625202E-02-7.60832471E-06 1.39784272E-09-9.86871188E-14 2 + 2.57831993E+04-1.54387855E+01 2.56532733E+00 2.39244964E-02 1.38115950E-05 3 +-3.10269360E-08 1.25444431E-11 2.77900540E+04 1.56311184E+01 4 + +! Thermo group additivity estimation: group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C4H5(35) C 4H 5 G 100.000 5000.000 935.58 1 + 1.13227703E+01 8.94049131E-03-2.08006868E-06 3.38974080E-10-2.61949890E-14 2 + 3.83166548E+04-3.40911798E+01 2.61016310E+00 2.04314979E-02 2.07961080E-05 3 +-4.53910308E-08 2.00574491E-11 4.10742701E+04 1.33868405E+01 4 + +! Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(Cs-CsHHH) + ring(Cyclopropane) + radical(Isobutyl) +C4H7(41) C 4H 7 G 100.000 5000.000 926.07 1 + 1.02346424E+01 1.41131644E-02-2.99925371E-06 4.56620522E-10-3.49799664E-14 2 + 2.27933498E+04-2.92349187E+01 3.04736554E+00 5.45571385E-03 7.53308215E-05 3 +-1.02226599E-07 4.01828021E-11 2.58269388E+04 1.40791072E+01 4 + +! Thermo group additivity estimation: group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + group(Cds-CdsHH) +C4H6(42) C 4H 6 G 100.000 5000.000 940.95 1 + 1.10823465E+01 1.17735303E-02-3.11414472E-06 5.37745823E-10-4.10623132E-14 2 + 8.42127950E+03-3.51696040E+01 2.68205225E+00 1.69322825E-02 3.73648473E-05 3 +-6.26479964E-08 2.59146511E-11 1.13546018E+04 1.20324202E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + radical(Allyl_P) + +! radical(Allyl_P) +C4H6(43) C 4H 6 G 100.000 5000.000 961.83 1 + 9.92849001E+00 1.51088208E-02-5.13560211E-06 9.43569819E-10-6.92734560E-14 2 + 3.02829926E+04-2.74906163E+01 2.65638077E+00 1.89337507E-02 3.00987228E-05 3 +-5.20344307E-08 2.11232146E-11 3.29038799E+04 1.36624695E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + radical(Allyl_P) +C4H7(45) C 4H 7 G 100.000 5000.000 998.56 1 + 7.82800811E+00 2.08400863E-02-7.96754424E-06 1.47337839E-09-1.04525635E-13 2 + 1.26472412E+04-1.58820365E+01 2.64214371E+00 2.15952609E-02 2.09688717E-05 3 +-3.79216452E-08 1.47847719E-11 1.46809427E+04 1.41266132E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + group(Cdd-CdsCds) +C4H6(69) C 4H 6 G 100.000 5000.000 1063.05 1 + 6.93544552E+00 1.97136368E-02-7.88231275E-06 1.45446865E-09-1.01396113E-13 2 + 1.61162804E+04-1.12054239E+01 2.67091213E+00 2.38372295E-02 3.12253865E-06 3 +-1.59972758E-08 6.48389677E-12 1.76966515E+04 1.27978754E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + ring(Cyclobutene) +C4H6(88) C 4H 6 G 100.000 5000.000 950.24 1 + 9.42741835E+00 1.39644294E-02-4.06892046E-06 7.75033524E-10-6.20421269E-14 2 + 1.43343164E+04-2.81799733E+01 3.39621343E+00-3.43725308E-03 9.09465048E-05 3 +-1.13274520E-07 4.24110728E-11 1.74123946E+04 1.07743991E+01 4 + +! Thermo group additivity estimation: group(Cs-CtHHH) + group(Cs-CtHHH) + group(Ct-CtCs) + group(Ct-CtCs) + radical(Propargyl) +C4H5(144) C 4H 5 G 100.000 5000.000 942.37 1 + 6.33626737E+00 1.64827848E-02-5.56208397E-06 9.43126364E-10-6.35802263E-14 2 + 3.32941157E+04-6.00339957E+00 2.92156480E+00 1.88274652E-02 1.00444412E-05 3 +-2.37783426E-08 1.01241167E-11 3.44771699E+04 1.31301921E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + ring(Cyclopropene) + +! radical(Isobutyl) +C4H5(185) C 4H 5 G 100.000 5000.000 922.39 1 + 7.72013271E+00 1.42822671E-02-4.41414586E-06 7.16675938E-10-4.76705841E-14 2 + 5.22310734E+04-1.47167968E+01 2.73381733E+00 2.27303683E-02 3.27346179E-06 3 +-2.03255440E-08 9.85275484E-12 5.37114183E+04 1.19746599E+01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #2 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), ethane(1); CH3(4), ethane(1); +! Matched reaction 9 CH3 + CH3 <=> C2H6 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing] +! family: R_Recombination +CH3(4)+CH3(4)=ethane(1) 9.450000e+14 -0.538 0.135 + +! Reaction index: Chemkin #2; RMG #5 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); ethane(1), C2H5(5); +! Matched reaction 215 C2H6 + CH3_r3 <=> C2H5b + CH4 in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;C_methyl] +! family: H_Abstraction +CH3(4)+ethane(1)=CH4(3)+C2H5(5) 3.500000e+01 3.440 10.384 + +! Reaction index: Chemkin #3; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: C2H5(5), ethane(1); H(6), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #4; RMG #12 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), CH4(3); H(6), CH4(3); +! Matched reaction 57 H + CH3 <=> CH4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C] +! family: R_Recombination +H(6)+CH3(4)=CH4(3) 1.930000e+14 0.000 0.270 + +! Reaction index: Chemkin #5; RMG #24 +! Template reaction: R_Recombination +! Flux pairs: H(6), ethane(1); C2H5(5), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #6; RMG #9 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H4(9), C2H5(5); H(6), C2H5(5); +! 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(6)+C2H4(9)=C2H5(5) 4.620000e+08 1.640 1.010 + +! Reaction index: Chemkin #7; RMG #13 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); CH3(4), CH4(3); +! Matched reaction 5 CH3 + C2H5 <=> CH4 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_methyl;Cmethyl_Csrad] +! family: Disproportionation +CH3(4)+C2H5(5)=CH4(3)+C2H4(9) 6.570000e+14 -0.680 0.000 + +! Reaction index: Chemkin #8; RMG #17 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); C2H5(5), ethane(1); +! Matched reaction 6 C2H5 + C2H5-2 <=> C2H6 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_rad/H2/Cs;Cmethyl_Csrad] +! family: Disproportionation +C2H5(5)+C2H5(5)=C2H4(9)+ethane(1) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #9; RMG #20 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); ethane(1), C2H5(5); +! Matched reaction 210 C2H6 + H <=> C2H5b + H2_p in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;H_rad] +! family: H_Abstraction +H(6)+ethane(1)=H2(11)+C2H5(5) 1.150000e+08 1.900 7.530 + +! Reaction index: Chemkin #10; RMG #22 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); H(6), H2(11); +! Matched reaction 4 H + C2H5 <=> H2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [H_rad;Cmethyl_Csrad] +! family: Disproportionation +H(6)+C2H5(5)=H2(11)+C2H4(9) 1.083000e+13 0.000 0.000 + +! Reaction index: Chemkin #11; RMG #25 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); CH4(3), CH3(4); +! Matched reaction 186 CH4b + H <=> CH3_p1 + H2_p in H_Abstraction/training +! This reaction matched rate rule [C_methane;H_rad] +! family: H_Abstraction +H(6)+CH4(3)=H2(11)+CH3(4) 4.100000e+03 3.156 8.755 + +! Reaction index: Chemkin #12; RMG #26 +! Template reaction: R_Recombination +! Flux pairs: H(6), H2(11); H(6), H2(11); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(6)+H(6)=H2(11) 5.450000e+10 0.000 1.500 + +! Reaction index: Chemkin #13; RMG #31 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H7(16); C2H4(9), C3H7(16); +! Matched reaction 219 CH3 + C2H4 <=> C3H7 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C2H4(9)=C3H7(16) 4.180000e+04 2.410 5.630 + +! Reaction index: Chemkin #14; RMG #27 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C2H4(9); H(6), C2H4(9); +! Matched reaction 60 H + C2H3 <=> C2H4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! family: R_Recombination +H(6)+C2H3(14)=C2H4(9) 1.210000e+14 0.000 0.000 + +! Reaction index: Chemkin #15; RMG #30 +! Template reaction: H_Abstraction +! Flux pairs: CH4(3), CH3(4); C2H3(14), C2H4(9); +! Matched reaction 843 C2H3 + CH4b <=> C2H4 + CH3_p23 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_methyl] +! family: H_Abstraction +CH4(3)+C2H3(14)=CH3(4)+C2H4(9) 2.236000e-02 4.340 5.700 + +! Reaction index: Chemkin #16; RMG #34 +! Template reaction: H_Abstraction +! Flux pairs: ethane(1), C2H5(5); C2H3(14), C2H4(9); +! Matched reaction 775 C2H3 + C2H6 <=> C2H4 + C2H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! family: H_Abstraction +C2H3(14)+ethane(1)=C2H4(9)+C2H5(5) 1.080000e-03 4.550 3.500 + +! Reaction index: Chemkin #17; RMG #36 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); C2H4(9), C2H3(14); +! Matched reaction 217 C2H4 + H <=> C2H3_p + H2_p in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;H_rad] +! family: H_Abstraction +H(6)+C2H4(9)=H2(11)+C2H3(14) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #18; RMG #39 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C2H4(9); C2H5(5), C2H4(9); +! Matched reaction 11 C2H3-2 + C2H5 <=> C2H4-2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Cd_pri_rad;Cmethyl_Csrad] +! family: Disproportionation +C2H3(14)+C2H5(5)=C2H4(9)+C2H4(9) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #19; RMG #55 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C#C(27), C2H3(14); H(6), C2H3(14); +! Matched reaction 2697 H + C2H2 <=> C2H3-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;HJ] +! family: R_Addition_MultipleBond +H(6)+C#C(27)=C2H3(14) 1.030000e+09 1.640 2.110 + +! Reaction index: Chemkin #20; RMG #66 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), ethane(1); C2H3(14), C#C(27); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cs;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H5(5)=C#C(27)+ethane(1) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #21; RMG #74 +! Template reaction: Disproportionation +! Flux pairs: CH3(4), CH4(3); C2H3(14), C#C(27); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_methyl;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C2H3(14)=CH4(3)+C#C(27) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #22; RMG #77 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(27); C2H3(14), C2H4(9); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H3(14)=C#C(27)+C2H4(9) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #23; RMG #79 +! Template reaction: Disproportionation +! Flux pairs: H(6), H2(11); C2H3(14), C#C(27); +! Estimated using template [H_rad;Cds/H2_d_Rrad] for rate rule [H_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C2H3(14)=H2(11)+C#C(27) 6.788225e+08 1.500 -0.890 + +! Reaction index: Chemkin #24; RMG #65 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H2(31), C#C(27); +! Estimated using template [singletcarbene_CH;singletcarbene;CH] for rate rule [CdJ2=C;CdJ2;CdH2] +! Euclidian distance = 1.7320508075688772 +! Multiplied by reaction path degeneracy 2.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H2(31)=C#C(27) 1.599708e+13 -0.202 8.145 + +! Reaction index: Chemkin #25; RMG #62 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H7(29); C2H4(9), C4H7(29); +! Matched reaction 234 C2H3 + C2H4 <=> C4H7-3 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CdsJ-H] +! family: R_Addition_MultipleBond +C2H3(14)+C2H4(9)=C4H7(29) 2.860000e+04 2.410 1.800 + +! Reaction index: Chemkin #26; RMG #91 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H7(29), C4H7(41); +! Matched reaction 335 C4H7 <=> C4H7-2 in Intra_R_Add_Exocyclic/training +! This reaction matched rate rule [R4_S_D;doublebond_intra_2H_pri;radadd_intra_cs2H] +! family: Intra_R_Add_Exocyclic +C4H7(29)=C4H7(41) 6.320000e+08 0.970 8.900 + +! Reaction index: Chemkin #27; RMG #73 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H5(5), C4H7(33); C#C(27), C4H7(33); +! Matched reaction 2254 C2H2 + C2H5 <=> C4H7-6 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-CsHH] +! family: R_Addition_MultipleBond +C#C(27)+C2H5(5)=C4H7(33) 1.360000e+04 2.410 6.200 + +! Reaction index: Chemkin #28; RMG #99 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(29); +! Estimated using template [R4H_DSS;Cd_rad_out_singleH;Cs_H_out] for rate rule [R4H_DSS;Cd_rad_out_singleH;Cs_H_out_2H] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: intra_H_migration +C4H7(33)=C4H7(29) 1.113000e+05 2.230 10.590 + +! Reaction index: Chemkin #29; RMG #97 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(29), C4H7(45); +! Matched reaction 84 C:CC[CH2] <=> C:C[CH]C in intra_H_migration/training +! This reaction matched rate rule [R2H_S;C_rad_out_2H;Cs_H_out_H/Cd] +! family: intra_H_migration +C4H7(29)=C4H7(45) 1.720000e+06 1.990 27.200 + +! Reaction index: Chemkin #30; RMG #146 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(45); +! Matched reaction 194 C4H7-4 <=> C4H7-5 in intra_H_migration/training +! This reaction matched rate rule [R3H_DS;Cd_rad_out_singleH;Cs_H_out_H/NonDeC] +! family: intra_H_migration +C4H7(33)=C4H7(45) 1.846000e+10 0.740 34.700 + +! Reaction index: Chemkin #31; RMG #92 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(42), C4H7(29); H(6), C4H7(29); +! Matched reaction 2580 H + C4H6-2 <=> C4H7-11 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-CdH_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(42)=C4H7(29) 3.240000e+08 1.640 2.400 + +! Reaction index: Chemkin #32; RMG #160 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(42), C4H7(45); H(6), C4H7(45); +! Matched reaction 2544 H + C4H6 <=> C4H7-9 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-CdH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(42)=C4H7(45) 4.620000e+08 1.640 -0.470 + +! Reaction index: Chemkin #33; RMG #213 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C4H6(42); C2H3(14), C4H6(42); +! Matched reaction 89 C2H3 + C2H3 <=> C4H6-4 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_N-Sp-3R!H-2R_N-3R!H->O_N-Sp-3CCSS#2R_Ext-1C-R] +! family: R_Recombination +C2H3(14)+C2H3(14)=C4H6(42) 3.615000e+13 0.000 0.000 + +! Reaction index: Chemkin #34; RMG #218 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), ethane(1); C4H7(29), C4H6(42); +! Estimated using template [C_rad/H2/Cs;Cpri_Rrad] for rate rule [C_rad/H2/Cs;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H7(29)=ethane(1)+C4H6(42) 2.900000e+12 0.000 0.000 + +! Reaction index: Chemkin #35; RMG #219 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cs;Cmethyl_Csrad] for rate rule [C_rad/H2/Cs;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H7(45)=ethane(1)+C4H6(42) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #36; RMG #234 +! Template reaction: Disproportionation +! Flux pairs: CH3(4), CH4(3); C4H7(29), C4H6(42); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [C_methyl;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H7(29)=CH4(3)+C4H6(42) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #37; RMG #235 +! Template reaction: Disproportionation +! Estimated using template [Cs_rad;Cmethyl_Csrad/H/Cd] for rate rule [C_methyl;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +CH3(4)+C4H7(45)=CH4(3)+C4H6(42) 1.500000e+11 0.000 0.000 + +! Reaction index: Chemkin #38; RMG #243 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C4H6(42); C4H7(29), C2H4(9); +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H7(29)=C2H4(9)+C4H6(42) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #39; RMG #244 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H3(14)+C4H7(45)=C2H4(9)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #40; RMG #247 +! Template reaction: Disproportionation +! Flux pairs: H(6), H2(11); C4H7(29), C4H6(42); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [H_rad;C/H2/Cd_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H7(29)=H2(11)+C4H6(42) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #41; RMG #248 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad;Cmethyl_Csrad/H/Cd] + [H_rad;Cmethyl_Csrad] for rate rule [H_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +H(6)+C4H7(45)=H2(11)+C4H6(42) 1.274559e+12 0.000 0.000 + +! Reaction index: Chemkin #42; RMG #209 +! Template reaction: Intra_2+2_cycloaddition_Cd +! Flux pairs: C4H6(42), C4H6(88); +! Estimated using template [1,3-butadiene_backbone;C=C_1;C=C_2] for rate rule [1,3-butadiene_backbone;CdH2_1;CdH2_2] +! Euclidian distance = 1.4142135623730951 +! family: Intra_2+2_cycloaddition_Cd +C4H6(42)=C4H6(88) 4.999980e+11 0.056 29.257 + +! Reaction index: Chemkin #43; RMG #94 +! Template reaction: R_Recombination +! Flux pairs: C4H6(43), C4H7(29); H(6), C4H7(29); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(43)=C4H7(29) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #44; RMG #107 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(43)=C2H4(9)+C4H7(29) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #45; RMG #120 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(43)=C#C(27)+C4H7(29) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #46; RMG #154 +! Template reaction: R_Recombination +! Flux pairs: C4H6(43), C4H7(45); H(6), C4H7(45); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(43)=C4H7(45) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #47; RMG #179 +! Template reaction: Disproportionation +! From training reaction 7 used for C_rad/H2/Cd;Cmethyl_Csrad +! Exact match found for rate rule [C_rad/H2/Cd;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(43)=C2H4(9)+C4H7(45) 1.374000e+14 -0.350 -0.130 + +! Reaction index: Chemkin #48; RMG #200 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cd;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(43)=C#C(27)+C4H7(45) 1.640928e+07 1.877 -1.115 + +! Reaction index: Chemkin #49; RMG #275 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cd;Cpri_Rrad] for rate rule [C_rad/H2/Cd;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(43)+C4H7(29)=C4H6(42)+C4H7(45) 5.800000e+12 0.000 -0.130 + +! Reaction index: Chemkin #50; RMG #276 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cd;Cmethyl_Csrad] for rate rule [C_rad/H2/Cd;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(43)+C4H7(45)=C4H6(42)+C4H7(45) 1.374000e+14 -0.350 -0.130 + +! Reaction index: Chemkin #51; RMG #312 +! Template reaction: Birad_recombination +! Flux pairs: C4H6(43), C4H6(88); +! Estimated using template [R4;C_rad_out_2H;Cpri_rad_out_2H] for rate rule [R4_SDS;C_rad_out_2H;Cpri_rad_out_2H] +! Euclidian distance = 1.0 +! family: Birad_recombination +C4H6(43)=C4H6(88) 1.620000e+12 -0.305 1.980 + +! Reaction index: Chemkin #52; RMG #348 +! Template reaction: 1,2-Birad_to_alkene +! Flux pairs: C4H6(43), C4H6(42); +! Matched reaction 5 C4H6 => C4H6-2 in 1,2-Birad_to_alkene/training +! This reaction matched rate rule [Y_12_01] +! family: 1,2-Birad_to_alkene +C4H6(43)=>C4H6(42) 5.010000e+07 0.000 0.000 + +! Reaction index: Chemkin #53; RMG #152 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(69), C4H7(45); H(6), C4H7(45); +! Matched reaction 2714 H + C4H6-4 <=> C4H7-13 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ca_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(69)=C4H7(45) 5.460000e+08 1.640 3.780 + +! Reaction index: Chemkin #54; RMG #342 +! Template reaction: Intra_Disproportionation +! Flux pairs: C4H6(43), C4H6(69); +! Estimated using an average for rate rule [R3radExo;Y_rad;XH_Rrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Intra_Disproportionation +C4H6(43)=C4H6(69) 1.487400e+09 1.045 15.153 + +! Reaction index: Chemkin #55; RMG #367 +! Template reaction: Disproportionation +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H5(5)+C4H7(45)=ethane(1)+C4H6(69) 9.640000e+11 0.000 6.000 + +! Reaction index: Chemkin #56; RMG #370 +! Template reaction: Disproportionation +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +CH3(4)+C4H7(45)=CH4(3)+C4H6(69) 3.354068e+12 0.000 6.000 + +! Reaction index: Chemkin #57; RMG #376 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H3(14)+C4H7(45)=C2H4(9)+C4H6(69) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #58; RMG #382 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +H(6)+C4H7(45)=H2(11)+C4H6(69) 3.010000e+12 0.000 6.000 + +! Reaction index: Chemkin #59; RMG #361 +! Template reaction: R_Recombination +! Flux pairs: C4H5(144), C4H6(69); H(6), C4H6(69); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(144)=C4H6(69) 1.554090e+97 -24.703 0.000 + +! Reaction index: Chemkin #60; RMG #378 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(144)=C2H4(9)+C4H6(69) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #61; RMG #390 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_rad/NonDeC;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(144)=C#C(27)+C4H6(69) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #62; RMG #407 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cpri_Rrad] for rate rule [Cd_rad/NonDeC;C/H2/Cd_Csrad] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(144)+C4H7(29)=C4H6(69)+C4H6(42) 2.420000e+12 0.000 0.000 + +! Reaction index: Chemkin #63; RMG #410 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(144)+C4H7(45)=C4H6(69)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #64; RMG #425 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); C2H5(5), ethane(1); +! Estimated using an average for rate rule [Cd_allenic;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! family: H_Abstraction +C2H5(5)+C4H6(69)=ethane(1)+C4H5(144) 5.450000e-03 4.340 5.900 + +! Reaction index: Chemkin #65; RMG #436 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); C2H3(14), C2H4(9); +! Estimated using an average for rate rule [Cd_allenic;Cd_Cd\H2_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C2H3(14)+C4H6(69)=C2H4(9)+C4H5(144) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #66; RMG #442 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); H(6), H2(11); +! Estimated using an average for rate rule [Cd_allenic;H_rad] +! Euclidian distance = 0 +! family: H_Abstraction +H(6)+C4H6(69)=H2(11)+C4H5(144) 3.532500e+00 3.852 3.502 + +! Reaction index: Chemkin #67; RMG #69 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H5(32); C#C(27), C3H5(32); +! Matched reaction 2253 C2H2 + CH3 <=> C3H5-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C#C(27)=C3H5(32) 1.338000e+05 2.410 6.770 + +! Reaction index: Chemkin #68; RMG #84 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H5(35); C#C(27), C4H5(35); +! Matched reaction 196 C2H2 + C2H3 <=> C4H5-8 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CdsJ-H] +! family: R_Addition_MultipleBond +C#C(27)+C2H3(14)=C4H5(35) 1.168000e+07 1.997 5.452 + +! Reaction index: Chemkin #69; RMG #215 +! Template reaction: R_Recombination +! Flux pairs: C4H5(35), C4H6(42); H(6), C4H6(42); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C +! Total Standard Deviation in ln(k): 6.83519320067 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(35)=C4H6(42) 9.988280e+13 0.006 0.000 + +! Reaction index: Chemkin #70; RMG #223 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(42), C4H5(35); +! From training reaction 1567 used for Cd/H2/NonDeC;C_methyl +! Exact match found for rate rule [Cd/H2/NonDeC;C_methyl] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +CH3(4)+C4H6(42)=CH4(3)+C4H5(35) 3.432000e-02 4.340 20.710 + +! Reaction index: Chemkin #71; RMG #231 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(42), C4H5(35); +! From training reaction 344 used for Cd/H2/NonDeC;C_rad/H2/Cs\H3 +! Exact match found for rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +C2H5(5)+C4H6(42)=ethane(1)+C4H5(35) 6.320000e+02 3.130 18.000 + +! Reaction index: Chemkin #72; RMG #237 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); C4H6(42), C4H5(35); +! From training reaction 217 used for Cd/H2/NonDeC;H_rad +! Exact match found for rate rule [Cd/H2/NonDeC;H_rad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +H(6)+C4H6(42)=H2(11)+C4H5(35) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #73; RMG #246 +! Template reaction: Disproportionation +! From training reaction 11 used for Cd_pri_rad;Cmethyl_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(35)=C2H4(9)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #74; RMG #256 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(42), C4H5(35); +! Matched reaction 177 C4H6-3 + C2H3 <=> C2H4 + C4H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;Cd_Cd\H2_pri_rad] +! family: H_Abstraction +C2H3(14)+C4H6(42)=C2H4(9)+C4H5(35) 3.437000e-04 4.732 6.579 + +! Reaction index: Chemkin #75; RMG #265 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(35)=C#C(27)+C4H6(42) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #76; RMG #309 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(35)+C4H7(29)=C4H6(42)+C4H6(42) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #77; RMG #310 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(35)+C4H7(45)=C4H6(42)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #78; RMG #405 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C4H5(35)+C4H7(45)=C4H6(69)+C4H6(42) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #79; RMG #466 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H5(35), C4H5(185); +! From training reaction 14 used for R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH +! Exact match found for rate rule [R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH] +! Euclidian distance = 0 +! family: Intra_R_Add_Exocyclic +C4H5(35)=C4H5(185) 2.540000e+10 0.690 25.170 + +END + diff --git a/examples/scripts/mergeModels/Models/minimal_ml_chem.inp b/examples/scripts/mergeModels/Models/minimal_ml_chem.inp new file mode 100644 index 0000000000..8bf029ae53 --- /dev/null +++ b/examples/scripts/mergeModels/Models/minimal_ml_chem.inp @@ -0,0 +1,1118 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + ethane(1) ! ethane(1) + CH4(3) ! CH4(3) + CH3(4) ! [CH3](4) + C2H5(5) ! C[CH2](5) + H(6) ! H(6) + C2H4(9) ! C=C(9) + H2(13) ! H2(13) + C2H3(14) ! [CH]=C(14) + C2H4(15) ! [CH]C(15) + C3H7(16) ! [CH2]CC(16) + C#C(30) ! C#C(30) + C4H7(33) ! [CH2]CC=C(33) + C4H6(35) ! C=CC=C(35) + C2H2(37) ! [C]=C(37) + C3H5(38) ! [CH]=CC(38) + C4H7(39) ! [CH]=CCC(39) + C4H5(43) ! [CH]=CC=C(43) + C4H7(49) ! [CH2]C1CC1(49) + C4H6(50) ! [CH2][CH]C=C(50) + C4H7(52) ! C=C[CH]C(52) + C4H6(118) ! C=C=CC(118) + C4H6(204) ! C1=CCC1(204) + C4H6(206) ! C=C[C]C(206) + C4H6(262) ! [C]1CCC1(262) + C4H5(302) ! C=C=[C]C(302) + C4H5(611) ! [CH2]C1C=C1(611) + C4H5(731) ! C[C]1C=C1(731) + C4H4(812) ! CC1=C=C1(812) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) +ethane(1) C 2H 6 G 100.000 5000.000 954.51 1 + 4.58979444E+00 1.41508381E-02-4.75965886E-06 8.60303158E-10-6.21724057E-14 2 +-1.27217503E+04-3.61718429E+00 3.78034607E+00-3.24276485E-03 5.52385525E-05 3 +-6.38587905E-08 2.28640069E-11-1.16203414E+04 5.21029625E+00 4 + +! Thermo library: primaryThermoLibrary +CH4(3) C 1H 4 G 100.000 5000.000 1084.12 1 + 9.08265721E-01 1.14540858E-02-4.57173828E-06 8.29191671E-10-5.66314895E-14 2 +-9.71997444E+03 1.39930944E+01 4.20541524E+00-5.35557362E-03 2.51123265E-05 3 +-2.13762843E-08 5.97523937E-12-1.01619433E+04-9.21279283E-01 4 + +! Thermo library: primaryThermoLibrary + radical(CH3) +CH3(4) C 1H 3 G 100.000 5000.000 1337.63 1 + 3.54145749E+00 4.76786834E-03-1.82148425E-06 3.28876586E-10-2.22545593E-14 2 + 1.62239579E+04 1.66034967E+00 3.91546761E+00 1.84154323E-03 3.48741760E-06 3 +-3.32747607E-09 8.49956882E-13 1.62856394E+04 3.51741490E-01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) + radical(CCJ) +C2H5(5) C 2H 5 G 100.000 5000.000 900.31 1 + 5.15621623E+00 9.43121232E-03-1.81945206E-06 2.21193866E-10-1.43479695E-14 2 + 1.20640796E+04-2.91102815E+00 3.82183329E+00-3.43357093E-03 5.09256026E-05 3 +-6.20209847E-08 2.37072520E-11 1.30660130E+04 7.61644314E+00 4 + +! Thermo library: primaryThermoLibrary +H(6) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) +C2H4(9) C 2H 4 G 100.000 5000.000 940.45 1 + 5.20299386E+00 7.82442468E-03-2.12683407E-06 3.79690544E-10-2.94670706E-14 2 + 3.93628131E+03-6.62410904E+00 3.97974441E+00-7.57559895E-03 5.52973238E-05 3 +-6.36221688E-08 2.31767197E-11 5.07746086E+03 4.04622760E+00 4 + +! Thermo library: primaryThermoLibrary +H2(13) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C2H3(14) C 2H 3 G 100.000 5000.000 931.96 1 + 5.44796550E+00 4.98356138E-03-1.08820775E-06 1.79837309E-10-1.45096285E-14 2 + 3.38297746E+04-4.87808224E+00 3.90670547E+00-4.06241062E-03 3.86780039E-05 3 +-4.62976404E-08 1.72900384E-11 3.47971783E+04 6.09788968E+00 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(CsJ2_singlet-CsH) +C2H4(15) C 2H 4 G 100.000 5000.000 1066.91 1 + 3.48115209E+00 1.16883236E-02-4.78434464E-06 8.90802946E-10-6.22433678E-14 2 + 4.22812570E+04 5.54898688E+00 3.71555285E+00 3.77628865E-03 1.62276340E-05 3 +-1.84174082E-08 5.90989211E-12 4.26315359E+04 6.27891490E+00 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsHHH) + group(Cs-CsHHH) + radical(RCCJ) +C3H7(16) C 3H 7 G 100.000 5000.000 995.41 1 + 5.69430979E+00 1.96033402E-02-7.42049648E-06 1.35882956E-09-9.56214889E-14 2 + 8.87584826E+03-4.32889887E+00 3.09191302E+00 1.32172474E-02 2.75847569E-05 3 +-3.90848844E-08 1.43313303E-11 1.02284118E+04 1.24057873E+01 4 + +! Thermo group additivity estimation: group(Ct-CtH) + group(Ct-CtH) +C#C(30) C 2H 2 G 100.000 5000.000 888.63 1 + 5.76204511E+00 2.37158782E-03-1.49582699E-07-2.19154662E-11 2.21779207E-15 2 + 2.50944501E+04-9.82608488E+00 3.03574736E+00 7.71239020E-03 2.53493006E-06 3 +-1.08133128E-08 5.50757058E-12 2.58526443E+04 4.54461297E+00 4 + +! ML Estimation + radical(RCCJ) +C4H7(33) C 4H 7 G 100.000 5000.000 1078.87 1 + 6.92232595E+00 2.17046609E-02-8.80220064E-06 1.64803378E-09-1.15890851E-13 2 + 2.06387442E+04-8.11802065E+00 2.65124021E+00 2.36511400E-02 7.80192789E-06 3 +-2.05446655E-08 7.79173851E-12 2.23686405E+04 1.65578190E+01 4 + +! ML Estimation +C4H6(35) C 4H 6 G 100.000 5000.000 954.15 1 + 1.03676849E+01 1.45821037E-02-4.67321619E-06 8.49490466E-10-6.30414970E-14 2 + 9.49991045E+03-3.15226171E+01 2.66951022E+00 1.75997221E-02 3.65733116E-05 3 +-6.01029274E-08 2.43266090E-11 1.23006441E+04 1.22337040E+01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(CdJ2_singlet-Cds) +C2H2(37) C 2H 2 G 100.000 5000.000 1423.26 1 + 4.43041986E+00 4.87757420E-03-1.79374459E-06 3.04085410E-10-1.96652162E-14 2 + 4.78744103E+04-1.67075241E-01 3.69251650E+00 6.06584723E-03-2.11277596E-06 3 + 1.63533182E-11 1.07665581E-13 4.81741496E+04 3.96842354E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C3H5(38) C 3H 5 G 100.000 5000.000 997.87 1 + 5.66465812E+00 1.44326998E-02-5.46743137E-06 1.00159120E-09-7.04869894E-14 2 + 2.93871077E+04-4.48482420E+00 3.23409465E+00 1.18206723E-02 1.70311418E-05 3 +-2.64373876E-08 9.91250979E-12 3.04873059E+04 1.03182315E+01 4 + +! ML Estimation + radical(Cds_P) +C4H7(39) C 4H 7 G 100.000 5000.000 1088.26 1 + 7.43030619E+00 2.10639706E-02-8.47867811E-06 1.57836912E-09-1.10522887E-13 2 + 2.55981431E+04-1.18519505E+01 2.53129347E+00 2.65456472E-02 1.22972909E-06 3 +-1.49450091E-08 6.11489161E-12 2.74060971E+04 1.56049405E+01 4 + +! ML Estimation + radical(Cds_P) +C4H5(43) C 4H 5 G 100.000 5000.000 955.64 1 + 1.06970014E+01 1.16010512E-02-3.57840830E-06 6.50033015E-10-4.86684885E-14 2 + 3.93608497E+04-3.09400155E+01 2.59081659E+00 2.12230334E-02 1.94729288E-05 3 +-4.20477294E-08 1.80843530E-11 4.20201271E+04 1.36072333E+01 4 + +! ML Estimation + radical(Isobutyl) +C4H7(49) C 4H 7 G 100.000 5000.000 950.84 1 + 8.61925602E+00 1.82848485E-02-5.82529494E-06 1.02602280E-09-7.35115648E-14 2 + 2.35749926E+04-1.93423218E+01 2.79233123E+00 1.58871755E-02 4.04099284E-05 3 +-6.11563015E-08 2.41018651E-11 2.58995634E+04 1.48723527E+01 4 + +! ML Estimation + radical(Allyl_P) + radical(Allyl_P) +C4H6(50) C 4H 6 G 100.000 5000.000 969.78 1 + 1.06933497E+01 1.31713172E-02-4.38797708E-06 8.51730358E-10-6.56940995E-14 2 + 3.03684785E+04-3.12144405E+01 2.72144234E+00 1.61881624E-02 3.71381701E-05 3 +-5.94494929E-08 2.36653401E-11 3.33190199E+04 1.42412818E+01 4 + +! ML Estimation + radical(Allyl_S) +C4H7(52) C 4H 7 G 100.000 5000.000 1024.08 1 + 6.98983798E+00 2.18068950E-02-8.71735467E-06 1.65319806E-09-1.18476776E-13 2 + 1.27222580E+04-1.24039020E+01 2.82652717E+00 1.75496097E-02 2.75728801E-05 3 +-4.15364349E-08 1.52012493E-11 1.46509312E+04 1.30340126E+01 4 + +! ML Estimation +C4H6(118) C 4H 6 G 100.000 5000.000 1050.31 1 + 6.91247067E+00 1.99659125E-02-8.06240299E-06 1.50325964E-09-1.05713842E-13 2 + 1.64740179E+04-1.08687975E+01 2.73020124E+00 2.18889508E-02 9.19221257E-06 3 +-2.21442289E-08 8.54482949E-12 1.81250129E+04 1.31908301E+01 4 + +! ML Estimation +C4H6(204) C 4H 6 G 100.000 5000.000 947.33 1 + 1.05003503E+01 1.34263547E-02-3.60393361E-06 6.93428896E-10-5.78005007E-14 2 + 1.41891065E+04-3.45159152E+01 3.39236739E+00-5.91857845E-03 1.05179439E-04 3 +-1.30859407E-07 4.91729935E-11 1.77505918E+04 1.10808957E+01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + group(CsJ2_singlet-CsH) +C4H6(206) C 4H 6 G 100.000 5000.000 2271.47 1 + 1.33033726E+01 1.41297275E-02-5.59015002E-06 9.21036568E-10-5.59628753E-14 2 + 4.39060412E+04-3.81544793E+01 2.68371413E+00 2.99287729E-02-1.41069865E-05 3 + 2.85826650E-09-2.07275399E-13 4.94791199E+04 2.34397882E+01 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(CsJ2_singlet-CsH) + ring(Cyclobutane) +C4H6(262) C 4H 6 G 100.000 5000.000 980.35 1 + 7.14704703E+00 2.10751316E-02-8.03260328E-06 1.52842626E-09-1.12007748E-13 2 + 5.09852626E+04-5.31313006E+00 3.16723720E+00 6.09463614E-03 6.26555185E-05 3 +-7.90245960E-08 2.87134488E-11 5.32657784E+04 2.14595013E+01 4 + +! ML Estimation + radical(Propargyl) +C4H5(302) C 4H 5 G 100.000 5000.000 1315.39 1 + 6.41498474E+00 1.79030746E-02-7.80803478E-06 1.46794405E-09-1.01382140E-13 2 + 3.28267991E+04-7.49357269E+00 2.93432630E+00 2.04689916E-02-1.59024215E-06 3 +-6.31762105E-09 2.25909769E-12 3.44361872E+04 1.28896247E+01 4 + +! ML Estimation + radical(Isobutyl) +C4H5(611) C 4H 5 G 100.000 5000.000 950.98 1 + 8.82100219E+00 1.64207490E-02-5.37530809E-06 9.43871506E-10-6.70140255E-14 2 + 4.09646430E+04-1.89209939E+01 2.71545999E+00 1.90191720E-02 2.69349209E-05 3 +-4.72303461E-08 1.93072123E-11 4.31696444E+04 1.57156143E+01 4 + +! ML Estimation + radical(Allyl_T) +C4H5(731) C 4H 5 G 100.000 5000.000 973.27 1 + 7.85854152E+00 1.86771894E-02-6.82738449E-06 1.27242853E-09-9.24592617E-14 2 + 3.21495813E+04-1.86936558E+01 2.97128106E+00 1.19781979E-02 4.47781461E-05 3 +-6.23528344E-08 2.35140773E-11 3.43695061E+04 1.12693601E+01 4 + +! ML Estimation +C4H4(812) C 4H 4 G 100.000 5000.000 1014.00 1 + 7.80825107E+00 2.01036086E-02-8.15845347E-06 1.52095603E-09-1.07480874E-13 2 + 3.32703654E+04-1.48110962E+01 2.62421107E+00 2.26939729E-02 1.44287845E-05 3 +-3.06987273E-08 1.21185930E-11 3.52398502E+04 1.47983764E+01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #2 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), ethane(1); CH3(4), ethane(1); +! Matched reaction 9 CH3 + CH3 <=> C2H6 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing] +! family: R_Recombination +CH3(4)+CH3(4)=ethane(1) 9.450000e+14 -0.538 0.135 + +! Reaction index: Chemkin #2; RMG #5 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); ethane(1), C2H5(5); +! Matched reaction 215 C2H6 + CH3_r3 <=> C2H5b + CH4 in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;C_methyl] +! family: H_Abstraction +CH3(4)+ethane(1)=CH4(3)+C2H5(5) 3.500000e+01 3.440 10.384 + +! Reaction index: Chemkin #3; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: C2H5(5), ethane(1); H(6), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #4; RMG #19 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), CH4(3); H(6), CH4(3); +! Matched reaction 57 H + CH3 <=> CH4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C] +! family: R_Recombination +H(6)+CH3(4)=CH4(3) 1.930000e+14 0.000 0.270 + +! Reaction index: Chemkin #5; RMG #24 +! Template reaction: R_Recombination +! Flux pairs: H(6), ethane(1); C2H5(5), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #6; RMG #9 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H4(9), C2H5(5); H(6), C2H5(5); +! 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(6)+C2H4(9)=C2H5(5) 4.620000e+08 1.640 1.010 + +! Reaction index: Chemkin #7; RMG #11 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); CH3(4), CH4(3); +! Matched reaction 5 CH3 + C2H5 <=> CH4 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_methyl;Cmethyl_Csrad] +! family: Disproportionation +CH3(4)+C2H5(5)=CH4(3)+C2H4(9) 6.570000e+14 -0.680 0.000 + +! Reaction index: Chemkin #8; RMG #15 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); C2H5(5), ethane(1); +! Matched reaction 6 C2H5 + C2H5-2 <=> C2H6 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_rad/H2/Cs;Cmethyl_Csrad] +! family: Disproportionation +C2H5(5)+C2H5(5)=C2H4(9)+ethane(1) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #9; RMG #20 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); ethane(1), C2H5(5); +! Matched reaction 210 C2H6 + H <=> C2H5b + H2_p in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;H_rad] +! family: H_Abstraction +H(6)+ethane(1)=H2(13)+C2H5(5) 1.150000e+08 1.900 7.530 + +! Reaction index: Chemkin #10; RMG #22 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); H(6), H2(13); +! Matched reaction 4 H + C2H5 <=> H2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [H_rad;Cmethyl_Csrad] +! family: Disproportionation +H(6)+C2H5(5)=H2(13)+C2H4(9) 1.083000e+13 0.000 0.000 + +! Reaction index: Chemkin #11; RMG #25 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); CH4(3), CH3(4); +! Matched reaction 186 CH4b + H <=> CH3_p1 + H2_p in H_Abstraction/training +! This reaction matched rate rule [C_methane;H_rad] +! family: H_Abstraction +H(6)+CH4(3)=H2(13)+CH3(4) 4.100000e+03 3.156 8.755 + +! Reaction index: Chemkin #12; RMG #26 +! Template reaction: R_Recombination +! Flux pairs: H(6), H2(13); H(6), H2(13); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(6)+H(6)=H2(13) 5.450000e+10 0.000 1.500 + +! Reaction index: Chemkin #13; RMG #28 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H4(15), C2H4(9); +! Estimated using template [CsJ2-C;singletcarbene;CH] for rate rule [CsJ2-C;CsJ2H;CH3] +! Euclidian distance = 1.4142135623730951 +! Multiplied by reaction path degeneracy 3.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H4(15)=C2H4(9) 1.582654e+14 -0.573 -7.598 + +! Reaction index: Chemkin #14; RMG #31 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H7(16); C2H4(9), C3H7(16); +! Matched reaction 219 CH3 + C2H4 <=> C3H7 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C2H4(9)=C3H7(16) 4.180000e+04 2.410 5.630 + +! Reaction index: Chemkin #15; RMG #27 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C2H4(9); H(6), C2H4(9); +! Matched reaction 60 H + C2H3 <=> C2H4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! family: R_Recombination +H(6)+C2H3(14)=C2H4(9) 1.210000e+14 0.000 0.000 + +! Reaction index: Chemkin #16; RMG #30 +! Template reaction: H_Abstraction +! Flux pairs: CH4(3), CH3(4); C2H3(14), C2H4(9); +! Matched reaction 843 C2H3 + CH4b <=> C2H4 + CH3_p23 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_methyl] +! family: H_Abstraction +CH4(3)+C2H3(14)=CH3(4)+C2H4(9) 2.236000e-02 4.340 5.700 + +! Reaction index: Chemkin #17; RMG #34 +! Template reaction: H_Abstraction +! Flux pairs: ethane(1), C2H5(5); C2H3(14), C2H4(9); +! Matched reaction 775 C2H3 + C2H6 <=> C2H4 + C2H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! family: H_Abstraction +C2H3(14)+ethane(1)=C2H4(9)+C2H5(5) 1.080000e-03 4.550 3.500 + +! Reaction index: Chemkin #18; RMG #36 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C2H4(9), C2H3(14); +! Matched reaction 217 C2H4 + H <=> C2H3_p + H2_p in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;H_rad] +! family: H_Abstraction +H(6)+C2H4(9)=H2(13)+C2H3(14) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #19; RMG #39 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C2H4(9); C2H5(5), C2H4(9); +! Matched reaction 11 C2H3-2 + C2H5 <=> C2H4-2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Cd_pri_rad;Cmethyl_Csrad] +! family: Disproportionation +C2H3(14)+C2H5(5)=C2H4(9)+C2H4(9) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #20; RMG #77 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C#C(30), C2H3(14); H(6), C2H3(14); +! Matched reaction 2697 H + C2H2 <=> C2H3-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;HJ] +! family: R_Addition_MultipleBond +H(6)+C#C(30)=C2H3(14) 1.030000e+09 1.640 2.110 + +! Reaction index: Chemkin #21; RMG #80 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); CH3(4), CH4(3); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_methyl;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C2H3(14)=CH4(3)+C#C(30) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #22; RMG #85 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); C2H5(5), ethane(1); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cs;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H5(5)=C#C(30)+ethane(1) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #23; RMG #92 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); H(6), H2(13); +! Estimated using template [H_rad;Cds/H2_d_Rrad] for rate rule [H_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C2H3(14)=H2(13)+C#C(30) 6.788225e+08 1.500 -0.890 + +! Reaction index: Chemkin #24; RMG #108 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(30); C2H3(14), C2H4(9); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H3(14)=C#C(30)+C2H4(9) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #25; RMG #114 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H2(37), C#C(30); +! Estimated using template [singletcarbene_CH;singletcarbene;CH] for rate rule [CdJ2=C;CdJ2;CdH2] +! Euclidian distance = 1.7320508075688772 +! Multiplied by reaction path degeneracy 2.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H2(37)=C#C(30) 5.784457e+12 0.007 -0.632 + +! Reaction index: Chemkin #26; RMG #97 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H7(33); C2H4(9), C4H7(33); +! Matched reaction 234 C2H3 + C2H4 <=> C4H7-3 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CdsJ-H] +! family: R_Addition_MultipleBond +C2H3(14)+C2H4(9)=C4H7(33) 2.860000e+04 2.410 1.800 + +! Reaction index: Chemkin #27; RMG #142 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H7(33), C4H7(49); +! Matched reaction 335 C4H7 <=> C4H7-2 in Intra_R_Add_Exocyclic/training +! This reaction matched rate rule [R4_S_D;doublebond_intra_2H_pri;radadd_intra_cs2H] +! family: Intra_R_Add_Exocyclic +C4H7(33)=C4H7(49) 6.320000e+08 0.970 8.900 + +! Reaction index: Chemkin #28; RMG #121 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H5(5), C4H7(39); C#C(30), C4H7(39); +! Matched reaction 2254 C2H2 + C2H5 <=> C4H7-6 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-CsHH] +! family: R_Addition_MultipleBond +C#C(30)+C2H5(5)=C4H7(39) 1.360000e+04 2.410 6.200 + +! Reaction index: Chemkin #29; RMG #150 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(39), C4H7(33); +! Estimated using template [R4H_DSS;Cd_rad_out_singleH;Cs_H_out] for rate rule [R4H_DSS;Cd_rad_out_singleH;Cs_H_out_2H] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: intra_H_migration +C4H7(39)=C4H7(33) 1.113000e+05 2.230 10.590 + +! Reaction index: Chemkin #30; RMG #148 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(52); +! Matched reaction 84 C:CC[CH2] <=> C:C[CH]C in intra_H_migration/training +! This reaction matched rate rule [R2H_S;C_rad_out_2H;Cs_H_out_H/Cd] +! family: intra_H_migration +C4H7(33)=C4H7(52) 1.720000e+06 1.990 27.200 + +! Reaction index: Chemkin #31; RMG #351 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(39), C4H7(52); +! Matched reaction 194 C4H7-4 <=> C4H7-5 in intra_H_migration/training +! This reaction matched rate rule [R3H_DS;Cd_rad_out_singleH;Cs_H_out_H/NonDeC] +! family: intra_H_migration +C4H7(39)=C4H7(52) 1.846000e+10 0.740 34.700 + +! Reaction index: Chemkin #32; RMG #112 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C4H6(35); C2H3(14), C4H6(35); +! Matched reaction 89 C2H3 + C2H3 <=> C4H6-4 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_N-Sp-3R!H-2R_N-3R!H->O_N-Sp-3CCSS#2R_Ext-1C-R] +! family: R_Recombination +C2H3(14)+C2H3(14)=C4H6(35) 3.615000e+13 0.000 0.000 + +! Reaction index: Chemkin #33; RMG #143 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(35), C4H7(33); H(6), C4H7(33); +! Matched reaction 2580 H + C4H6-2 <=> C4H7-11 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-CdH_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(35)=C4H7(33) 3.240000e+08 1.640 2.400 + +! Reaction index: Chemkin #34; RMG #154 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); CH3(4), CH4(3); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [C_methyl;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H7(33)=CH4(3)+C4H6(35) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #35; RMG #164 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); C2H5(5), ethane(1); +! Estimated using template [C_rad/H2/Cs;Cpri_Rrad] for rate rule [C_rad/H2/Cs;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H7(33)=ethane(1)+C4H6(35) 2.900000e+12 0.000 0.000 + +! Reaction index: Chemkin #36; RMG #180 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); H(6), H2(13); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [H_rad;C/H2/Cd_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H7(33)=H2(13)+C4H6(35) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #37; RMG #219 +! Template reaction: Disproportionation +! Flux pairs: C4H7(33), C4H6(35); C2H3(14), C2H4(9); +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H7(33)=C2H4(9)+C4H6(35) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #38; RMG #464 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(35), C4H7(52); H(6), C4H7(52); +! Matched reaction 2544 H + C4H6 <=> C4H7-9 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-CdH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(35)=C4H7(52) 4.620000e+08 1.640 -0.470 + +! Reaction index: Chemkin #39; RMG #480 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cmethyl_Csrad/H/Cd] for rate rule [C_methyl;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +CH3(4)+C4H7(52)=CH4(3)+C4H6(35) 1.500000e+11 0.000 0.000 + +! Reaction index: Chemkin #40; RMG #494 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); C2H5(5), ethane(1); +! Estimated using template [C_rad/H2/Cs;Cmethyl_Csrad] for rate rule [C_rad/H2/Cs;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H7(52)=ethane(1)+C4H6(35) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #41; RMG #518 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); H(6), H2(13); +! Estimated using average of templates [Y_rad;Cmethyl_Csrad/H/Cd] + [H_rad;Cmethyl_Csrad] for rate rule [H_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +H(6)+C4H7(52)=H2(13)+C4H6(35) 1.274559e+12 0.000 0.000 + +! Reaction index: Chemkin #42; RMG #576 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(35); C2H3(14), C2H4(9); +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H3(14)+C4H7(52)=C2H4(9)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #43; RMG #759 +! Template reaction: Intra_2+2_cycloaddition_Cd +! Flux pairs: C4H6(35), C4H6(204); +! Estimated using template [1,3-butadiene_backbone;C=C_1;C=C_2] for rate rule [1,3-butadiene_backbone;CdH2_1;CdH2_2] +! Euclidian distance = 1.4142135623730951 +! family: Intra_2+2_cycloaddition_Cd +C4H6(35)=C4H6(204) 4.999980e+11 0.056 29.257 + +! Reaction index: Chemkin #44; RMG #765 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(206), C4H6(35); +! Estimated using template [CsJ2-C;CsJ2(C=C);CH] for rate rule [CsJ2-C;CsJ2(C=C);CH3] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(206)=C4H6(35) 6.011024e+12 -0.766 -14.909 + +! Reaction index: Chemkin #45; RMG #465 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(118), C4H7(52); H(6), C4H7(52); +! Matched reaction 2714 H + C4H6-4 <=> C4H7-13 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ca_Cds-CsH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(118)=C4H7(52) 5.460000e+08 1.640 3.780 + +! Reaction index: Chemkin #46; RMG #481 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +CH3(4)+C4H7(52)=CH4(3)+C4H6(118) 3.354068e+12 0.000 6.000 + +! Reaction index: Chemkin #47; RMG #495 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); C2H5(5), ethane(1); +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H5(5)+C4H7(52)=ethane(1)+C4H6(118) 9.640000e+11 0.000 6.000 + +! Reaction index: Chemkin #48; RMG #519 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); H(6), H2(13); +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +H(6)+C4H7(52)=H2(13)+C4H6(118) 3.010000e+12 0.000 6.000 + +! Reaction index: Chemkin #49; RMG #577 +! Template reaction: Disproportionation +! Flux pairs: C4H7(52), C4H6(118); C2H3(14), C2H4(9); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H3(14)+C4H7(52)=C2H4(9)+C4H6(118) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #50; RMG #1019 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(206), C4H6(118); +! Estimated using an average for rate rule [CsJ2-C;CsJ2C;CH=C] +! Euclidian distance = 0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(206)=C4H6(118) 5.275512e+13 -0.573 -7.598 + +! Reaction index: Chemkin #51; RMG #1041 +! Template reaction: R_Recombination +! Flux pairs: C4H5(302), C4H6(118); H(6), C4H6(118); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(302)=C4H6(118) 1.554090e+97 -24.703 0.000 + +! Reaction index: Chemkin #52; RMG #1050 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;C_methyl] +! Euclidian distance = 0 +! family: H_Abstraction +CH3(4)+C4H6(118)=CH4(3)+C4H5(302) 7.130000e+00 3.317 6.610 + +! Reaction index: Chemkin #53; RMG #1062 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! family: H_Abstraction +C2H5(5)+C4H6(118)=ethane(1)+C4H5(302) 5.450000e-03 4.340 5.900 + +! Reaction index: Chemkin #54; RMG #1070 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;H_rad] +! Euclidian distance = 0 +! family: H_Abstraction +H(6)+C4H6(118)=H2(13)+C4H5(302) 3.532500e+00 3.852 3.502 + +! Reaction index: Chemkin #55; RMG #1080 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(302)=C2H4(9)+C4H6(118) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #56; RMG #1111 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(118), C4H5(302); +! Estimated using an average for rate rule [Cd_allenic;Cd_Cd\H2_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C2H3(14)+C4H6(118)=C2H4(9)+C4H5(302) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #57; RMG #1123 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_rad/NonDeC;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(302)=C#C(30)+C4H6(118) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #58; RMG #1248 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cpri_Rrad] for rate rule [Cd_rad/NonDeC;C/H2/Cd_Csrad] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(302)+C4H7(33)=C4H6(118)+C4H6(35) 2.420000e+12 0.000 0.000 + +! Reaction index: Chemkin #59; RMG #1251 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(302)+C4H7(52)=C4H6(118)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #60; RMG #1276 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cdpri_Csrad] for rate rule [Cd_rad/NonDeC;Cdpri_Csrad] +! Euclidian distance = 2.0 +! family: Disproportionation +C4H5(302)+C4H7(52)=C4H6(118)+C4H6(118) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #61; RMG #916 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C4H6(262), C4H6(204); +! Estimated using template [CsJ2-C;CsJ2(CsC);CH] for rate rule [CsJ2-C;CsJ2(CsC);CH2(C)] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Singlet_Carbene_Intra_Disproportionation +C4H6(262)=C4H6(204) 5.555998e+15 -0.380 -0.286 + +! Reaction index: Chemkin #62; RMG #145 +! Template reaction: R_Recombination +! Flux pairs: C4H6(50), C4H7(33); H(6), C4H7(33); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(50)=C4H7(33) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #63; RMG #194 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(50)=C2H4(9)+C4H7(33) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #64; RMG #241 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(50)=C#C(30)+C4H7(33) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #65; RMG #466 +! Template reaction: R_Recombination +! Flux pairs: C4H6(50), C4H7(52); H(6), C4H7(52); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(50)=C4H7(52) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #66; RMG #534 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(50)=C2H4(9)+C4H7(52) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #67; RMG #604 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(50)=C#C(30)+C4H7(52) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #68; RMG #827 +! Template reaction: Disproportionation +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [Y_rad;C/H2/Cd_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(50)+C4H7(33)=C4H6(35)+C4H7(33) 4.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #69; RMG #828 +! Template reaction: Disproportionation +! Estimated using an average for rate rule [Y_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(35)+C4H7(33) 3.000000e+11 0.000 0.000 + +! Reaction index: Chemkin #70; RMG #874 +! Template reaction: Disproportionation +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [Y_rad;C/H2/Cd_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(50)+C4H7(33)=C4H6(35)+C4H7(52) 4.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #71; RMG #875 +! Template reaction: Disproportionation +! Estimated using an average for rate rule [Y_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(35)+C4H7(52) 3.000000e+11 0.000 0.000 + +! Reaction index: Chemkin #72; RMG #911 +! Template reaction: Birad_recombination +! Flux pairs: C4H6(50), C4H6(204); +! Estimated using template [R4;C_rad_out_2H;Cpri_rad_out_2H] for rate rule [R4_SDS;C_rad_out_2H;Cpri_rad_out_2H] +! Euclidian distance = 1.0 +! family: Birad_recombination +C4H6(50)=C4H6(204) 1.620000e+12 -0.305 1.980 + +! Reaction index: Chemkin #73; RMG #1037 +! Template reaction: Intra_Disproportionation +! Flux pairs: C4H6(50), C4H6(118); +! Estimated using an average for rate rule [R3radExo;Y_rad;XH_Rrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Intra_Disproportionation +C4H6(50)=C4H6(118) 1.487400e+09 1.045 15.153 + +! Reaction index: Chemkin #74; RMG #1136 +! Template reaction: Disproportionation +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(118)+C4H7(33) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #75; RMG #1202 +! Template reaction: Disproportionation +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H6(50)+C4H7(52)=C4H6(118)+C4H7(52) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #76; RMG #1649 +! Template reaction: 1,2-Birad_to_alkene +! Flux pairs: C4H6(50), C4H6(35); +! Matched reaction 5 C4H6 => C4H6-2 in 1,2-Birad_to_alkene/training +! This reaction matched rate rule [Y_12_01] +! family: 1,2-Birad_to_alkene +C4H6(50)=>C4H6(35) 5.010000e+07 0.000 0.000 + +! Reaction index: Chemkin #77; RMG #117 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H5(38); C#C(30), C3H5(38); +! Matched reaction 2253 C2H2 + CH3 <=> C3H5-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C#C(30)=C3H5(38) 1.338000e+05 2.410 6.770 + +! Reaction index: Chemkin #78; RMG #135 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H5(43); C#C(30), C4H5(43); +! Matched reaction 196 C2H2 + C2H3 <=> C4H5-8 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CdsJ-H] +! family: R_Addition_MultipleBond +C#C(30)+C2H3(14)=C4H5(43) 1.168000e+07 1.997 5.452 + +! Reaction index: Chemkin #79; RMG #764 +! Template reaction: R_Recombination +! Flux pairs: C4H5(43), C4H6(35); H(6), C4H6(35); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C +! Total Standard Deviation in ln(k): 6.83519320067 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(43)=C4H6(35) 9.988280e+13 0.006 0.000 + +! Reaction index: Chemkin #80; RMG #770 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(35), C4H5(43); +! From training reaction 1567 used for Cd/H2/NonDeC;C_methyl +! Exact match found for rate rule [Cd/H2/NonDeC;C_methyl] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +CH3(4)+C4H6(35)=CH4(3)+C4H5(43) 3.432000e-02 4.340 20.710 + +! Reaction index: Chemkin #81; RMG #778 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(35), C4H5(43); +! From training reaction 344 used for Cd/H2/NonDeC;C_rad/H2/Cs\H3 +! Exact match found for rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +C2H5(5)+C4H6(35)=ethane(1)+C4H5(43) 6.320000e+02 3.130 18.000 + +! Reaction index: Chemkin #82; RMG #782 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(13); C4H6(35), C4H5(43); +! From training reaction 217 used for Cd/H2/NonDeC;H_rad +! Exact match found for rate rule [Cd/H2/NonDeC;H_rad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +H(6)+C4H6(35)=H2(13)+C4H5(43) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #83; RMG #789 +! Template reaction: Disproportionation +! From training reaction 11 used for Cd_pri_rad;Cmethyl_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(43)=C2H4(9)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #84; RMG #808 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(35), C4H5(43); +! Matched reaction 177 C4H6-3 + C2H3 <=> C2H4 + C4H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;Cd_Cd\H2_pri_rad] +! family: H_Abstraction +C2H3(14)+C4H6(35)=C2H4(9)+C4H5(43) 3.437000e-04 4.732 6.579 + +! Reaction index: Chemkin #85; RMG #817 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(43)=C#C(30)+C4H6(35) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #86; RMG #908 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(43)+C4H7(33)=C4H6(35)+C4H6(35) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #87; RMG #909 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(43)+C4H7(52)=C4H6(35)+C4H6(35) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #88; RMG #1246 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C4H5(43)+C4H7(52)=C4H6(118)+C4H6(35) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #89; RMG #1563 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(118), C4H5(302); C4H5(43), C4H6(35); +! Estimated using an average for rate rule [Cd_allenic;Cd_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C4H5(43)+C4H6(118)=C4H5(302)+C4H6(35) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #90; RMG #2163 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H5(43), C4H5(611); +! From training reaction 14 used for R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH +! Exact match found for rate rule [R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH] +! Euclidian distance = 0 +! family: Intra_R_Add_Exocyclic +C4H5(43)=C4H5(611) 2.540000e+10 0.690 20.376 + +! Reaction index: Chemkin #91; RMG #2615 +! Template reaction: intra_H_migration +! Flux pairs: C4H5(611), C4H5(731); +! Estimated using an average for rate rule [R2H_S;C_rad_out_2H;Cs_H_out_noH] +! Euclidian distance = 0 +! family: intra_H_migration +C4H5(611)=C4H5(731) 5.846148e+01 3.158 23.534 + +! Reaction index: Chemkin #92; RMG #2917 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H4(812), C4H5(731); H(6), C4H5(731); +! Estimated using an average for rate rule [Cdd_Cds;HJ] +! Euclidian distance = 0 +! family: R_Addition_MultipleBond +H(6)+C4H4(812)=C4H5(731) 7.956368e+08 1.576 4.912 + +! Reaction index: Chemkin #93; RMG #2932 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); CH3(4), CH4(3); +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H5(731)=CH4(3)+C4H4(812) 6.708136e+12 0.000 6.000 + +! Reaction index: Chemkin #94; RMG #2943 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C2H5(5), ethane(1); +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H5(731)=ethane(1)+C4H4(812) 1.928000e+12 0.000 6.000 + +! Reaction index: Chemkin #95; RMG #2962 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); H(6), H2(13); +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H5(731)=H2(13)+C4H4(812) 6.020000e+12 0.000 6.000 + +! Reaction index: Chemkin #96; RMG #3006 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C2H3(14), C2H4(9); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(731)=C2H4(9)+C4H4(812) 4.820000e+12 0.000 6.000 + +! Reaction index: Chemkin #97; RMG #3259 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H5(302), C4H6(118); +! Estimated using template [Cd_rad;Cdpri_Csrad] for rate rule [Cd_rad/NonDeC;Cdpri_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(302)+C4H5(731)=C4H4(812)+C4H6(118) 4.820000e+12 0.000 6.000 + +! Reaction index: Chemkin #98; RMG #3270 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H6(50), C4H7(52); +! From training reaction 48 used for C_rad/H2/Cd;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cd;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H5(731)+C4H6(50)=C4H4(812)+C4H7(52) 3.372000e+11 0.000 6.000 + +! Reaction index: Chemkin #99; RMG #3291 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H6(50), C4H7(33); +! From training reaction 46 used for Y_rad;Cdpri_Csrad +! Exact match found for rate rule [Y_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H5(731)+C4H6(50)=C4H4(812)+C4H7(33) 1.204000e+13 0.000 6.000 + +! Reaction index: Chemkin #100; RMG #3324 +! Template reaction: Disproportionation +! Flux pairs: C4H5(731), C4H4(812); C4H5(43), C4H6(35); +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(731)+C4H5(43)=C4H4(812)+C4H6(35) 4.820000e+12 0.000 6.000 + +END + diff --git a/examples/scripts/mergeModels/Models/minimal_ml_species_dictionary.txt b/examples/scripts/mergeModels/Models/minimal_ml_species_dictionary.txt new file mode 100644 index 0000000000..4e197877c3 --- /dev/null +++ b/examples/scripts/mergeModels/Models/minimal_ml_species_dictionary.txt @@ -0,0 +1,302 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +ethane(1) +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} + +CH3(4) +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} + +C2H5(5) +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} + +CH4(3) +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} + +H(6) +multiplicity 2 +1 H u1 p0 c0 + +C2H4(9) +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} + +H2(13) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +C2H4(15) +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p1 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} + +C3H7(16) +multiplicity 2 +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 u1 p0 c0 {1,S} {9,S} {10,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} + +C2H3(14) +multiplicity 2 +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u1 p0 c0 {1,D} {5,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} + +C#C(30) +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} + +C2H2(37) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p1 c0 {1,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C4H7(33) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,D} {7,S} +3 C u1 p0 c0 {1,S} {8,S} {9,S} +4 C u0 p0 c0 {2,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(49) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} +3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} +4 C u1 p0 c0 {1,S} {10,S} {11,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 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(39) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {7,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,D} {10,S} +4 C u1 p0 c0 {3,D} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} +10 H u0 p0 c0 {3,S} +11 H u0 p0 c0 {4,S} + +C4H7(52) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {1,S} {3,S} {8,S} +3 C u0 p0 c0 {2,S} {4,D} {9,S} +4 C u0 p0 c0 {3,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H6(35) +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u0 p0 c0 {2,D} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(204) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {9,S} +4 C u0 p0 c0 {2,S} {3,D} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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 {4,S} + +C4H6(206) +1 C u0 p0 c0 {4,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {3,D} {4,S} {8,S} +3 C u0 p0 c0 {2,D} {9,S} {10,S} +4 C u0 p1 c0 {1,S} {2,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H6(118) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {4,D} {8,S} +3 C u0 p0 c0 {4,D} {9,S} {10,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H5(302) +multiplicity 2 +1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {4,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,T} +4 C u0 p0 c0 {2,S} {3,T} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} + +C4H6(262) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S} +4 C u0 p1 c0 {2,S} {3,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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} + +C4H6(50) +multiplicity 3 +1 C u0 p0 c0 {2,D} {3,S} {5,S} +2 C u0 p0 c0 {1,D} {4,S} {6,S} +3 C u1 p0 c0 {1,S} {7,S} {8,S} +4 C u1 p0 c0 {2,S} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C3H5(38) +multiplicity 2 +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 C u1 p0 c0 {2,D} {8,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} + +C4H5(43) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u1 p0 c0 {2,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H5(611) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,D} {6,S} +3 C u0 p0 c0 {1,S} {2,D} {7,S} +4 C u1 p0 c0 {1,S} {8,S} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {4,S} +9 H u0 p0 c0 {4,S} + +C4H5(731) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {1,S} {3,S} {4,S} +3 C u0 p0 c0 {2,S} {4,D} {8,S} +4 C u0 p0 c0 {2,S} {3,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H4(812) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {3,S} {4,D} +3 C u0 p0 c0 {2,S} {4,D} {8,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {3,S} + diff --git a/examples/scripts/mergeModels/Models/minimal_species_dictionary.txt b/examples/scripts/mergeModels/Models/minimal_species_dictionary.txt new file mode 100644 index 0000000000..d9cf2f5695 --- /dev/null +++ b/examples/scripts/mergeModels/Models/minimal_species_dictionary.txt @@ -0,0 +1,248 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +ethane(1) +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} + +CH3(4) +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} + +C2H5(5) +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} + +CH4(3) +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} + +H(6) +multiplicity 2 +1 H u1 p0 c0 + +C2H4(9) +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} + +H2(11) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +C3H7(16) +multiplicity 2 +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 u1 p0 c0 {1,S} {9,S} {10,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} + +C2H3(14) +multiplicity 2 +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u1 p0 c0 {1,D} {5,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} + +C#C(27) +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} + +C2H2(31) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p1 c0 {1,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C4H7(29) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,D} {7,S} +3 C u1 p0 c0 {1,S} {8,S} {9,S} +4 C u0 p0 c0 {2,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(41) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} +3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} +4 C u1 p0 c0 {1,S} {10,S} {11,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 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(33) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {7,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,D} {10,S} +4 C u1 p0 c0 {3,D} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} +10 H u0 p0 c0 {3,S} +11 H u0 p0 c0 {4,S} + +C4H7(45) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {3,D} {8,S} +3 C u0 p0 c0 {2,D} {4,S} {9,S} +4 C u1 p0 c0 {3,S} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H6(42) +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u0 p0 c0 {2,D} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(88) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {9,S} +4 C u0 p0 c0 {2,S} {3,D} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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 {4,S} + +C4H6(43) +multiplicity 3 +1 C u0 p0 c0 {2,D} {3,S} {5,S} +2 C u0 p0 c0 {1,D} {4,S} {6,S} +3 C u1 p0 c0 {1,S} {7,S} {8,S} +4 C u1 p0 c0 {2,S} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(69) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {4,D} {8,S} +3 C u0 p0 c0 {4,D} {9,S} {10,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H5(144) +multiplicity 2 +1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {4,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,T} +4 C u0 p0 c0 {2,S} {3,T} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} + +C3H5(32) +multiplicity 2 +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 C u1 p0 c0 {2,D} {8,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} + +C4H5(35) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u1 p0 c0 {2,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H5(185) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,D} {6,S} +3 C u0 p0 c0 {1,S} {2,D} {7,S} +4 C u1 p0 c0 {1,S} {8,S} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {4,S} +9 H u0 p0 c0 {4,S} + diff --git a/examples/scripts/mergeModels/Models/superminimal_chem.inp b/examples/scripts/mergeModels/Models/superminimal_chem.inp new file mode 100644 index 0000000000..b0799a6c0c --- /dev/null +++ b/examples/scripts/mergeModels/Models/superminimal_chem.inp @@ -0,0 +1,279 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + H2(1) ! H2(1) + O2(2) ! O2(2) + H(3) ! H(3) + HO2(4) ! [O]O(4) + OH(D)(5) ! OH(D)(5) + O(T)(6) ! O(T)(6) + OO(7) ! OO(7) + H2O(10) ! H2O(10) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 +H2(1) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo library: primaryThermoLibrary +O2(2) O 2 G 100.000 5000.000 1074.56 1 + 3.15382425E+00 1.67803802E-03-7.69971022E-07 1.51274714E-10-1.08781801E-14 2 +-1.04081878E+03 6.16753884E+00 3.53732181E+00-1.21570930E-03 5.31617826E-06 3 +-4.89443424E-09 1.45845042E-12-1.03858846E+03 4.68368406E+00 4 + +! Thermo library: primaryThermoLibrary +H(3) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) + radical(HOOJ) +HO2(4) O 2H 1 G 100.000 5000.000 932.13 1 + 3.21021575E+00 3.67945961E-03-1.27703899E-06 2.18050820E-10-1.46342588E-14 2 +-9.10359190E+02 8.18304670E+00 4.04595233E+00-1.73474005E-03 1.03769950E-05 3 +-1.02207268E-08 3.34930151E-12-9.86754562E+02 4.63578650E+00 4 + +! Thermo library: primaryThermoLibrary +OH(D)(5) O 1H 1 G 100.000 5000.000 1145.75 1 + 3.07194246E+00 6.04011411E-04-1.39759127E-08-2.13451563E-11 2.48070095E-15 2 + 3.57938557E+03 4.57798500E+00 3.51456768E+00 2.92814373E-05-5.32176582E-07 3 + 1.01950588E-09-3.85951152E-13 3.41425421E+03 2.10435015E+00 4 + +! Thermo library: primaryThermoLibrary +O(T)(6) O 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.92302441E+04 5.12616433E+00 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.92302441E+04 5.12616427E+00 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) +OO(7) O 2H 2 G 100.000 5000.000 908.86 1 + 5.41576461E+00 2.61012083E-03-4.39915287E-07 4.91143478E-11-3.35235545E-15 2 +-1.83029432E+04-4.02235599E+00 3.73136642E+00 3.35060430E-03 9.35072698E-06 3 +-1.52105192E-08 6.41611128E-12-1.77211712E+04 5.45907862E+00 4 + +! Thermo library: primaryThermoLibrary +H2O(10) O 1H 2 G 100.000 5000.000 1130.24 1 + 2.84324866E+00 2.75108838E-03-7.81033120E-07 1.07244016E-10-5.79395308E-15 2 +-2.99586120E+04 5.91043011E+00 4.05763610E+00-7.87938871E-04 2.90878480E-06 3 +-1.47520039E-09 2.12847506E-13-3.02815866E+04-3.11365027E-01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #1 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #2; RMG #4 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #3; RMG #2 +! Template reaction: H_Abstraction +! Flux pairs: O2(2), HO2(4); H2(1), H(3); +! Matched reaction 306 H2 + O2 <=> HO2_r12 + H in H_Abstraction/training +! This reaction matched rate rule [H2;O2b] +! family: H_Abstraction +O2(2)+H2(1)=H(3)+HO2(4) 2.900000e+14 0.000 56.640 + +! Reaction index: Chemkin #4; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: H(3), HO2(4); O2(2), HO2(4); +! Matched reaction 104 O2 + H <=> HO2-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! family: R_Recombination +O2(2)+H(3)=HO2(4) 8.790000e+10 1.000 0.450 + +! Reaction index: Chemkin #5; RMG #6 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); H(3), H2(1); +! Estimated using average of templates [O/H/NonDeO;H_rad] + [H2O2;Y_rad] for rate rule [H2O2;H_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +H(3)+OO(7)=HO2(4)+H2(1) 1.235020e+06 1.634 6.086 + +! Reaction index: Chemkin #6; RMG #8 +! Template reaction: R_Recombination +! Flux pairs: HO2(4), OO(7); H(3), OO(7); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(3)+HO2(4)=OO(7) 5.250690e+09 1.273 0.000 + +! Reaction index: Chemkin #7; RMG #9 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), OO(7); HO2(4), O2(2); +! Matched reaction 405 HO2_r3 + HO2_r12 <=> H2O2 + O2 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_rad/NonDeO] +! family: H_Abstraction +HO2(4)+HO2(4)=O2(2)+OO(7) 1.750000e+10 0.000 -3.275 + +! Reaction index: Chemkin #8; RMG #11 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), OO(7); OH(D)(5), OO(7); +! Matched reaction 96 OH + OH <=> H2O2 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_1COS->O_N-2R->C] +! family: R_Recombination +OH(D)(5)+OH(D)(5)=OO(7) 7.850000e+12 0.000 0.000 + +! Reaction index: Chemkin #9; RMG #13 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); H2(1), H(3); +! Matched reaction 312 H2 + OH <=> H2O_p + H_p in H_Abstraction/training +! This reaction matched rate rule [H2;O_pri_rad] +! family: H_Abstraction +OH(D)(5)+H2(1)=H(3)+H2O(10) 1.820000e+09 1.210 20.070 + +! Reaction index: Chemkin #10; RMG #17 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), H2O(10); H(3), H2O(10); +! Matched reaction 64 H + OH <=> H2O in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C] +! family: R_Recombination +H(3)+OH(D)(5)=H2O(10) 1.620000e+14 0.000 0.150 + +! Reaction index: Chemkin #11; RMG #18 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O2(2), HO2(4); +! Matched reaction 379 H2O + O2 <=> HO2_r12 + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_pri_rad] +! family: H_Abstraction +O2(2)+H2O(10)=OH(D)(5)+HO2(4) 9.300000e+12 0.000 74.120 + +! Reaction index: Chemkin #12; RMG #21 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); OO(7), HO2(4); +! Estimated using average of templates [O/H/NonDeO;O_pri_rad] + [H2O2;O_rad] for rate rule [H2O2;O_pri_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +OH(D)(5)+OO(7)=HO2(4)+H2O(10) 4.994995e+05 1.927 6.325 + +! Reaction index: Chemkin #13; RMG #5 +! Template reaction: Birad_R_Recombination +! Flux pairs: OH(D)(5), HO2(4); O(T)(6), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +! Reaction index: Chemkin #14; RMG #12 +! Template reaction: Birad_R_Recombination +! Flux pairs: H(3), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 4 H + O <=> HO in Birad_R_Recombination/training +! This reaction matched rate rule [H_rad;O_birad] +! family: Birad_R_Recombination +O(T)(6)+H(3)=OH(D)(5) 1.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #15; RMG #14 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), O2(2); O(T)(6), OH(D)(5); +! Estimated using average of templates [X_H;O_atom_triplet] + [Orad_O_H;Y_rad_birad_trirad_quadrad] for rate rule [Orad_O_H;O_atom_triplet] +! Euclidian distance = 2.0 +! family: H_Abstraction +O(T)(6)+HO2(4)=O2(2)+OH(D)(5) 3.680392e+09 0.678 5.899 + +! Reaction index: Chemkin #16; RMG #16 +! Template reaction: H_Abstraction +! Flux pairs: H2(1), H(3); O(T)(6), OH(D)(5); +! Matched reaction 285 H2 + O_rad <=> HO + H in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;H_rad] +! family: H_Abstraction +O(T)(6)+H2(1)=H(3)+OH(D)(5) 3.400000e+08 1.500 22.950 + +! Reaction index: Chemkin #17; RMG #19 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); O(T)(6), OH(D)(5); +! Estimated using template [O/H/NonDeO;O_atom_triplet] for rate rule [H2O2;O_atom_triplet] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +O(T)(6)+OO(7)=OH(D)(5)+HO2(4) 1.740000e+13 0.000 4.750 + +! Reaction index: Chemkin #18; RMG #22 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 380 H2O + O_rad <=> HO + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;O_pri_rad] +! family: H_Abstraction +O(T)(6)+H2O(10)=OH(D)(5)+OH(D)(5) 5.260000e+09 1.200 17.830 + +! Reaction index: Chemkin #19; RMG #25 +! Template reaction: Birad_R_Recombination +! Flux pairs: O(T)(6), HO2(4); OH(D)(5), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +END + diff --git a/examples/scripts/mergeModels/Models/superminimal_species_dictionary.txt b/examples/scripts/mergeModels/Models/superminimal_species_dictionary.txt new file mode 100644 index 0000000000..910547a04c --- /dev/null +++ b/examples/scripts/mergeModels/Models/superminimal_species_dictionary.txt @@ -0,0 +1,52 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +H2(1) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +O2(2) +multiplicity 3 +1 O u1 p2 c0 {2,S} +2 O u1 p2 c0 {1,S} + +H(3) +multiplicity 2 +1 H u1 p0 c0 + +HO2(4) +multiplicity 2 +1 O u0 p2 c0 {2,S} {3,S} +2 O u1 p2 c0 {1,S} +3 H u0 p0 c0 {1,S} + +OO(7) +1 O u0 p2 c0 {2,S} {3,S} +2 O u0 p2 c0 {1,S} {4,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} + +OH(D)(5) +multiplicity 2 +1 O u1 p2 c0 {2,S} +2 H u0 p0 c0 {1,S} + +H2O(10) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +O(T)(6) +multiplicity 3 +1 O u2 p2 c0 + diff --git a/examples/scripts/mergeModels/run.sh b/examples/scripts/mergeModels/run.sh new file mode 100644 index 0000000000..99ed8d16f4 --- /dev/null +++ b/examples/scripts/mergeModels/run.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +# merging two models +python ../../../scripts/mergeModels.py --model1 Models/minimal_chem.inp Models/minimal_species_dictionary.txt --model2 Models/superminimal_chem.inp Models/superminimal_species_dictionary.txt + +# merging three models +#python ../../../scripts/mergeModels.py --model1 Models/minimal_chem.inp Models/minimal_species_dictionary.txt --model2 Models/superminimal_chem.inp Models/superminimal_species_dictionary.txt --model3 Models/minimal_ml_chem.inp Models/minimal_ml_species_dictionary.txt From e8c774f197ae8496253f770ea8f2508d748c16aa Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 15:08:42 -0500 Subject: [PATCH 5/7] Example for generateFluxDiagram is added An example for scripts/generateFluxDiagram.py is added --- .../generateFluxDiagram/chem_annotated.inp | 279 ++++++++++++++++++ examples/scripts/generateFluxDiagram/input.py | 55 ++++ examples/scripts/generateFluxDiagram/run.sh | 4 + .../species_dictionary.txt | 52 ++++ 4 files changed, 390 insertions(+) create mode 100644 examples/scripts/generateFluxDiagram/chem_annotated.inp create mode 100644 examples/scripts/generateFluxDiagram/input.py create mode 100755 examples/scripts/generateFluxDiagram/run.sh create mode 100644 examples/scripts/generateFluxDiagram/species_dictionary.txt diff --git a/examples/scripts/generateFluxDiagram/chem_annotated.inp b/examples/scripts/generateFluxDiagram/chem_annotated.inp new file mode 100644 index 0000000000..b0799a6c0c --- /dev/null +++ b/examples/scripts/generateFluxDiagram/chem_annotated.inp @@ -0,0 +1,279 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + H2(1) ! H2(1) + O2(2) ! O2(2) + H(3) ! H(3) + HO2(4) ! [O]O(4) + OH(D)(5) ! OH(D)(5) + O(T)(6) ! O(T)(6) + OO(7) ! OO(7) + H2O(10) ! H2O(10) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 +H2(1) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo library: primaryThermoLibrary +O2(2) O 2 G 100.000 5000.000 1074.56 1 + 3.15382425E+00 1.67803802E-03-7.69971022E-07 1.51274714E-10-1.08781801E-14 2 +-1.04081878E+03 6.16753884E+00 3.53732181E+00-1.21570930E-03 5.31617826E-06 3 +-4.89443424E-09 1.45845042E-12-1.03858846E+03 4.68368406E+00 4 + +! Thermo library: primaryThermoLibrary +H(3) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) + radical(HOOJ) +HO2(4) O 2H 1 G 100.000 5000.000 932.13 1 + 3.21021575E+00 3.67945961E-03-1.27703899E-06 2.18050820E-10-1.46342588E-14 2 +-9.10359190E+02 8.18304670E+00 4.04595233E+00-1.73474005E-03 1.03769950E-05 3 +-1.02207268E-08 3.34930151E-12-9.86754562E+02 4.63578650E+00 4 + +! Thermo library: primaryThermoLibrary +OH(D)(5) O 1H 1 G 100.000 5000.000 1145.75 1 + 3.07194246E+00 6.04011411E-04-1.39759127E-08-2.13451563E-11 2.48070095E-15 2 + 3.57938557E+03 4.57798500E+00 3.51456768E+00 2.92814373E-05-5.32176582E-07 3 + 1.01950588E-09-3.85951152E-13 3.41425421E+03 2.10435015E+00 4 + +! Thermo library: primaryThermoLibrary +O(T)(6) O 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.92302441E+04 5.12616433E+00 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.92302441E+04 5.12616427E+00 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) +OO(7) O 2H 2 G 100.000 5000.000 908.86 1 + 5.41576461E+00 2.61012083E-03-4.39915287E-07 4.91143478E-11-3.35235545E-15 2 +-1.83029432E+04-4.02235599E+00 3.73136642E+00 3.35060430E-03 9.35072698E-06 3 +-1.52105192E-08 6.41611128E-12-1.77211712E+04 5.45907862E+00 4 + +! Thermo library: primaryThermoLibrary +H2O(10) O 1H 2 G 100.000 5000.000 1130.24 1 + 2.84324866E+00 2.75108838E-03-7.81033120E-07 1.07244016E-10-5.79395308E-15 2 +-2.99586120E+04 5.91043011E+00 4.05763610E+00-7.87938871E-04 2.90878480E-06 3 +-1.47520039E-09 2.12847506E-13-3.02815866E+04-3.11365027E-01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #1 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #2; RMG #4 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #3; RMG #2 +! Template reaction: H_Abstraction +! Flux pairs: O2(2), HO2(4); H2(1), H(3); +! Matched reaction 306 H2 + O2 <=> HO2_r12 + H in H_Abstraction/training +! This reaction matched rate rule [H2;O2b] +! family: H_Abstraction +O2(2)+H2(1)=H(3)+HO2(4) 2.900000e+14 0.000 56.640 + +! Reaction index: Chemkin #4; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: H(3), HO2(4); O2(2), HO2(4); +! Matched reaction 104 O2 + H <=> HO2-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! family: R_Recombination +O2(2)+H(3)=HO2(4) 8.790000e+10 1.000 0.450 + +! Reaction index: Chemkin #5; RMG #6 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); H(3), H2(1); +! Estimated using average of templates [O/H/NonDeO;H_rad] + [H2O2;Y_rad] for rate rule [H2O2;H_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +H(3)+OO(7)=HO2(4)+H2(1) 1.235020e+06 1.634 6.086 + +! Reaction index: Chemkin #6; RMG #8 +! Template reaction: R_Recombination +! Flux pairs: HO2(4), OO(7); H(3), OO(7); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(3)+HO2(4)=OO(7) 5.250690e+09 1.273 0.000 + +! Reaction index: Chemkin #7; RMG #9 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), OO(7); HO2(4), O2(2); +! Matched reaction 405 HO2_r3 + HO2_r12 <=> H2O2 + O2 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_rad/NonDeO] +! family: H_Abstraction +HO2(4)+HO2(4)=O2(2)+OO(7) 1.750000e+10 0.000 -3.275 + +! Reaction index: Chemkin #8; RMG #11 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), OO(7); OH(D)(5), OO(7); +! Matched reaction 96 OH + OH <=> H2O2 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_1COS->O_N-2R->C] +! family: R_Recombination +OH(D)(5)+OH(D)(5)=OO(7) 7.850000e+12 0.000 0.000 + +! Reaction index: Chemkin #9; RMG #13 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); H2(1), H(3); +! Matched reaction 312 H2 + OH <=> H2O_p + H_p in H_Abstraction/training +! This reaction matched rate rule [H2;O_pri_rad] +! family: H_Abstraction +OH(D)(5)+H2(1)=H(3)+H2O(10) 1.820000e+09 1.210 20.070 + +! Reaction index: Chemkin #10; RMG #17 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), H2O(10); H(3), H2O(10); +! Matched reaction 64 H + OH <=> H2O in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C] +! family: R_Recombination +H(3)+OH(D)(5)=H2O(10) 1.620000e+14 0.000 0.150 + +! Reaction index: Chemkin #11; RMG #18 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O2(2), HO2(4); +! Matched reaction 379 H2O + O2 <=> HO2_r12 + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_pri_rad] +! family: H_Abstraction +O2(2)+H2O(10)=OH(D)(5)+HO2(4) 9.300000e+12 0.000 74.120 + +! Reaction index: Chemkin #12; RMG #21 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); OO(7), HO2(4); +! Estimated using average of templates [O/H/NonDeO;O_pri_rad] + [H2O2;O_rad] for rate rule [H2O2;O_pri_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +OH(D)(5)+OO(7)=HO2(4)+H2O(10) 4.994995e+05 1.927 6.325 + +! Reaction index: Chemkin #13; RMG #5 +! Template reaction: Birad_R_Recombination +! Flux pairs: OH(D)(5), HO2(4); O(T)(6), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +! Reaction index: Chemkin #14; RMG #12 +! Template reaction: Birad_R_Recombination +! Flux pairs: H(3), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 4 H + O <=> HO in Birad_R_Recombination/training +! This reaction matched rate rule [H_rad;O_birad] +! family: Birad_R_Recombination +O(T)(6)+H(3)=OH(D)(5) 1.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #15; RMG #14 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), O2(2); O(T)(6), OH(D)(5); +! Estimated using average of templates [X_H;O_atom_triplet] + [Orad_O_H;Y_rad_birad_trirad_quadrad] for rate rule [Orad_O_H;O_atom_triplet] +! Euclidian distance = 2.0 +! family: H_Abstraction +O(T)(6)+HO2(4)=O2(2)+OH(D)(5) 3.680392e+09 0.678 5.899 + +! Reaction index: Chemkin #16; RMG #16 +! Template reaction: H_Abstraction +! Flux pairs: H2(1), H(3); O(T)(6), OH(D)(5); +! Matched reaction 285 H2 + O_rad <=> HO + H in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;H_rad] +! family: H_Abstraction +O(T)(6)+H2(1)=H(3)+OH(D)(5) 3.400000e+08 1.500 22.950 + +! Reaction index: Chemkin #17; RMG #19 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); O(T)(6), OH(D)(5); +! Estimated using template [O/H/NonDeO;O_atom_triplet] for rate rule [H2O2;O_atom_triplet] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +O(T)(6)+OO(7)=OH(D)(5)+HO2(4) 1.740000e+13 0.000 4.750 + +! Reaction index: Chemkin #18; RMG #22 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 380 H2O + O_rad <=> HO + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;O_pri_rad] +! family: H_Abstraction +O(T)(6)+H2O(10)=OH(D)(5)+OH(D)(5) 5.260000e+09 1.200 17.830 + +! Reaction index: Chemkin #19; RMG #25 +! Template reaction: Birad_R_Recombination +! Flux pairs: O(T)(6), HO2(4); OH(D)(5), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +END + diff --git a/examples/scripts/generateFluxDiagram/input.py b/examples/scripts/generateFluxDiagram/input.py new file mode 100644 index 0000000000..98be011097 --- /dev/null +++ b/examples/scripts/generateFluxDiagram/input.py @@ -0,0 +1,55 @@ +# Data sources +database( + thermoLibraries = ['primaryThermoLibrary'], + reactionLibraries = [], + seedMechanisms = [], + kineticsDepositories = ['training'], + kineticsFamilies = ['H_Abstraction','Disproportionation','R_Recombination', + 'Birad_recombination', 'Birad_R_Recombination'], + kineticsEstimator = 'rate rules', +) + +# List of species +species( + label='H2', + reactive=True, + structure=SMILES("[H][H]"), +) +species( + label='O2', + reactive=True, + structure=SMILES("[O][O]"), +) + +# Reaction systems +simpleReactor( + temperature=(1000,'K'), + pressure=(1.0,'bar'), + initialMoleFractions={ + 'H2':.67, 'O2':.33, + }, + terminationConversion={ + 'H2': 0.9, + }, + terminationTime=(1e6,'s'), +) + +simulator( + atol=1e-16, + rtol=1e-8, +) + +model( + toleranceKeepInEdge=0.0, + toleranceMoveToCore=0.001, + toleranceInterruptSimulation=0.001, + maximumEdgeSpecies=100000, +) + +options( + units='si', + generateOutputHTML=True, + generatePlots=False, + saveEdgeSpecies=True, + saveSimulationProfiles=True, +) diff --git a/examples/scripts/generateFluxDiagram/run.sh b/examples/scripts/generateFluxDiagram/run.sh new file mode 100755 index 0000000000..77a36c91cb --- /dev/null +++ b/examples/scripts/generateFluxDiagram/run.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Run generateFluxDiagram.py on a RMG input file, a Chemkin input file, and a RMG species dictionary file +python ../../../scripts/generateFluxDiagram.py input.py chem_annotated.inp species_dictionary.txt diff --git a/examples/scripts/generateFluxDiagram/species_dictionary.txt b/examples/scripts/generateFluxDiagram/species_dictionary.txt new file mode 100644 index 0000000000..910547a04c --- /dev/null +++ b/examples/scripts/generateFluxDiagram/species_dictionary.txt @@ -0,0 +1,52 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +H2(1) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +O2(2) +multiplicity 3 +1 O u1 p2 c0 {2,S} +2 O u1 p2 c0 {1,S} + +H(3) +multiplicity 2 +1 H u1 p0 c0 + +HO2(4) +multiplicity 2 +1 O u0 p2 c0 {2,S} {3,S} +2 O u1 p2 c0 {1,S} +3 H u0 p0 c0 {1,S} + +OO(7) +1 O u0 p2 c0 {2,S} {3,S} +2 O u0 p2 c0 {1,S} {4,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} + +OH(D)(5) +multiplicity 2 +1 O u1 p2 c0 {2,S} +2 H u0 p0 c0 {1,S} + +H2O(10) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +O(T)(6) +multiplicity 3 +1 O u2 p2 c0 + From fa822af08923944ee730eed2f452646eed862d62 Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Wed, 27 Nov 2019 16:36:58 -0500 Subject: [PATCH 6/7] added an example for standardizeModelSpeceisNames An exmaple for scripts/standardizeModelSpeceisNames.py is added --- .../Models/minimal_chem.inp | 892 ++++++++++++++++++ .../Models/minimal_species_dictionary.txt | 248 +++++ .../Models/superminimal_chem.inp | 279 ++++++ .../superminimal_species_dictionary.txt | 52 + .../standardizeModelSpeciesNames/run.sh | 4 + 5 files changed, 1475 insertions(+) create mode 100644 examples/scripts/standardizeModelSpeciesNames/Models/minimal_chem.inp create mode 100644 examples/scripts/standardizeModelSpeciesNames/Models/minimal_species_dictionary.txt create mode 100644 examples/scripts/standardizeModelSpeciesNames/Models/superminimal_chem.inp create mode 100644 examples/scripts/standardizeModelSpeciesNames/Models/superminimal_species_dictionary.txt create mode 100644 examples/scripts/standardizeModelSpeciesNames/run.sh diff --git a/examples/scripts/standardizeModelSpeciesNames/Models/minimal_chem.inp b/examples/scripts/standardizeModelSpeciesNames/Models/minimal_chem.inp new file mode 100644 index 0000000000..32e0e375ca --- /dev/null +++ b/examples/scripts/standardizeModelSpeciesNames/Models/minimal_chem.inp @@ -0,0 +1,892 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + ethane(1) ! ethane(1) + CH4(3) ! CH4(3) + CH3(4) ! [CH3](4) + C2H5(5) ! C[CH2](5) + H(6) ! H(6) + C2H4(9) ! C=C(9) + H2(11) ! H2(11) + C2H3(14) ! [CH]=C(14) + C3H7(16) ! [CH2]CC(16) + C#C(27) ! C#C(27) + C4H7(29) ! [CH2]CC=C(29) + C2H2(31) ! [C]=C(31) + C3H5(32) ! [CH]=CC(32) + C4H7(33) ! [CH]=CCC(33) + C4H5(35) ! [CH]=CC=C(35) + C4H7(41) ! [CH2]C1CC1(41) + C4H6(42) ! C=CC=C(42) + C4H6(43) ! [CH2][CH]C=C(43) + C4H7(45) ! C=C[CH]C(45) + C4H6(69) ! C=C=CC(69) + C4H6(88) ! C1=CCC1(88) + C4H5(144) ! C=C=[C]C(144) + C4H5(185) ! [CH2]C1C=C1(185) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) +ethane(1) C 2H 6 G 100.000 5000.000 954.51 1 + 4.58979444E+00 1.41508381E-02-4.75965886E-06 8.60303158E-10-6.21724057E-14 2 +-1.27217503E+04-3.61718429E+00 3.78034607E+00-3.24276485E-03 5.52385525E-05 3 +-6.38587905E-08 2.28640069E-11-1.16203414E+04 5.21029625E+00 4 + +! Thermo library: primaryThermoLibrary +CH4(3) C 1H 4 G 100.000 5000.000 1084.12 1 + 9.08265721E-01 1.14540858E-02-4.57173828E-06 8.29191671E-10-5.66314895E-14 2 +-9.71997444E+03 1.39930944E+01 4.20541524E+00-5.35557362E-03 2.51123265E-05 3 +-2.13762843E-08 5.97523937E-12-1.01619433E+04-9.21279283E-01 4 + +! Thermo library: primaryThermoLibrary + radical(CH3) +CH3(4) C 1H 3 G 100.000 5000.000 1337.63 1 + 3.54145749E+00 4.76786834E-03-1.82148425E-06 3.28876586E-10-2.22545593E-14 2 + 1.62239579E+04 1.66034967E+00 3.91546761E+00 1.84154323E-03 3.48741760E-06 3 +-3.32747607E-09 8.49956882E-13 1.62856394E+04 3.51741490E-01 4 + +! Thermo group additivity estimation: group(Cs-CsHHH) + group(Cs-CsHHH) + radical(CCJ) +C2H5(5) C 2H 5 G 100.000 5000.000 900.31 1 + 5.15621623E+00 9.43121232E-03-1.81945206E-06 2.21193866E-10-1.43479695E-14 2 + 1.20640796E+04-2.91102815E+00 3.82183329E+00-3.43357093E-03 5.09256026E-05 3 +-6.20209847E-08 2.37072520E-11 1.30660130E+04 7.61644314E+00 4 + +! Thermo library: primaryThermoLibrary +H(6) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) +C2H4(9) C 2H 4 G 100.000 5000.000 940.45 1 + 5.20299386E+00 7.82442468E-03-2.12683407E-06 3.79690544E-10-2.94670706E-14 2 + 3.93628131E+03-6.62410904E+00 3.97974441E+00-7.57559895E-03 5.52973238E-05 3 +-6.36221688E-08 2.31767197E-11 5.07746086E+03 4.04622760E+00 4 + +! Thermo library: primaryThermoLibrary +H2(11) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C2H3(14) C 2H 3 G 100.000 5000.000 931.96 1 + 5.44796550E+00 4.98356138E-03-1.08820775E-06 1.79837309E-10-1.45096285E-14 2 + 3.38297746E+04-4.87808224E+00 3.90670547E+00-4.06241062E-03 3.86780039E-05 3 +-4.62976404E-08 1.72900384E-11 3.47971783E+04 6.09788968E+00 4 + +! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsHHH) + group(Cs-CsHHH) + radical(RCCJ) +C3H7(16) C 3H 7 G 100.000 5000.000 995.41 1 + 5.69430979E+00 1.96033402E-02-7.42049648E-06 1.35882956E-09-9.56214889E-14 2 + 8.87584826E+03-4.32889887E+00 3.09191302E+00 1.32172474E-02 2.75847569E-05 3 +-3.90848844E-08 1.43313303E-11 1.02284118E+04 1.24057873E+01 4 + +! Thermo group additivity estimation: group(Ct-CtH) + group(Ct-CtH) +C#C(27) C 2H 2 G 100.000 5000.000 888.63 1 + 5.76204511E+00 2.37158782E-03-1.49582699E-07-2.19154662E-11 2.21779207E-15 2 + 2.50944501E+04-9.82608488E+00 3.03574736E+00 7.71239020E-03 2.53493006E-06 3 +-1.08133128E-08 5.50757058E-12 2.58526443E+04 4.54461297E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(RCCJ) +C4H7(29) C 4H 7 G 100.000 5000.000 1000.95 1 + 7.59479951E+00 2.06424593E-02-7.89782526E-06 1.45964270E-09-1.03413353E-13 2 + 2.08073058E+04-1.19159668E+01 2.68059468E+00 2.10828055E-02 2.02114983E-05 3 +-3.64232761E-08 1.41440404E-11 2.27528020E+04 1.66009256E+01 4 + +! Thermo group additivity estimation: group(Cds-CdsHH) + group(CdJ2_singlet-Cds) +C2H2(31) C 2H 2 G 100.000 5000.000 1423.26 1 + 4.43041986E+00 4.87757420E-03-1.79374459E-06 3.04085410E-10-1.96652162E-14 2 + 4.78744103E+04-1.67075241E-01 3.69251650E+00 6.06584723E-03-2.11277596E-06 3 + 1.63533182E-11 1.07665581E-13 4.81741496E+04 3.96842354E+00 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C3H5(32) C 3H 5 G 100.000 5000.000 997.87 1 + 5.66465812E+00 1.44326998E-02-5.46743137E-06 1.00159120E-09-7.04869894E-14 2 + 2.93871077E+04-4.48482420E+00 3.23409465E+00 1.18206723E-02 1.70311418E-05 3 +-2.64373876E-08 9.91250979E-12 3.04873059E+04 1.03182315E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P) +C4H7(33) C 4H 7 G 100.000 5000.000 999.92 1 + 8.06557472E+00 2.00625202E-02-7.60832471E-06 1.39784272E-09-9.86871188E-14 2 + 2.57831993E+04-1.54387855E+01 2.56532733E+00 2.39244964E-02 1.38115950E-05 3 +-3.10269360E-08 1.25444431E-11 2.77900540E+04 1.56311184E+01 4 + +! Thermo group additivity estimation: group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + group(Cds-CdsHH) + radical(Cds_P) +C4H5(35) C 4H 5 G 100.000 5000.000 935.58 1 + 1.13227703E+01 8.94049131E-03-2.08006868E-06 3.38974080E-10-2.61949890E-14 2 + 3.83166548E+04-3.40911798E+01 2.61016310E+00 2.04314979E-02 2.07961080E-05 3 +-4.53910308E-08 2.00574491E-11 4.10742701E+04 1.33868405E+01 4 + +! Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-CsCsHH) + group(Cs-CsCsHH) + group(Cs-CsHHH) + ring(Cyclopropane) + radical(Isobutyl) +C4H7(41) C 4H 7 G 100.000 5000.000 926.07 1 + 1.02346424E+01 1.41131644E-02-2.99925371E-06 4.56620522E-10-3.49799664E-14 2 + 2.27933498E+04-2.92349187E+01 3.04736554E+00 5.45571385E-03 7.53308215E-05 3 +-1.02226599E-07 4.01828021E-11 2.58269388E+04 1.40791072E+01 4 + +! Thermo group additivity estimation: group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + group(Cds-CdsHH) +C4H6(42) C 4H 6 G 100.000 5000.000 940.95 1 + 1.10823465E+01 1.17735303E-02-3.11414472E-06 5.37745823E-10-4.10623132E-14 2 + 8.42127950E+03-3.51696040E+01 2.68205225E+00 1.69322825E-02 3.73648473E-05 3 +-6.26479964E-08 2.59146511E-11 1.13546018E+04 1.20324202E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + radical(Allyl_P) + +! radical(Allyl_P) +C4H6(43) C 4H 6 G 100.000 5000.000 961.83 1 + 9.92849001E+00 1.51088208E-02-5.13560211E-06 9.43569819E-10-6.92734560E-14 2 + 3.02829926E+04-2.74906163E+01 2.65638077E+00 1.89337507E-02 3.00987228E-05 3 +-5.20344307E-08 2.11232146E-11 3.29038799E+04 1.36624695E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + radical(Allyl_P) +C4H7(45) C 4H 7 G 100.000 5000.000 998.56 1 + 7.82800811E+00 2.08400863E-02-7.96754424E-06 1.47337839E-09-1.04525635E-13 2 + 1.26472412E+04-1.58820365E+01 2.64214371E+00 2.15952609E-02 2.09688717E-05 3 +-3.79216452E-08 1.47847719E-11 1.46809427E+04 1.41266132E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + group(Cdd-CdsCds) +C4H6(69) C 4H 6 G 100.000 5000.000 1063.05 1 + 6.93544552E+00 1.97136368E-02-7.88231275E-06 1.45446865E-09-1.01396113E-13 2 + 1.61162804E+04-1.12054239E+01 2.67091213E+00 2.38372295E-02 3.12253865E-06 3 +-1.59972758E-08 6.48389677E-12 1.76966515E+04 1.27978754E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + ring(Cyclobutene) +C4H6(88) C 4H 6 G 100.000 5000.000 950.24 1 + 9.42741835E+00 1.39644294E-02-4.06892046E-06 7.75033524E-10-6.20421269E-14 2 + 1.43343164E+04-2.81799733E+01 3.39621343E+00-3.43725308E-03 9.09465048E-05 3 +-1.13274520E-07 4.24110728E-11 1.74123946E+04 1.07743991E+01 4 + +! Thermo group additivity estimation: group(Cs-CtHHH) + group(Cs-CtHHH) + group(Ct-CtCs) + group(Ct-CtCs) + radical(Propargyl) +C4H5(144) C 4H 5 G 100.000 5000.000 942.37 1 + 6.33626737E+00 1.64827848E-02-5.56208397E-06 9.43126364E-10-6.35802263E-14 2 + 3.32941157E+04-6.00339957E+00 2.92156480E+00 1.88274652E-02 1.00444412E-05 3 +-2.37783426E-08 1.01241167E-11 3.44771699E+04 1.31301921E+01 4 + +! Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsHHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + ring(Cyclopropene) + +! radical(Isobutyl) +C4H5(185) C 4H 5 G 100.000 5000.000 922.39 1 + 7.72013271E+00 1.42822671E-02-4.41414586E-06 7.16675938E-10-4.76705841E-14 2 + 5.22310734E+04-1.47167968E+01 2.73381733E+00 2.27303683E-02 3.27346179E-06 3 +-2.03255440E-08 9.85275484E-12 5.37114183E+04 1.19746599E+01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #2 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), ethane(1); CH3(4), ethane(1); +! Matched reaction 9 CH3 + CH3 <=> C2H6 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing] +! family: R_Recombination +CH3(4)+CH3(4)=ethane(1) 9.450000e+14 -0.538 0.135 + +! Reaction index: Chemkin #2; RMG #5 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); ethane(1), C2H5(5); +! Matched reaction 215 C2H6 + CH3_r3 <=> C2H5b + CH4 in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;C_methyl] +! family: H_Abstraction +CH3(4)+ethane(1)=CH4(3)+C2H5(5) 3.500000e+01 3.440 10.384 + +! Reaction index: Chemkin #3; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: C2H5(5), ethane(1); H(6), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #4; RMG #12 +! Template reaction: R_Recombination +! Flux pairs: CH3(4), CH4(3); H(6), CH4(3); +! Matched reaction 57 H + CH3 <=> CH4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C] +! family: R_Recombination +H(6)+CH3(4)=CH4(3) 1.930000e+14 0.000 0.270 + +! Reaction index: Chemkin #5; RMG #24 +! Template reaction: R_Recombination +! Flux pairs: H(6), ethane(1); C2H5(5), ethane(1); +! Matched reaction 58 H + C2H5 <=> C2H6-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N-Sp-3R!H=2C_3R!H->C_Sp-3C-2C] +! family: R_Recombination +H(6)+C2H5(5)=ethane(1) 1.000000e+14 0.000 0.000 +DUPLICATE + +! Reaction index: Chemkin #6; RMG #9 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H4(9), C2H5(5); H(6), C2H5(5); +! 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(6)+C2H4(9)=C2H5(5) 4.620000e+08 1.640 1.010 + +! Reaction index: Chemkin #7; RMG #13 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); CH3(4), CH4(3); +! Matched reaction 5 CH3 + C2H5 <=> CH4 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_methyl;Cmethyl_Csrad] +! family: Disproportionation +CH3(4)+C2H5(5)=CH4(3)+C2H4(9) 6.570000e+14 -0.680 0.000 + +! Reaction index: Chemkin #8; RMG #17 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); C2H5(5), ethane(1); +! Matched reaction 6 C2H5 + C2H5-2 <=> C2H6 + C2H4 in Disproportionation/training +! This reaction matched rate rule [C_rad/H2/Cs;Cmethyl_Csrad] +! family: Disproportionation +C2H5(5)+C2H5(5)=C2H4(9)+ethane(1) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #9; RMG #20 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); ethane(1), C2H5(5); +! Matched reaction 210 C2H6 + H <=> C2H5b + H2_p in H_Abstraction/training +! This reaction matched rate rule [C/H3/Cs\H3;H_rad] +! family: H_Abstraction +H(6)+ethane(1)=H2(11)+C2H5(5) 1.150000e+08 1.900 7.530 + +! Reaction index: Chemkin #10; RMG #22 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), C2H4(9); H(6), H2(11); +! Matched reaction 4 H + C2H5 <=> H2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [H_rad;Cmethyl_Csrad] +! family: Disproportionation +H(6)+C2H5(5)=H2(11)+C2H4(9) 1.083000e+13 0.000 0.000 + +! Reaction index: Chemkin #11; RMG #25 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); CH4(3), CH3(4); +! Matched reaction 186 CH4b + H <=> CH3_p1 + H2_p in H_Abstraction/training +! This reaction matched rate rule [C_methane;H_rad] +! family: H_Abstraction +H(6)+CH4(3)=H2(11)+CH3(4) 4.100000e+03 3.156 8.755 + +! Reaction index: Chemkin #12; RMG #26 +! Template reaction: R_Recombination +! Flux pairs: H(6), H2(11); H(6), H2(11); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(6)+H(6)=H2(11) 5.450000e+10 0.000 1.500 + +! Reaction index: Chemkin #13; RMG #31 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H7(16); C2H4(9), C3H7(16); +! Matched reaction 219 CH3 + C2H4 <=> C3H7 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C2H4(9)=C3H7(16) 4.180000e+04 2.410 5.630 + +! Reaction index: Chemkin #14; RMG #27 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C2H4(9); H(6), C2H4(9); +! Matched reaction 60 H + C2H3 <=> C2H4 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! family: R_Recombination +H(6)+C2H3(14)=C2H4(9) 1.210000e+14 0.000 0.000 + +! Reaction index: Chemkin #15; RMG #30 +! Template reaction: H_Abstraction +! Flux pairs: CH4(3), CH3(4); C2H3(14), C2H4(9); +! Matched reaction 843 C2H3 + CH4b <=> C2H4 + CH3_p23 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_methyl] +! family: H_Abstraction +CH4(3)+C2H3(14)=CH3(4)+C2H4(9) 2.236000e-02 4.340 5.700 + +! Reaction index: Chemkin #16; RMG #34 +! Template reaction: H_Abstraction +! Flux pairs: ethane(1), C2H5(5); C2H3(14), C2H4(9); +! Matched reaction 775 C2H3 + C2H6 <=> C2H4 + C2H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! family: H_Abstraction +C2H3(14)+ethane(1)=C2H4(9)+C2H5(5) 1.080000e-03 4.550 3.500 + +! Reaction index: Chemkin #17; RMG #36 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); C2H4(9), C2H3(14); +! Matched reaction 217 C2H4 + H <=> C2H3_p + H2_p in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;H_rad] +! family: H_Abstraction +H(6)+C2H4(9)=H2(11)+C2H3(14) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #18; RMG #39 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C2H4(9); C2H5(5), C2H4(9); +! Matched reaction 11 C2H3-2 + C2H5 <=> C2H4-2 + C2H4 in Disproportionation/training +! This reaction matched rate rule [Cd_pri_rad;Cmethyl_Csrad] +! family: Disproportionation +C2H3(14)+C2H5(5)=C2H4(9)+C2H4(9) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #19; RMG #55 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C#C(27), C2H3(14); H(6), C2H3(14); +! Matched reaction 2697 H + C2H2 <=> C2H3-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;HJ] +! family: R_Addition_MultipleBond +H(6)+C#C(27)=C2H3(14) 1.030000e+09 1.640 2.110 + +! Reaction index: Chemkin #20; RMG #66 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), ethane(1); C2H3(14), C#C(27); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cs;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H5(5)=C#C(27)+ethane(1) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #21; RMG #74 +! Template reaction: Disproportionation +! Flux pairs: CH3(4), CH4(3); C2H3(14), C#C(27); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_methyl;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C2H3(14)=CH4(3)+C#C(27) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #22; RMG #77 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C#C(27); C2H3(14), C2H4(9); +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C2H3(14)=C#C(27)+C2H4(9) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #23; RMG #79 +! Template reaction: Disproportionation +! Flux pairs: H(6), H2(11); C2H3(14), C#C(27); +! Estimated using template [H_rad;Cds/H2_d_Rrad] for rate rule [H_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C2H3(14)=H2(11)+C#C(27) 6.788225e+08 1.500 -0.890 + +! Reaction index: Chemkin #24; RMG #65 +! Template reaction: Singlet_Carbene_Intra_Disproportionation +! Flux pairs: C2H2(31), C#C(27); +! Estimated using template [singletcarbene_CH;singletcarbene;CH] for rate rule [CdJ2=C;CdJ2;CdH2] +! Euclidian distance = 1.7320508075688772 +! Multiplied by reaction path degeneracy 2.0 +! family: Singlet_Carbene_Intra_Disproportionation +C2H2(31)=C#C(27) 1.599708e+13 -0.202 8.145 + +! Reaction index: Chemkin #25; RMG #62 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H7(29); C2H4(9), C4H7(29); +! Matched reaction 234 C2H3 + C2H4 <=> C4H7-3 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-HH;CdsJ-H] +! family: R_Addition_MultipleBond +C2H3(14)+C2H4(9)=C4H7(29) 2.860000e+04 2.410 1.800 + +! Reaction index: Chemkin #26; RMG #91 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H7(29), C4H7(41); +! Matched reaction 335 C4H7 <=> C4H7-2 in Intra_R_Add_Exocyclic/training +! This reaction matched rate rule [R4_S_D;doublebond_intra_2H_pri;radadd_intra_cs2H] +! family: Intra_R_Add_Exocyclic +C4H7(29)=C4H7(41) 6.320000e+08 0.970 8.900 + +! Reaction index: Chemkin #27; RMG #73 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H5(5), C4H7(33); C#C(27), C4H7(33); +! Matched reaction 2254 C2H2 + C2H5 <=> C4H7-6 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-CsHH] +! family: R_Addition_MultipleBond +C#C(27)+C2H5(5)=C4H7(33) 1.360000e+04 2.410 6.200 + +! Reaction index: Chemkin #28; RMG #99 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(29); +! Estimated using template [R4H_DSS;Cd_rad_out_singleH;Cs_H_out] for rate rule [R4H_DSS;Cd_rad_out_singleH;Cs_H_out_2H] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: intra_H_migration +C4H7(33)=C4H7(29) 1.113000e+05 2.230 10.590 + +! Reaction index: Chemkin #29; RMG #97 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(29), C4H7(45); +! Matched reaction 84 C:CC[CH2] <=> C:C[CH]C in intra_H_migration/training +! This reaction matched rate rule [R2H_S;C_rad_out_2H;Cs_H_out_H/Cd] +! family: intra_H_migration +C4H7(29)=C4H7(45) 1.720000e+06 1.990 27.200 + +! Reaction index: Chemkin #30; RMG #146 +! Template reaction: intra_H_migration +! Flux pairs: C4H7(33), C4H7(45); +! Matched reaction 194 C4H7-4 <=> C4H7-5 in intra_H_migration/training +! This reaction matched rate rule [R3H_DS;Cd_rad_out_singleH;Cs_H_out_H/NonDeC] +! family: intra_H_migration +C4H7(33)=C4H7(45) 1.846000e+10 0.740 34.700 + +! Reaction index: Chemkin #31; RMG #92 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(42), C4H7(29); H(6), C4H7(29); +! Matched reaction 2580 H + C4H6-2 <=> C4H7-11 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-CdH_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(42)=C4H7(29) 3.240000e+08 1.640 2.400 + +! Reaction index: Chemkin #32; RMG #160 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(42), C4H7(45); H(6), C4H7(45); +! Matched reaction 2544 H + C4H6 <=> C4H7-9 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Cds-HH_Cds-CdH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(42)=C4H7(45) 4.620000e+08 1.640 -0.470 + +! Reaction index: Chemkin #33; RMG #213 +! Template reaction: R_Recombination +! Flux pairs: C2H3(14), C4H6(42); C2H3(14), C4H6(42); +! Matched reaction 89 C2H3 + C2H3 <=> C4H6-4 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_N-1COS->O_1CS->C_N-1C-inRing_Ext-2R-R_N-Sp-3R!H-2R_N-3R!H->O_N-Sp-3CCSS#2R_Ext-1C-R] +! family: R_Recombination +C2H3(14)+C2H3(14)=C4H6(42) 3.615000e+13 0.000 0.000 + +! Reaction index: Chemkin #34; RMG #218 +! Template reaction: Disproportionation +! Flux pairs: C2H5(5), ethane(1); C4H7(29), C4H6(42); +! Estimated using template [C_rad/H2/Cs;Cpri_Rrad] for rate rule [C_rad/H2/Cs;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H5(5)+C4H7(29)=ethane(1)+C4H6(42) 2.900000e+12 0.000 0.000 + +! Reaction index: Chemkin #35; RMG #219 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cs;Cmethyl_Csrad] for rate rule [C_rad/H2/Cs;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H7(45)=ethane(1)+C4H6(42) 6.900000e+13 -0.350 0.000 + +! Reaction index: Chemkin #36; RMG #234 +! Template reaction: Disproportionation +! Flux pairs: CH3(4), CH4(3); C4H7(29), C4H6(42); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [C_methyl;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +CH3(4)+C4H7(29)=CH4(3)+C4H6(42) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #37; RMG #235 +! Template reaction: Disproportionation +! Estimated using template [Cs_rad;Cmethyl_Csrad/H/Cd] for rate rule [C_methyl;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +CH3(4)+C4H7(45)=CH4(3)+C4H6(42) 1.500000e+11 0.000 0.000 + +! Reaction index: Chemkin #38; RMG #243 +! Template reaction: Disproportionation +! Flux pairs: C2H3(14), C4H6(42); C4H7(29), C2H4(9); +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H7(29)=C2H4(9)+C4H6(42) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #39; RMG #244 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H3(14)+C4H7(45)=C2H4(9)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #40; RMG #247 +! Template reaction: Disproportionation +! Flux pairs: H(6), H2(11); C4H7(29), C4H6(42); +! Estimated using template [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] for rate rule [H_rad;C/H2/Cd_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +H(6)+C4H7(29)=H2(11)+C4H6(42) 2.000000e+10 0.000 0.000 + +! Reaction index: Chemkin #41; RMG #248 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad;Cmethyl_Csrad/H/Cd] + [H_rad;Cmethyl_Csrad] for rate rule [H_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +H(6)+C4H7(45)=H2(11)+C4H6(42) 1.274559e+12 0.000 0.000 + +! Reaction index: Chemkin #42; RMG #209 +! Template reaction: Intra_2+2_cycloaddition_Cd +! Flux pairs: C4H6(42), C4H6(88); +! Estimated using template [1,3-butadiene_backbone;C=C_1;C=C_2] for rate rule [1,3-butadiene_backbone;CdH2_1;CdH2_2] +! Euclidian distance = 1.4142135623730951 +! family: Intra_2+2_cycloaddition_Cd +C4H6(42)=C4H6(88) 4.999980e+11 0.056 29.257 + +! Reaction index: Chemkin #43; RMG #94 +! Template reaction: R_Recombination +! Flux pairs: C4H6(43), C4H7(29); H(6), C4H7(29); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(43)=C4H7(29) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #44; RMG #107 +! Template reaction: Disproportionation +! From training reaction 5 used for Y_rad;Cmethyl_Csrad +! Exact match found for rate rule [Y_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(43)=C2H4(9)+C4H7(29) 1.314000e+15 -0.680 0.000 + +! Reaction index: Chemkin #45; RMG #120 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;Cds/H2_d_Crad] + [Y_rad;Cds/H2_d_Rrad] for rate rule [Y_rad;Cds/H2_d_Crad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(43)=C#C(27)+C4H7(29) 4.131060e+11 0.309 1.097 + +! Reaction index: Chemkin #46; RMG #154 +! Template reaction: R_Recombination +! Flux pairs: C4H6(43), C4H7(45); H(6), C4H7(45); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_N- +! Sp-3R!H=2C_3R!H->C_Sp-3C-2C_Ext-3C-R_Sp-4R!H=3C_N-3C-inRing] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: R_Recombination +H(6)+C4H6(43)=C4H7(45) 3.251960e+13 0.255 0.000 + +! Reaction index: Chemkin #47; RMG #179 +! Template reaction: Disproportionation +! From training reaction 7 used for C_rad/H2/Cd;Cmethyl_Csrad +! Exact match found for rate rule [C_rad/H2/Cd;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C2H5(5)+C4H6(43)=C2H4(9)+C4H7(45) 1.374000e+14 -0.350 -0.130 + +! Reaction index: Chemkin #48; RMG #200 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [C_rad/H2/Cd;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C2H3(14)+C4H6(43)=C#C(27)+C4H7(45) 1.640928e+07 1.877 -1.115 + +! Reaction index: Chemkin #49; RMG #275 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cd;Cpri_Rrad] for rate rule [C_rad/H2/Cd;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 4.0 +! family: Disproportionation +C4H6(43)+C4H7(29)=C4H6(42)+C4H7(45) 5.800000e+12 0.000 -0.130 + +! Reaction index: Chemkin #50; RMG #276 +! Template reaction: Disproportionation +! Estimated using template [C_rad/H2/Cd;Cmethyl_Csrad] for rate rule [C_rad/H2/Cd;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 6.0 +! family: Disproportionation +C4H6(43)+C4H7(45)=C4H6(42)+C4H7(45) 1.374000e+14 -0.350 -0.130 + +! Reaction index: Chemkin #51; RMG #312 +! Template reaction: Birad_recombination +! Flux pairs: C4H6(43), C4H6(88); +! Estimated using template [R4;C_rad_out_2H;Cpri_rad_out_2H] for rate rule [R4_SDS;C_rad_out_2H;Cpri_rad_out_2H] +! Euclidian distance = 1.0 +! family: Birad_recombination +C4H6(43)=C4H6(88) 1.620000e+12 -0.305 1.980 + +! Reaction index: Chemkin #52; RMG #348 +! Template reaction: 1,2-Birad_to_alkene +! Flux pairs: C4H6(43), C4H6(42); +! Matched reaction 5 C4H6 => C4H6-2 in 1,2-Birad_to_alkene/training +! This reaction matched rate rule [Y_12_01] +! family: 1,2-Birad_to_alkene +C4H6(43)=>C4H6(42) 5.010000e+07 0.000 0.000 + +! Reaction index: Chemkin #53; RMG #152 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C4H6(69), C4H7(45); H(6), C4H7(45); +! Matched reaction 2714 H + C4H6-4 <=> C4H7-13 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ca_Cds-HH;HJ] +! family: R_Addition_MultipleBond +H(6)+C4H6(69)=C4H7(45) 5.460000e+08 1.640 3.780 + +! Reaction index: Chemkin #54; RMG #342 +! Template reaction: Intra_Disproportionation +! Flux pairs: C4H6(43), C4H6(69); +! Estimated using an average for rate rule [R3radExo;Y_rad;XH_Rrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 2.0 +! family: Intra_Disproportionation +C4H6(43)=C4H6(69) 1.487400e+09 1.045 15.153 + +! Reaction index: Chemkin #55; RMG #367 +! Template reaction: Disproportionation +! From training reaction 47 used for C_rad/H2/Cs;Cdpri_Csrad +! Exact match found for rate rule [C_rad/H2/Cs;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H5(5)+C4H7(45)=ethane(1)+C4H6(69) 9.640000e+11 0.000 6.000 + +! Reaction index: Chemkin #56; RMG #370 +! Template reaction: Disproportionation +! Estimated using template [Cs_rad;Cdpri_Csrad] for rate rule [C_methyl;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +CH3(4)+C4H7(45)=CH4(3)+C4H6(69) 3.354068e+12 0.000 6.000 + +! Reaction index: Chemkin #57; RMG #376 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C2H3(14)+C4H7(45)=C2H4(9)+C4H6(69) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #58; RMG #382 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cdpri_Csrad] for rate rule [H_rad;Cdpri_Csrad] +! Euclidian distance = 1.0 +! family: Disproportionation +H(6)+C4H7(45)=H2(11)+C4H6(69) 3.010000e+12 0.000 6.000 + +! Reaction index: Chemkin #59; RMG #361 +! Template reaction: R_Recombination +! Flux pairs: C4H5(144), C4H6(69); H(6), C4H6(69); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_Ext-2C-R_Ext-3R!H-R] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(144)=C4H6(69) 1.554090e+97 -24.703 0.000 + +! Reaction index: Chemkin #60; RMG #378 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad] +! Euclidian distance = 2.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(144)=C2H4(9)+C4H6(69) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #61; RMG #390 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_rad/NonDeC;Cds/H2_d_Crad] +! Euclidian distance = 3.1622776601683795 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(144)=C#C(27)+C4H6(69) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #62; RMG #407 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cpri_Rrad] for rate rule [Cd_rad/NonDeC;C/H2/Cd_Csrad] +! Euclidian distance = 3.605551275463989 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(144)+C4H7(29)=C4H6(69)+C4H6(42) 2.420000e+12 0.000 0.000 + +! Reaction index: Chemkin #63; RMG #410 +! Template reaction: Disproportionation +! Estimated using template [Cd_rad;Cmethyl_Csrad] for rate rule [Cd_rad/NonDeC;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(144)+C4H7(45)=C4H6(69)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #64; RMG #425 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); C2H5(5), ethane(1); +! Estimated using an average for rate rule [Cd_allenic;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! family: H_Abstraction +C2H5(5)+C4H6(69)=ethane(1)+C4H5(144) 5.450000e-03 4.340 5.900 + +! Reaction index: Chemkin #65; RMG #436 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); C2H3(14), C2H4(9); +! Estimated using an average for rate rule [Cd_allenic;Cd_Cd\H2_pri_rad] +! Euclidian distance = 0 +! family: H_Abstraction +C2H3(14)+C4H6(69)=C2H4(9)+C4H5(144) 4.170000e-02 4.340 1.000 + +! Reaction index: Chemkin #66; RMG #442 +! Template reaction: H_Abstraction +! Flux pairs: C4H6(69), C4H5(144); H(6), H2(11); +! Estimated using an average for rate rule [Cd_allenic;H_rad] +! Euclidian distance = 0 +! family: H_Abstraction +H(6)+C4H6(69)=H2(11)+C4H5(144) 3.532500e+00 3.852 3.502 + +! Reaction index: Chemkin #67; RMG #69 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: CH3(4), C3H5(32); C#C(27), C3H5(32); +! Matched reaction 2253 C2H2 + CH3 <=> C3H5-2 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CsJ-HHH] +! family: R_Addition_MultipleBond +CH3(4)+C#C(27)=C3H5(32) 1.338000e+05 2.410 6.770 + +! Reaction index: Chemkin #68; RMG #84 +! Template reaction: R_Addition_MultipleBond +! Flux pairs: C2H3(14), C4H5(35); C#C(27), C4H5(35); +! Matched reaction 196 C2H2 + C2H3 <=> C4H5-8 in R_Addition_MultipleBond/training +! This reaction matched rate rule [Ct-H_Ct-H;CdsJ-H] +! family: R_Addition_MultipleBond +C#C(27)+C2H3(14)=C4H5(35) 1.168000e+07 1.997 5.452 + +! Reaction index: Chemkin #69; RMG #215 +! Template reaction: R_Recombination +! Flux pairs: C4H5(35), C4H6(42); H(6), C4H6(42); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C +! Total Standard Deviation in ln(k): 6.83519320067 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_2CNO->C_Ext-2C-R_Sp-3R!H=2C_3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(6)+C4H5(35)=C4H6(42) 9.988280e+13 0.006 0.000 + +! Reaction index: Chemkin #70; RMG #223 +! Template reaction: H_Abstraction +! Flux pairs: CH3(4), CH4(3); C4H6(42), C4H5(35); +! From training reaction 1567 used for Cd/H2/NonDeC;C_methyl +! Exact match found for rate rule [Cd/H2/NonDeC;C_methyl] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +CH3(4)+C4H6(42)=CH4(3)+C4H5(35) 3.432000e-02 4.340 20.710 + +! Reaction index: Chemkin #71; RMG #231 +! Template reaction: H_Abstraction +! Flux pairs: C2H5(5), ethane(1); C4H6(42), C4H5(35); +! From training reaction 344 used for Cd/H2/NonDeC;C_rad/H2/Cs\H3 +! Exact match found for rate rule [Cd/H2/NonDeC;C_rad/H2/Cs\H3] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +C2H5(5)+C4H6(42)=ethane(1)+C4H5(35) 6.320000e+02 3.130 18.000 + +! Reaction index: Chemkin #72; RMG #237 +! Template reaction: H_Abstraction +! Flux pairs: H(6), H2(11); C4H6(42), C4H5(35); +! From training reaction 217 used for Cd/H2/NonDeC;H_rad +! Exact match found for rate rule [Cd/H2/NonDeC;H_rad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 4.0 +! family: H_Abstraction +H(6)+C4H6(42)=H2(11)+C4H5(35) 2.400000e+02 3.620 11.266 + +! Reaction index: Chemkin #73; RMG #246 +! Template reaction: Disproportionation +! From training reaction 11 used for Cd_pri_rad;Cmethyl_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cmethyl_Csrad] +! Euclidian distance = 0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C2H5(5)+C4H5(35)=C2H4(9)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #74; RMG #256 +! Template reaction: H_Abstraction +! Flux pairs: C2H3(14), C2H4(9); C4H6(42), C4H5(35); +! Matched reaction 177 C4H6-3 + C2H3 <=> C2H4 + C4H5 in H_Abstraction/training +! This reaction matched rate rule [Cd/H2/NonDeC;Cd_Cd\H2_pri_rad] +! family: H_Abstraction +C2H3(14)+C4H6(42)=C2H4(9)+C4H5(35) 3.437000e-04 4.732 6.579 + +! Reaction index: Chemkin #75; RMG #265 +! Template reaction: Disproportionation +! Estimated using template [Y_rad;Cds/H2_d_Rrad] for rate rule [Cd_pri_rad;Cds/H2_d_Crad] +! Euclidian distance = 2.23606797749979 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C2H3(14)+C4H5(35)=C#C(27)+C4H6(42) 8.204641e+06 1.877 -1.115 + +! Reaction index: Chemkin #76; RMG #309 +! Template reaction: Disproportionation +! Estimated using average of templates [Y_rad_birad_trirad_quadrad;C/H2/Cd_Csrad] + [Cd_pri_rad;Cpri_Rrad] for rate rule [Cd_pri_rad;C/H2/Cd_Csrad] +! Euclidian distance = 3.0 +! Multiplied by reaction path degeneracy 2.0 +! family: Disproportionation +C4H5(35)+C4H7(29)=C4H6(42)+C4H6(42) 2.200000e+11 0.000 0.000 + +! Reaction index: Chemkin #77; RMG #310 +! Template reaction: Disproportionation +! Estimated using template [Cd_pri_rad;Cmethyl_Csrad] for rate rule [Cd_pri_rad;Cmethyl_Csrad/H/Cd] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 3.0 +! family: Disproportionation +C4H5(35)+C4H7(45)=C4H6(42)+C4H6(42) 4.560000e+14 -0.700 0.000 + +! Reaction index: Chemkin #78; RMG #405 +! Template reaction: Disproportionation +! From training reaction 51 used for Cd_pri_rad;Cdpri_Csrad +! Exact match found for rate rule [Cd_pri_rad;Cdpri_Csrad] +! Euclidian distance = 0 +! family: Disproportionation +C4H5(35)+C4H7(45)=C4H6(69)+C4H6(42) 2.410000e+12 0.000 6.000 + +! Reaction index: Chemkin #79; RMG #466 +! Template reaction: Intra_R_Add_Exocyclic +! Flux pairs: C4H5(35), C4H5(185); +! From training reaction 14 used for R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH +! Exact match found for rate rule [R4_D_D;doublebond_intra_2H_pri;radadd_intra_cdsingleH] +! Euclidian distance = 0 +! family: Intra_R_Add_Exocyclic +C4H5(35)=C4H5(185) 2.540000e+10 0.690 25.170 + +END + diff --git a/examples/scripts/standardizeModelSpeciesNames/Models/minimal_species_dictionary.txt b/examples/scripts/standardizeModelSpeciesNames/Models/minimal_species_dictionary.txt new file mode 100644 index 0000000000..d9cf2f5695 --- /dev/null +++ b/examples/scripts/standardizeModelSpeciesNames/Models/minimal_species_dictionary.txt @@ -0,0 +1,248 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +ethane(1) +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} + +CH3(4) +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} + +C2H5(5) +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} + +CH4(3) +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} + +H(6) +multiplicity 2 +1 H u1 p0 c0 + +C2H4(9) +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} + +H2(11) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +C3H7(16) +multiplicity 2 +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 u1 p0 c0 {1,S} {9,S} {10,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} + +C2H3(14) +multiplicity 2 +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u1 p0 c0 {1,D} {5,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} + +C#C(27) +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} + +C2H2(31) +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p1 c0 {1,D} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C4H7(29) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,D} {7,S} +3 C u1 p0 c0 {1,S} {8,S} {9,S} +4 C u0 p0 c0 {2,D} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(41) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} +3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} +4 C u1 p0 c0 {1,S} {10,S} {11,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 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H7(33) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {7,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,D} {10,S} +4 C u1 p0 c0 {3,D} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} +10 H u0 p0 c0 {3,S} +11 H u0 p0 c0 {4,S} + +C4H7(45) +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {3,D} {8,S} +3 C u0 p0 c0 {2,D} {4,S} {9,S} +4 C u1 p0 c0 {3,S} {10,S} {11,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {4,S} + +C4H6(42) +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u0 p0 c0 {2,D} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(88) +1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {9,S} +4 C u0 p0 c0 {2,S} {3,D} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,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 {4,S} + +C4H6(43) +multiplicity 3 +1 C u0 p0 c0 {2,D} {3,S} {5,S} +2 C u0 p0 c0 {1,D} {4,S} {6,S} +3 C u1 p0 c0 {1,S} {7,S} {8,S} +4 C u1 p0 c0 {2,S} {9,S} {10,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} +10 H u0 p0 c0 {4,S} + +C4H6(69) +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {4,D} {8,S} +3 C u0 p0 c0 {4,D} {9,S} {10,S} +4 C u0 p0 c0 {2,D} {3,D} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +C4H5(144) +multiplicity 2 +1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {4,S} {8,S} {9,S} +3 C u0 p0 c0 {1,S} {4,T} +4 C u0 p0 c0 {2,S} {3,T} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} + +C3H5(32) +multiplicity 2 +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 C u1 p0 c0 {2,D} {8,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} + +C4H5(35) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,D} {5,S} +2 C u0 p0 c0 {1,S} {4,D} {6,S} +3 C u0 p0 c0 {1,D} {7,S} {8,S} +4 C u1 p0 c0 {2,D} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {4,S} + +C4H5(185) +multiplicity 2 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,D} {6,S} +3 C u0 p0 c0 {1,S} {2,D} {7,S} +4 C u1 p0 c0 {1,S} {8,S} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {4,S} +9 H u0 p0 c0 {4,S} + diff --git a/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_chem.inp b/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_chem.inp new file mode 100644 index 0000000000..b0799a6c0c --- /dev/null +++ b/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_chem.inp @@ -0,0 +1,279 @@ +ELEMENTS + H + D /2.014/ + T /3.016/ + C + CI /13.003/ + O + OI /18.000/ + N + Ne + Ar + He + Si + S + Cl + X /195.083/ +END + +SPECIES + Ar ! Ar + He ! He + Ne ! Ne + N2 ! N2 + H2(1) ! H2(1) + O2(2) ! O2(2) + H(3) ! H(3) + HO2(4) ! [O]O(4) + OH(D)(5) ! OH(D)(5) + O(T)(6) ! O(T)(6) + OO(7) ! OO(7) + H2O(10) ! H2O(10) +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 +He He 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 9.28724000E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28724000E-01 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 +H2(1) H 2 G 100.000 5000.000 1959.08 1 + 2.78816583E+00 5.87640942E-04 1.59010417E-07-5.52739026E-11 4.34310984E-15 2 +-5.96144270E+02 1.12732655E-01 3.43536412E+00 2.12710353E-04-2.78625043E-07 3 + 3.40267167E-10-7.76031998E-14-1.03135984E+03-3.90841732E+00 4 + +! Thermo library: primaryThermoLibrary +O2(2) O 2 G 100.000 5000.000 1074.56 1 + 3.15382425E+00 1.67803802E-03-7.69971022E-07 1.51274714E-10-1.08781801E-14 2 +-1.04081878E+03 6.16753884E+00 3.53732181E+00-1.21570930E-03 5.31617826E-06 3 +-4.89443424E-09 1.45845042E-12-1.03858846E+03 4.68368406E+00 4 + +! Thermo library: primaryThermoLibrary +H(3) H 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.54742178E+04-4.44972842E-01 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.54742178E+04-4.44972896E-01 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) + radical(HOOJ) +HO2(4) O 2H 1 G 100.000 5000.000 932.13 1 + 3.21021575E+00 3.67945961E-03-1.27703899E-06 2.18050820E-10-1.46342588E-14 2 +-9.10359190E+02 8.18304670E+00 4.04595233E+00-1.73474005E-03 1.03769950E-05 3 +-1.02207268E-08 3.34930151E-12-9.86754562E+02 4.63578650E+00 4 + +! Thermo library: primaryThermoLibrary +OH(D)(5) O 1H 1 G 100.000 5000.000 1145.75 1 + 3.07194246E+00 6.04011411E-04-1.39759127E-08-2.13451563E-11 2.48070095E-15 2 + 3.57938557E+03 4.57798500E+00 3.51456768E+00 2.92814373E-05-5.32176582E-07 3 + 1.01950588E-09-3.85951152E-13 3.41425421E+03 2.10435015E+00 4 + +! Thermo library: primaryThermoLibrary +O(T)(6) O 1 G 100.000 5000.000 3459.60 1 + 2.49999999E+00 9.20455546E-12-3.58608293E-15 6.15198922E-19-3.92041801E-23 2 + 2.92302441E+04 5.12616433E+00 2.50000000E+00 9.24384602E-15-1.36779837E-17 3 + 6.66184769E-21-1.00106912E-24 2.92302441E+04 5.12616427E+00 4 + +! Thermo group additivity estimation: group(O2s-OsH) + group(O2s-OsH) +OO(7) O 2H 2 G 100.000 5000.000 908.86 1 + 5.41576461E+00 2.61012083E-03-4.39915287E-07 4.91143478E-11-3.35235545E-15 2 +-1.83029432E+04-4.02235599E+00 3.73136642E+00 3.35060430E-03 9.35072698E-06 3 +-1.52105192E-08 6.41611128E-12-1.77211712E+04 5.45907862E+00 4 + +! Thermo library: primaryThermoLibrary +H2O(10) O 1H 2 G 100.000 5000.000 1130.24 1 + 2.84324866E+00 2.75108838E-03-7.81033120E-07 1.07244016E-10-5.79395308E-15 2 +-2.99586120E+04 5.91043011E+00 4.05763610E+00-7.87938871E-04 2.90878480E-06 3 +-1.47520039E-09 2.12847506E-13-3.02815866E+04-3.11365027E-01 4 + +END + + + +REACTIONS KCAL/MOLE MOLES + +! Reaction index: Chemkin #1; RMG #1 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #2; RMG #4 +! Template reaction: R_Recombination +! Flux pairs: H(3), H2(1); H(3), H2(1); +! Matched reaction 56 H + H <=> H2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_2R->H] +! family: R_Recombination +H(3)+H(3)=H2(1) 5.450000e+10 0.000 1.500 +DUPLICATE + +! Reaction index: Chemkin #3; RMG #2 +! Template reaction: H_Abstraction +! Flux pairs: O2(2), HO2(4); H2(1), H(3); +! Matched reaction 306 H2 + O2 <=> HO2_r12 + H in H_Abstraction/training +! This reaction matched rate rule [H2;O2b] +! family: H_Abstraction +O2(2)+H2(1)=H(3)+HO2(4) 2.900000e+14 0.000 56.640 + +! Reaction index: Chemkin #4; RMG #3 +! Template reaction: R_Recombination +! Flux pairs: H(3), HO2(4); O2(2), HO2(4); +! Matched reaction 104 O2 + H <=> HO2-2 in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! family: R_Recombination +O2(2)+H(3)=HO2(4) 8.790000e+10 1.000 0.450 + +! Reaction index: Chemkin #5; RMG #6 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); H(3), H2(1); +! Estimated using average of templates [O/H/NonDeO;H_rad] + [H2O2;Y_rad] for rate rule [H2O2;H_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +H(3)+OO(7)=HO2(4)+H2(1) 1.235020e+06 1.634 6.086 + +! Reaction index: Chemkin #6; RMG #8 +! Template reaction: R_Recombination +! Flux pairs: HO2(4), OO(7); H(3), OO(7); +! BM rule fitted to 2 training reactions at node Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C +! Total Standard Deviation in ln(k): 11.5401827615 +! Exact match found for rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C_Ext-2NO-R_N-2NO->N_N-3R!H->C] +! Euclidian distance = 0 +! family: R_Recombination +H(3)+HO2(4)=OO(7) 5.250690e+09 1.273 0.000 + +! Reaction index: Chemkin #7; RMG #9 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), OO(7); HO2(4), O2(2); +! Matched reaction 405 HO2_r3 + HO2_r12 <=> H2O2 + O2 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_rad/NonDeO] +! family: H_Abstraction +HO2(4)+HO2(4)=O2(2)+OO(7) 1.750000e+10 0.000 -3.275 + +! Reaction index: Chemkin #8; RMG #11 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), OO(7); OH(D)(5), OO(7); +! Matched reaction 96 OH + OH <=> H2O2 in R_Recombination/training +! This reaction matched rate rule [Root_N-1R->H_N-1CClNOSSi->N_1COS->O_N-2R->C] +! family: R_Recombination +OH(D)(5)+OH(D)(5)=OO(7) 7.850000e+12 0.000 0.000 + +! Reaction index: Chemkin #9; RMG #13 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); H2(1), H(3); +! Matched reaction 312 H2 + OH <=> H2O_p + H_p in H_Abstraction/training +! This reaction matched rate rule [H2;O_pri_rad] +! family: H_Abstraction +OH(D)(5)+H2(1)=H(3)+H2O(10) 1.820000e+09 1.210 20.070 + +! Reaction index: Chemkin #10; RMG #17 +! Template reaction: R_Recombination +! Flux pairs: OH(D)(5), H2O(10); H(3), H2O(10); +! Matched reaction 64 H + OH <=> H2O in R_Recombination/training +! This reaction matched rate rule [Root_1R->H_N-2R-inRing_N-2R->H_N-2CNOS->S_N-2CNO->C] +! family: R_Recombination +H(3)+OH(D)(5)=H2O(10) 1.620000e+14 0.000 0.150 + +! Reaction index: Chemkin #11; RMG #18 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O2(2), HO2(4); +! Matched reaction 379 H2O + O2 <=> HO2_r12 + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [Orad_O_H;O_pri_rad] +! family: H_Abstraction +O2(2)+H2O(10)=OH(D)(5)+HO2(4) 9.300000e+12 0.000 74.120 + +! Reaction index: Chemkin #12; RMG #21 +! Template reaction: H_Abstraction +! Flux pairs: OH(D)(5), H2O(10); OO(7), HO2(4); +! Estimated using average of templates [O/H/NonDeO;O_pri_rad] + [H2O2;O_rad] for rate rule [H2O2;O_pri_rad] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +OH(D)(5)+OO(7)=HO2(4)+H2O(10) 4.994995e+05 1.927 6.325 + +! Reaction index: Chemkin #13; RMG #5 +! Template reaction: Birad_R_Recombination +! Flux pairs: OH(D)(5), HO2(4); O(T)(6), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +! Reaction index: Chemkin #14; RMG #12 +! Template reaction: Birad_R_Recombination +! Flux pairs: H(3), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 4 H + O <=> HO in Birad_R_Recombination/training +! This reaction matched rate rule [H_rad;O_birad] +! family: Birad_R_Recombination +O(T)(6)+H(3)=OH(D)(5) 1.000000e+13 0.000 0.000 + +! Reaction index: Chemkin #15; RMG #14 +! Template reaction: H_Abstraction +! Flux pairs: HO2(4), O2(2); O(T)(6), OH(D)(5); +! Estimated using average of templates [X_H;O_atom_triplet] + [Orad_O_H;Y_rad_birad_trirad_quadrad] for rate rule [Orad_O_H;O_atom_triplet] +! Euclidian distance = 2.0 +! family: H_Abstraction +O(T)(6)+HO2(4)=O2(2)+OH(D)(5) 3.680392e+09 0.678 5.899 + +! Reaction index: Chemkin #16; RMG #16 +! Template reaction: H_Abstraction +! Flux pairs: H2(1), H(3); O(T)(6), OH(D)(5); +! Matched reaction 285 H2 + O_rad <=> HO + H in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;H_rad] +! family: H_Abstraction +O(T)(6)+H2(1)=H(3)+OH(D)(5) 3.400000e+08 1.500 22.950 + +! Reaction index: Chemkin #17; RMG #19 +! Template reaction: H_Abstraction +! Flux pairs: OO(7), HO2(4); O(T)(6), OH(D)(5); +! Estimated using template [O/H/NonDeO;O_atom_triplet] for rate rule [H2O2;O_atom_triplet] +! Euclidian distance = 1.0 +! Multiplied by reaction path degeneracy 2.0 +! family: H_Abstraction +O(T)(6)+OO(7)=OH(D)(5)+HO2(4) 1.740000e+13 0.000 4.750 + +! Reaction index: Chemkin #18; RMG #22 +! Template reaction: H_Abstraction +! Flux pairs: H2O(10), OH(D)(5); O(T)(6), OH(D)(5); +! Matched reaction 380 H2O + O_rad <=> HO + OH_p23 in H_Abstraction/training +! This reaction matched rate rule [OH_rad_H;O_pri_rad] +! family: H_Abstraction +O(T)(6)+H2O(10)=OH(D)(5)+OH(D)(5) 5.260000e+09 1.200 17.830 + +! Reaction index: Chemkin #19; RMG #25 +! Template reaction: Birad_R_Recombination +! Flux pairs: O(T)(6), HO2(4); OH(D)(5), HO2(4); +! Estimated using template [O_rad;O_birad] for rate rule [O_pri_rad;O_birad] +! Euclidian distance = 1.0 +! family: Birad_R_Recombination +O(T)(6)+OH(D)(5)=HO2(4) 1.548026e+07 1.880 1.235 +DUPLICATE + +END + diff --git a/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_species_dictionary.txt b/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_species_dictionary.txt new file mode 100644 index 0000000000..910547a04c --- /dev/null +++ b/examples/scripts/standardizeModelSpeciesNames/Models/superminimal_species_dictionary.txt @@ -0,0 +1,52 @@ +Ar +1 Ar u0 p4 c0 + +He +1 He u0 p1 c0 + +Ne +1 Ne u0 p4 c0 + +N2 +1 N u0 p1 c0 {2,T} +2 N u0 p1 c0 {1,T} + +H2(1) +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +O2(2) +multiplicity 3 +1 O u1 p2 c0 {2,S} +2 O u1 p2 c0 {1,S} + +H(3) +multiplicity 2 +1 H u1 p0 c0 + +HO2(4) +multiplicity 2 +1 O u0 p2 c0 {2,S} {3,S} +2 O u1 p2 c0 {1,S} +3 H u0 p0 c0 {1,S} + +OO(7) +1 O u0 p2 c0 {2,S} {3,S} +2 O u0 p2 c0 {1,S} {4,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} + +OH(D)(5) +multiplicity 2 +1 O u1 p2 c0 {2,S} +2 H u0 p0 c0 {1,S} + +H2O(10) +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +O(T)(6) +multiplicity 3 +1 O u2 p2 c0 + diff --git a/examples/scripts/standardizeModelSpeciesNames/run.sh b/examples/scripts/standardizeModelSpeciesNames/run.sh new file mode 100644 index 0000000000..08e91359b5 --- /dev/null +++ b/examples/scripts/standardizeModelSpeciesNames/run.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# standardize species names for the two models +python ../../../scripts/standardizeModelSpeciesNames.py --model1 Models/minimal_chem.inp Models/minimal_species_dictionary.txt --model2 Models/superminimal_chem.inp Models/superminimal_species_dictionary.txt From 71f10d742e07c6b9e9564062e9a6c4983bcd3f36 Mon Sep 17 00:00:00 2001 From: yunsiechung Date: Tue, 3 Dec 2019 13:05:38 -0500 Subject: [PATCH 7/7] modified the description for generateTree script A few more lines are added in the description --- scripts/generateTree.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/generateTree.py b/scripts/generateTree.py index c4b6403625..34dd51ad55 100644 --- a/scripts/generateTree.py +++ b/scripts/generateTree.py @@ -29,9 +29,12 @@ """ This script cleans and generates new trees for the specified family running in parallel on the specified number of processors -`python generate_tree.py familyName nprocs` -ex: `python generate_tree.py intra_H_migration 6` +`python generateTree.py familyName nprocs` +ex: `python generateTree.py intra_H_migration 6` Note that 6 is the maximum number of processors used currently by this script +This script will work only for the certain reaction families that have been fixed to run this script. +Running this script on other reaction families will throw error. +The documentation for this script will be ready in the future. """ import argparse