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Example for generateFluxDiagram is added
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An example for scripts/generateFluxDiagram.py is added
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yunsiechung committed Dec 3, 2019
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279 changes: 279 additions & 0 deletions examples/scripts/generateFluxDiagram/chem_annotated.inp
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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

55 changes: 55 additions & 0 deletions examples/scripts/generateFluxDiagram/input.py
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# 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,
)
4 changes: 4 additions & 0 deletions examples/scripts/generateFluxDiagram/run.sh
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#!/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
52 changes: 52 additions & 0 deletions examples/scripts/generateFluxDiagram/species_dictionary.txt
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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

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