RMG.log

Global RMG Settings:
   test_data.directory  = /Users/rwest/Code/Cat/RMG-Py/rmgpy/test_data (Default, relative to RMG-Py source code)
   database.directory   = /Users/rwest/Code/Cat/RMG-database/input (Default, relative to RMG-Py source code)
RMG execution initiated at Tue Dec  4 16:42:12 2018

#########################################################
# RMG-Py - Reaction Mechanism Generator in Python       #
# Version: 2.2.1-Cat                                    #
# Authors: RMG Developers (rmg_dev@mit.edu)             #
# P.I.s:   William H. Green (whgreen@mit.edu)           #
#          Richard H. West (r.west@neu.edu)             #
# Website: http://reactionmechanismgenerator.github.io/ #
#                                                       #
#  This heterogeneous catalysis branch developed by:    #
#  Richard H. West (r.west@neu.edu)                     #
#  C. Franklin Goldsmith (franklin_goldsmith@brown.edu) #
#########################################################

The current git HEAD for RMG-Py is:
	f6f51c2091e531b0a14968717bb4f2055e391877
	Tue Dec 4 16:39:28 2018 -0500

The current git HEAD for RMG-database is:
	53563a9a0992aaab3baa66ed55c042451bcf4a62
	Tue Dec 4 16:40:31 2018 -0500

Reading input file "/Users/rwest/Code/Cat/cpox-methane/input.py"...
# Data sources
database(
    thermoLibraries=['surfaceThermoPt', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'],
    reactionLibraries = [('CPOX_Pt/Deutschmann2006', False)], # 'CPOX_Pt/Vlachos2007'
    seedMechanisms = [],
    kineticsDepositories = ['training'],
    kineticsFamilies =['surface','default'],
    kineticsEstimator = 'rate rules',
    bindingEnergies = { # default values
                       'C':(-6.364, 'eV/molecule'), # Pt(111)
                       'H':(-2.778, 'eV/molecule'), # Ni(111), until we find the vaule for Pt(111)
                       'O':(-3.481, 'eV/molecule'), # Pt(111)
                       }
)

# List of species
species(
    label='X',
    reactive=True,
    structure=adjacencyList("1 X u0"),
)

species(
    label='CH4',
    reactive=True,
    structure=SMILES("[CH4]"),
)
species(
   label='O2',
   reactive=True,
   structure=adjacencyList(
       """
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
"""),
)

species(
    label='N2',
    reactive=False,
    structure=SMILES("N#N"),
)

species(
    label='CO2',
    reactive=True,
    structure=SMILES("O=C=O"),
)

species(
    label='H2O',
    reactive=True,
    structure=SMILES("O"),
)

species(
    label='H2',
    reactive=True,
    structure=SMILES("[H][H]"),
)

species(
    label='CO',
    reactive=True,
    structure=SMILES("[C-]#[O+]"),
)

species(
    label='CH2O',
    reactive=True,
    structure=SMILES("C=O"),
)

species(
    label='CH3',
    reactive=True,
    structure=SMILES("[CH3]"),
)

species(
    label='H',
    reactive=True,
    structure=SMILES("[H]"),
)

species(
    label='CH3OH',
    reactive=True,
    structure=SMILES("CO"),
)

species(
    label='HCO',
    reactive=True,
    structure=SMILES("[CH]=O"),
)

species(
    label='OH',
    reactive=True,
    structure=SMILES("[OH]"),
)

#----------
# Reaction systems
surfaceReactor(
    temperature=(1000,'K'),
    initialPressure=(1.0, 'bar'),
    initialGasMoleFractions={
        "CH4": 0.1,
        "O2": 0.1,
        "N2": 0.8,
    },
    initialSurfaceCoverages={
        "X": 1.0,
    },
    surfaceVolumeRatio=(1.e5, 'm^-1'),
    surfaceSiteDensity=(2.9e-9, 'mol/cm^2'),
#    terminationConversion = { "CH4":0.9,},
    terminationTime=(10., 's'),
    terminationConversion={'O2': 0.95,}
)

simulator(
    atol=1e-18,
    rtol=1e-12,
)

model(
    toleranceKeepInEdge=0.0,
    toleranceMoveToCore=1e-4,
    toleranceInterruptSimulation=0.1,
    maximumEdgeSpecies=100000
)

options(
    units='si',
    saveRestartPeriod=None,
    generateOutputHTML=True,
    generatePlots=False,
    saveEdgeSpecies=True,
    saveSimulationProfiles=True,
)


Surface reaction system 1
Gas phase mole fractions:
  N2                   0.8
  CH4                  0.1
  O2                   0.1
Total gas phase:          1 moles
Pressure:                 1e+05 Pa
Temperature:              1000.0 K
Reactor volume:           0.0831 m3
Surface/volume ratio:     1e+05 m2/m3
Surface site density:     2.9e-05 mol/m2
Surface sites in reactor: 0.241 moles
Initial surface coverages (and amounts):
  X                  1 = 0.24112 moles
Warning: Generate Output HTML option was turned on. Note that this will slow down model generation.
Warning: Edge species saving was turned on. This will slow down model generation for large simulations.

Loading thermodynamics library from surfaceThermoPt.py in /Users/rwest/Code/Cat/RMG-database/input/thermo/libraries...
Loading thermodynamics library from primaryThermoLibrary.py in /Users/rwest/Code/Cat/RMG-database/input/thermo/libraries...
Loading thermodynamics library from thermo_DFT_CCSDTF12_BAC.py in /Users/rwest/Code/Cat/RMG-database/input/thermo/libraries...
Loading thermodynamics library from DFT_QCI_thermo.py in /Users/rwest/Code/Cat/RMG-database/input/thermo/libraries...
Loading thermodynamics group database from /Users/rwest/Code/Cat/RMG-database/input/thermo/groups...
Loading transport library from GRI-Mech.py in /Users/rwest/Code/Cat/RMG-database/input/transport/libraries...
Loading transport library from NOx2018.py in /Users/rwest/Code/Cat/RMG-database/input/transport/libraries...
Loading transport library from PrimaryTransportLibrary.py in /Users/rwest/Code/Cat/RMG-database/input/transport/libraries...
Loading transport group database from /Users/rwest/Code/Cat/RMG-database/input/transport/groups...
Warning: Requested depository /Users/rwest/Code/Cat/RMG-database/input/kinetics/families/Surface_Adsorption_Single/training/reactions.py does not exist
Warning: Requested depository /Users/rwest/Code/Cat/RMG-database/input/kinetics/families/Surface_Adsorption_vdW/training/reactions.py does not exist
Loading kinetics library CPOX_Pt/Deutschmann2006 from /Users/rwest/Code/Cat/RMG-database/input/kinetics/libraries/CPOX_Pt/Deutschmann2006/reactions.py...
Loading frequencies group database from /Users/rwest/Code/Cat/RMG-database/input/statmech/groups...
Loading Platts additivity group database from /Users/rwest/Code/Cat/RMG-database/input/solvation/groups...
Trimolecular reactions are turned on
Adding rate rules from training set in kinetics families...
Could not find training depository in family Surface_Adsorption_vdW.
Must be because you turned off the training depository.
Could not find training depository in family Surface_Adsorption_Single.
Must be because you turned off the training depository.
Filling in rate rules in kinetics families by averaging...
Adding reaction library CPOX_Pt/Deutschmann2006 to model edge...

Summary of Model Enlargement
---------------------------------
Added 0 new core species
Created 10 new edge species
    HX(14)
    OX(15)
    CH3X(16)
    HOX(17)
    H2OX(18)
    CO2X(19)
    OCX(20)
    CX(21)
    CH2X(22)
    CHX(23)
Added 0 new core reactions
Created 18 new edge reactions
    X(1) + X(1) + H2(6) <=> HX(14) + HX(14)
    X(1) + X(1) + O2(3) <=> OX(15) + OX(15)
    X(1) + CH4(2) + OX(15) <=> CH3X(16) + HOX(17)
    X(1) + CH4(2) + HOX(17) <=> CH3X(16) + H2OX(18)
    X(1) + H2O(5) <=> H2OX(18)
    X(1) + CO2(4) <=> CO2X(19)
    X(1) + CO(7) <=> OCX(20)
    OX(15) + CX(21) <=> X(1) + OCX(20)
    OX(15) + OCX(20) <=> X(1) + CO2X(19)
    HX(14) + CO2X(19) <=> HOX(17) + OCX(20)
    HX(14) + CH2X(22) <=> X(1) + CH3X(16)
    HX(14) + CHX(23) <=> X(1) + CH2X(22)
    X(1) + CHX(23) <=> HX(14) + CX(21)
    HX(14) + OX(15) <=> X(1) + HOX(17)
    OX(15) + H2OX(18) <=> HOX(17) + HOX(17)
    H2(6) + CX(21) <=> CH2X(22)
    HX(14) + HOX(17) <=> X(1) + H2OX(18)
    HX(14) + CH3X(16) <=> X(1) + X(1) + CH4(2)

After model enlargement:
    The model core has 0 species and 0 reactions
    The model edge has 24 species and 18 reactions

NOT generating reactions for unreactive species N2

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    N2
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 1 species and 0 reactions
    The model edge has 23 species and 18 reactions


NOT generating reactions for unreactive species Ar

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    Ar
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 2 species and 0 reactions
    The model edge has 23 species and 18 reactions


NOT generating reactions for unreactive species He

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    He
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 3 species and 0 reactions
    The model edge has 23 species and 18 reactions


NOT generating reactions for unreactive species Ne

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    Ne
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 4 species and 0 reactions
    The model edge has 23 species and 18 reactions


Adding species X(1) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    X(1)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 5 species and 0 reactions
    The model edge has 22 species and 18 reactions


Adding species CH4(2) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH4(2)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 6 species and 0 reactions
    The model edge has 21 species and 18 reactions


Adding species O2(3) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    O2(3)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 7 species and 0 reactions
    The model edge has 20 species and 18 reactions


Adding species CO2(4) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CO2(4)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 8 species and 0 reactions
    The model edge has 19 species and 18 reactions


Adding species H2O(5) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    H2O(5)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 9 species and 0 reactions
    The model edge has 18 species and 18 reactions


Adding species H2(6) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    H2(6)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 10 species and 0 reactions
    The model edge has 17 species and 18 reactions


Adding species CO(7) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CO(7)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 11 species and 0 reactions
    The model edge has 16 species and 18 reactions


Adding species CH2O(8) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH2O(8)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 12 species and 0 reactions
    The model edge has 15 species and 18 reactions


Adding species CH3(9) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH3(9)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 13 species and 0 reactions
    The model edge has 14 species and 18 reactions


Adding species H(10) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    H(10)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 14 species and 0 reactions
    The model edge has 13 species and 18 reactions


Adding species CH3OH(11) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH3OH(11)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 15 species and 0 reactions
    The model edge has 12 species and 18 reactions


Adding species HCO(12) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    HCO(12)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 16 species and 0 reactions
    The model edge has 11 species and 18 reactions


Adding species OH(13) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    OH(13)
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 17 species and 0 reactions
    The model edge has 10 species and 18 reactions


Initialization complete. Starting model generation.

Generating initial reactions...
Species with SMILES of [CH2] named CH2(S) based on thermo library name
Species with SMILES of [CH2] named CH2(T) based on thermo library name
Species with SMILES of C[O] named CH3O based on thermo library name
Species with SMILES of [CH2]O named CH2OH based on thermo library name
Species with SMILES of [O] named O(T) based on thermo library name
Species with SMILES of [C-]#[O+].[Ni] named COX based on thermo library name
Species with SMILES of [O]O named HO2 based on thermo library name
Species with SMILES of O=[C]O named HOCO based on thermo library name
Species with SMILES of [O]C=O named formyloxy based on thermo library name
Species with SMILES of COC=O named methyl_formate based on thermo library name
Species with SMILES of CC(=O)O named acetic_acid based on thermo library name
Species with SMILES of CC=O named CH3CHO based on thermo library name
Species with SMILES of [CH]O named HCOH(T) based on thermo library name
Species with SMILES of CO[O] named CH3OO based on thermo library name
Species with SMILES of [O]OC=O named formylperoxy based on thermo library name
Species with SMILES of O=CO named formic_acid based on thermo library name
Species with SMILES of CO[C]=O named CH3OCO based on thermo library name
Species with SMILES of CC([O])=O named acetyloxy based on thermo library name
Species with SMILES of C[C]=O named acetyl based on thermo library name
Species with SMILES of O=CCO named HOCH2CHO based on thermo library name
Species with SMILES of O=[C]C=O named OCHCO based on thermo library name
Species with SMILES of [CH2]OC named CH3OCH2 based on thermo library name
Species with SMILES of CC[O] named CH3CH2O based on thermo library name
Species with SMILES of [CH2]OC=O named CH2OCHO based on thermo library name
Species with SMILES of [O]CC=O named OCH2CHO based on thermo library name
Species with SMILES of [O]CO named HOCH2O based on thermo library name
Generating kinetics for new reactions...
For reaction CH4(2) + O2(3) <=> CH3(9) + HO2(38), Ea raised from 216.4 to 231.5 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CO2(4) <=> [O]OO[C]=O(45), Ea raised from 401.1 to 405.7 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CO2(4) <=> [O]OC([O])=O(46), Ea raised from 217.3 to 222.0 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CH2O(8) <=> [CH2]OO[O](47), Ea raised from 358.5 to 363.2 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CH2O(8) <=> [O]CO[O](48), Ea raised from 172.4 to 176.3 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CH2O(8) <=> HCO(12) + HO2(38), Ea raised from 158.7 to 162.5 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + CH3OH(11) <=> HO2(38) + CH2OH(27), Ea raised from 178.9 to 195.8 kJ/mol to match endothermicity of reaction.
For reaction O2(3) + OH(13) <=> [O]OO(51), Ea raised from 14.6 to 20.8 kJ/mol to match endothermicity of reaction.
For reaction CO2(4) + CH3(9) <=> CH3OCO(60), Ea raised from 88.5 to 94.8 kJ/mol to match endothermicity of reaction.
For reaction CO2(4) + CH3(9) <=> acetyloxy(61), Ea raised from 58.1 to 65.1 kJ/mol to match endothermicity of reaction.
For reaction CO2(4) + H(10) <=> formyloxy(40), Ea raised from 47.9 to 52.0 kJ/mol to match endothermicity of reaction.
For reaction CO2(4) + HCO(12) <=> [O]C(=O)C=O(65), Ea raised from 146.3 to 150.3 kJ/mol to match endothermicity of reaction.
For reaction CO2(4) + OH(13) <=> O=[C]OO(66), Ea raised from 264.1 to 266.3 kJ/mol to match endothermicity of reaction.
For reaction CH2O(8) + OH(13) <=> [CH2]OO(80), Ea raised from 140.4 to 146.2 kJ/mol to match endothermicity of reaction.
For reaction HCO(12) + OH(13) <=> formic_acid(55) Ea raised from -1.8 to -1.8 kJ/mol.

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 61 new edge species
    CH2(S)(24)
    CH2(T)(25)
    CH3O(26)
    CH2OH(27)
    [C]=O(28)
    O(T)(29)
    C.[Ni](30)
    [H][H].[Ni](31)
    COX(32)
    O=C[Ni](33)
    C=O.[Ni](34)
    CO[Ni](35)
    OC[Ni](36)
    CO.[Ni](37)
    HO2(38)
    HOCO(39)
    formyloxy(40)
    methyl_formate(41)
    acetic_acid(42)
    CH3CHO(43)
    HCOH(T)(44)
    [O]OO[C]=O(45)
    [O]OC([O])=O(46)
    [CH2]OO[O](47)
    [O]CO[O](48)
    CH3OO(49)
    formylperoxy(50)
    [O]OO(51)
    [O]C(=O)C([O])=O(52)
    [O]C(=O)O[C]=O(53)
    O=[C]OO[C]=O(54)
    formic_acid(55)
    [O]CC([O])=O(56)
    [CH2]OC([O])=O(57)
    [O]CO[C]=O(58)
    [CH2]OO[C]=O(59)
    CH3OCO(60)
    acetyloxy(61)
    O=COCO(62)
    O=C(O)CO(63)
    O=[C]OC=O(64)
    [O]C(=O)C=O(65)
    O=[C]OO(66)
    [O]C(=O)O(67)
    acetyl(68)
    HOCH2CHO(69)
    OCHCO(70)
    [O]CC[O](71)
    [CH2]OC[O](72)
    [CH2]OO[CH2](73)
    C1COO1(74)
    C1OCO1(75)
    CH3OCH2(76)
    CH3CH2O(77)
    CH2OCHO(78)
    OCH2CHO(79)
    [CH2]OO(80)
    HOCH2O(81)
    CC(82)
    O=CC=O(83)
    OO(84)
Added 17 new core reactions
    CH3(9) + H(10) <=> CH4(2)
    H(10) + OH(13) <=> H2O(5)
    H(10) + H(10) <=> H2(6)
    H(10) + HCO(12) <=> CH2O(8)
    H2(6) + CO(7) <=> CH2O(8)
    CH3(9) + OH(13) <=> CH3OH(11)
    CO(7) + H(10) <=> HCO(12)
    CH3(9) + HCO(12) <=> CH4(2) + CO(7)
    CH4(2) + H(10) <=> H2(6) + CH3(9)
    CH4(2) + HCO(12) <=> CH2O(8) + CH3(9)
    CH4(2) + OH(13) <=> H2O(5) + CH3(9)
    HCO(12) + OH(13) <=> H2O(5) + CO(7)
    H2(6) + OH(13) <=> H2O(5) + H(10)
    CH2O(8) + OH(13) <=> H2O(5) + HCO(12)
    H(10) + HCO(12) <=> H2(6) + CO(7)
    H2(6) + HCO(12) <=> CH2O(8) + H(10)
    HCO(12) + HCO(12) <=> CO(7) + CH2O(8)
Created 154 new edge reactions
    H2(6) + CH2(S)(24) <=> CH4(2)
    H(10) + CH2(T)(25) <=> CH3(9)
    H(10) + CH3O(26) <=> CH3OH(11)
    H(10) + CH2OH(27) <=> CH3OH(11)
    H2O(5) + CH2(S)(24) <=> CH3OH(11)
    H(10) + [C]=O(28) <=> HCO(12)
    H(10) + O(T)(29) <=> OH(13)
    X(1) + CH4(2) <=> C.[Ni](30)
    X(1) + X(1) + H2O(5) <=> HX(14) + HOX(17)
    X(1) + H2(6) <=> [H][H].[Ni](31)
    X(1) + CO(7) <=> COX(32)
    X(1) + X(1) + CH2O(8) <=> HX(14) + O=C[Ni](33)
    X(1) + CH2O(8) <=> C=O.[Ni](34)
    X(1) + CH3(9) <=> CH3X(16)
    X(1) + H(10) <=> HX(14)
    X(1) + X(1) + CH3OH(11) <=> CH3X(16) + HOX(17)
    X(1) + X(1) + CH3OH(11) <=> HX(14) + CO[Ni](35)
    X(1) + X(1) + CH3OH(11) <=> HX(14) + OC[Ni](36)
    X(1) + CH3OH(11) <=> CO.[Ni](37)
    X(1) + HCO(12) <=> O=C[Ni](33)
    X(1) + OH(13) <=> HOX(17)
    CH4(2) + O2(3) <=> CH3(9) + HO2(38)
    CH3(9) + HOCO(39) <=> CH4(2) + CO2(4)
    CH3(9) + formyloxy(40) <=> CH4(2) + CO2(4)
    CH4(2) + CO2(4) <=> methyl_formate(41)
    CH4(2) + CO2(4) <=> acetic_acid(42)
    CH4(2) + CO(7) <=> CH3CHO(43)
    CH3(9) + CH2OH(27) <=> CH4(2) + CH2O(8)
    CH3(9) + CH3O(26) <=> CH4(2) + CH2O(8)
    CH3(9) + HCOH(T)(44) <=> CH4(2) + HCO(12)
    O2(3) + CO2(4) <=> [O]OO[C]=O(45)
    O2(3) + CO2(4) <=> [O]OC([O])=O(46)
    O2(3) + H2O(5) <=> OH(13) + HO2(38)
    H2(6) + O2(3) <=> H(10) + HO2(38)
    O2(3) + CH2O(8) <=> [CH2]OO[O](47)
    O2(3) + CH2O(8) <=> [O]CO[O](48)
    O2(3) + CH2O(8) <=> HCO(12) + HO2(38)
    HO2(38) + CH2(T)(25) <=> O2(3) + CH3(9)
    CH3OO(49) <=> O2(3) + CH3(9)
    O2(3) + H(10) <=> HO2(38)
    HO2(38) + CH3O(26) <=> O2(3) + CH3OH(11)
    O2(3) + CH3OH(11) <=> HO2(38) + CH2OH(27)
    O2(3) + HCO(12) <=> CO(7) + HO2(38)
    [C]=O(28) + HO2(38) <=> O2(3) + HCO(12)
    O2(3) + HCO(12) <=> formylperoxy(50)
    O(T)(29) + HO2(38) <=> O2(3) + OH(13)
    O2(3) + OH(13) <=> [O]OO(51)
    [O]C(=O)C([O])=O(52) <=> CO2(4) + CO2(4)
    [O]C(=O)O[C]=O(53) <=> CO2(4) + CO2(4)
    O=[C]OO[C]=O(54) <=> CO2(4) + CO2(4)
    OH(13) + HOCO(39) <=> H2O(5) + CO2(4)
    OH(13) + formyloxy(40) <=> H2O(5) + CO2(4)
    H(10) + HOCO(39) <=> H2(6) + CO2(4)
    H(10) + formyloxy(40) <=> H2(6) + CO2(4)
    H2(6) + CO2(4) <=> formic_acid(55)
    HCO(12) + HOCO(39) <=> CO2(4) + CH2O(8)
    HCO(12) + formyloxy(40) <=> CO2(4) + CH2O(8)
    [O]CC([O])=O(56) <=> CO2(4) + CH2O(8)
    [CH2]OC([O])=O(57) <=> CO2(4) + CH2O(8)
    [O]CO[C]=O(58) <=> CO2(4) + CH2O(8)
    [CH2]OO[C]=O(59) <=> CO2(4) + CH2O(8)
    HOCO(39) + CH2(T)(25) <=> CO2(4) + CH3(9)
    formyloxy(40) + CH2(T)(25) <=> CO2(4) + CH3(9)
    CO2(4) + CH3(9) <=> CH3OCO(60)
    CO2(4) + CH3(9) <=> acetyloxy(61)
    CO2(4) + H(10) <=> HOCO(39)
    CO2(4) + H(10) <=> formyloxy(40)
    HOCO(39) + CH2OH(27) <=> CO2(4) + CH3OH(11)
    HOCO(39) + CH3O(26) <=> CO2(4) + CH3OH(11)
    formyloxy(40) + CH2OH(27) <=> CO2(4) + CH3OH(11)
    formyloxy(40) + CH3O(26) <=> CO2(4) + CH3OH(11)
    CO2(4) + CH3OH(11) <=> O=COCO(62)
    CO2(4) + CH3OH(11) <=> O=C(O)CO(63)
    HOCO(39) + [C]=O(28) <=> CO2(4) + HCO(12)
    formyloxy(40) + [C]=O(28) <=> CO2(4) + HCO(12)
    CO2(4) + HCO(12) <=> O=[C]OC=O(64)
    CO2(4) + HCO(12) <=> [O]C(=O)C=O(65)
    HOCO(39) + O(T)(29) <=> CO2(4) + OH(13)
    formyloxy(40) + O(T)(29) <=> CO2(4) + OH(13)
    CO2(4) + OH(13) <=> O=[C]OO(66)
    CO2(4) + OH(13) <=> [O]C(=O)O(67)
    H2O(5) + CO(7) <=> formic_acid(55)
    OH(13) + CH2OH(27) <=> H2O(5) + CH2O(8)
    OH(13) + CH3O(26) <=> H2O(5) + CH2O(8)
    OH(13) + HCOH(T)(44) <=> H2O(5) + HCO(12)
    H(10) + CH2OH(27) <=> H2(6) + CH2O(8)
    H(10) + CH3O(26) <=> H2(6) + CH2O(8)
    H(10) + HCOH(T)(44) <=> H2(6) + HCO(12)
    HCO(12) + CH2(T)(25) <=> CO(7) + CH3(9)
    CO(7) + CH3(9) <=> acetyl(68)
    HCO(12) + CH3O(26) <=> CO(7) + CH3OH(11)
    HCO(12) + CH2OH(27) <=> CO(7) + CH3OH(11)
    CO(7) + CH3OH(11) <=> methyl_formate(41)
    CO(7) + CH3OH(11) <=> HOCH2CHO(69)
    HCO(12) + [C]=O(28) <=> CO(7) + HCO(12)
    CO(7) + HCO(12) <=> OCHCO(70)
    HCO(12) + O(T)(29) <=> CO(7) + OH(13)
    CO(7) + OH(13) <=> HOCO(39)
    HCO(12) + CH2OH(27) <=> CH2O(8) + CH2O(8)
    HCO(12) + CH3O(26) <=> CH2O(8) + CH2O(8)
    [O]CC[O](71) <=> CH2O(8) + CH2O(8)
    [CH2]OC[O](72) <=> CH2O(8) + CH2O(8)
    [CH2]OO[CH2](73) <=> CH2O(8) + CH2O(8)
    CH2O(8) + CH2O(8) <=> C1COO1(74)
    CH2O(8) + CH2O(8) <=> C1OCO1(75)
    CH2OH(27) + CH2(T)(25) <=> CH2O(8) + CH3(9)
    CH3O(26) + CH2(T)(25) <=> CH2O(8) + CH3(9)
    CH2O(8) + CH3(9) <=> CH3OCH2(76)
    CH2O(8) + CH3(9) <=> CH3CH2O(77)
    CH2O(8) + H(10) <=> CH2OH(27)
    CH2O(8) + H(10) <=> CH3O(26)
    CH2OH(27) + CH2OH(27) <=> CH2O(8) + CH3OH(11)
    CH3O(26) + CH2OH(27) <=> CH2O(8) + CH3OH(11)
    CH3O(26) + CH2OH(27) <=> CH2O(8) + CH3OH(11)
    CH3O(26) + CH3O(26) <=> CH2O(8) + CH3OH(11)
    HCO(12) + HCOH(T)(44) <=> CH2O(8) + HCO(12)
    [C]=O(28) + CH2OH(27) <=> CH2O(8) + HCO(12)
    [C]=O(28) + CH3O(26) <=> CH2O(8) + HCO(12)
    CH2O(8) + HCO(12) <=> CH2OCHO(78)
    CH2O(8) + HCO(12) <=> OCH2CHO(79)
    O(T)(29) + CH2OH(27) <=> CH2O(8) + OH(13)
    O(T)(29) + CH3O(26) <=> CH2O(8) + OH(13)
    CH2O(8) + OH(13) <=> [CH2]OO(80)
    CH2O(8) + OH(13) <=> HOCH2O(81)
    CH4(2) + CH2(T)(25) <=> CH3(9) + CH3(9)
    CH3(9) + CH3(9) <=> CC(82)
    H2(6) + CH2(T)(25) <=> CH3(9) + H(10)
    CH4(2) + CH3O(26) <=> CH3(9) + CH3OH(11)
    CH3(9) + CH3OH(11) <=> CH4(2) + CH2OH(27)
    HCOH(T)(44) + CH2(T)(25) <=> CH3(9) + HCO(12)
    CH2O(8) + CH2(T)(25) <=> CH3(9) + HCO(12)
    CH4(2) + [C]=O(28) <=> CH3(9) + HCO(12)
    CH3(9) + HCO(12) <=> CH3CHO(43)
    CH3(9) + OH(13) <=> H2O(5) + CH2(T)(25)
    CH4(2) + O(T)(29) <=> CH3(9) + OH(13)
    H(10) + CH3OH(11) <=> H2(6) + CH3O(26)
    H(10) + CH3OH(11) <=> H2(6) + CH2OH(27)
    H2(6) + [C]=O(28) <=> H(10) + HCO(12)
    H2(6) + O(T)(29) <=> H(10) + OH(13)
    HCOH(T)(44) + CH2OH(27) <=> CH3OH(11) + HCO(12)
    HCOH(T)(44) + CH3O(26) <=> CH3OH(11) + HCO(12)
    CH2O(8) + CH3O(26) <=> CH3OH(11) + HCO(12)
    CH2O(8) + CH2OH(27) <=> CH3OH(11) + HCO(12)
    CH3OH(11) + OH(13) <=> H2O(5) + CH3O(26)
    CH3OH(11) + OH(13) <=> H2O(5) + CH2OH(27)
    HCOH(T)(44) + [C]=O(28) <=> HCO(12) + HCO(12)
    CH2O(8) + [C]=O(28) <=> HCO(12) + HCO(12)
    HCO(12) + HCO(12) <=> O=CC=O(83)
    HCOH(T)(44) + O(T)(29) <=> HCO(12) + OH(13)
    H2O(5) + [C]=O(28) <=> HCO(12) + OH(13)
    CH2O(8) + O(T)(29) <=> HCO(12) + OH(13)
    HCO(12) + OH(13) <=> formic_acid(55)
    H2O(5) + O(T)(29) <=> OH(13) + OH(13)
    OH(13) + OH(13) <=> OO(84)

After model enlargement:
    The model core has 17 species and 17 reactions
    The model edge has 71 species and 172 reactions


Completed initial enlarge edge step.

Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 0 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 0 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:08
    Memory used: 573.14 MB

Beginning model generation stage 1...

Conducting simulation of reaction system 1...
At time 0.0000e+00 s, species HX(14) at 14514021602.2 exceeded the minimum rate for simulation interruption of 0.1
At time 0.0000e+00 s, species OX(15) at 2.82024509718e+12 exceeded the minimum rate for simulation interruption of 0.1
At time 0.0000e+00 s, species CH3X(16) at 14514021602.2 exceeded the minimum rate for simulation interruption of 0.1
At time 0.0000e+00 s, species C.[Ni](30) at 8.05732696408e+12 exceeded the minimum rate for simulation interruption of 0.1
At time 0.0000e+00 s, species HO2(38) at 94.7578315176 exceeded the minimum rate for simulation interruption of 0.1
Exceeded max number of objects...removing excess objects
Reached max number of objects...preparing to terminate
At time 0.0000e+00 s, species C.[Ni](30) at rate ratio 8.05732696408e+12 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species C.[Ni](30) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    C.[Ni](30)
Created 0 new edge species
Moved 1 reactions from edge to core
    X(1) + CH4(2) <=> C.[Ni](30)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 18 species and 18 reactions
    The model edge has 70 species and 171 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 18 species and 18 reactions
    The model edge has 70 species and 171 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 1 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 1 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:11
    Memory used: 580.72 MB

Conducting simulation of reaction system 1...
At time 0.0000e+00 s, species OX(15) at 0.202085539447 exceeded the minimum rate for simulation interruption of 0.1
Exceeded max number of objects...removing excess objects
Reached max number of objects...preparing to terminate
At time 0.0000e+00 s, species OX(15) at rate ratio 0.202085539447 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species OX(15) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    OX(15)
Created 0 new edge species
Moved 1 reactions from edge to core
    X(1) + X(1) + O2(3) <=> OX(15) + OX(15)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 19 species and 19 reactions
    The model edge has 69 species and 170 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 19 species and 19 reactions
    The model edge has 69 species and 170 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 2 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 2 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 32 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:14
    Memory used: 589.36 MB

Conducting simulation of reaction system 1...
Exceeded max number of objects...removing excess objects
Reached max number of objects...preparing to terminate
At time 0.0000e+00 s, species CH3X(16) at rate ratio 0.000903419983614 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species CH3X(16) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH3X(16)
Created 0 new edge species
Moved 1 reactions from edge to core
    X(1) + CH3(9) <=> CH3X(16)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 20 species and 20 reactions
    The model edge has 68 species and 169 reactions


Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 3 new edge reactions
    HOX(17) + CH2X(22) <=> OX(15) + CH3X(16)
    X(1) + CO[Ni](35) <=> OX(15) + CH3X(16)
    X(1) + X(1) + CC(82) <=> CH3X(16) + CH3X(16)

After model enlargement:
    The model core has 20 species and 20 reactions
    The model edge has 68 species and 172 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 3 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 3 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 35 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 35 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:18
    Memory used: 594.97 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 0.0000e+00 s, species HX(14) at rate ratio 0.000903419983614 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species HX(14) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    HX(14)
Created 0 new edge species
Moved 3 reactions from edge to core
    X(1) + X(1) + H2(6) <=> HX(14) + HX(14)
    HX(14) + CH3X(16) <=> X(1) + X(1) + CH4(2)
    X(1) + H(10) <=> HX(14)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 21 species and 23 reactions
    The model edge has 67 species and 169 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 21 species and 23 reactions
    The model edge has 67 species and 169 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 6 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 6 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 35 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 35 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:21
    Memory used: 600.33 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 5.1167e-13 s, species CH2X(22) at rate ratio 0.000101270333768 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species CH2X(22) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CH2X(22)
Created 0 new edge species
Moved 1 reactions from edge to core
    HX(14) + CH2X(22) <=> X(1) + CH3X(16)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 22 species and 24 reactions
    The model edge has 66 species and 168 reactions


Generating kinetics for new reactions...
For reaction HOX(17) + CHX(23) <=> OX(15) + CH2X(22), Ea raised from 42.4 to 43.7 kJ/mol to match endothermicity of reaction.

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 1 new edge species
    CC[Ni](85)
Added 0 new core reactions
Created 3 new edge reactions
    HOX(17) + CHX(23) <=> OX(15) + CH2X(22)
    X(1) + CC[Ni](85) <=> CH3X(16) + CH2X(22)
    CH2X(22) + CH2X(22) <=> CH3X(16) + CHX(23)

After model enlargement:
    The model core has 22 species and 24 reactions
    The model edge has 67 species and 171 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 7 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 7 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 38 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 38 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:24
    Memory used: 606.83 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 8.6116e-15 s, species CHX(23) at rate ratio 0.000285791066535 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species CHX(23) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CHX(23)
Created 0 new edge species
Moved 2 reactions from edge to core
    HX(14) + CHX(23) <=> X(1) + CH2X(22)
    CH2X(22) + CH2X(22) <=> CH3X(16) + CHX(23)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 23 species and 26 reactions
    The model edge has 66 species and 169 reactions


Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 1 new edge species
    CC=[Ni](86)
Added 0 new core reactions
Created 4 new edge reactions
    HOX(17) + CX(21) <=> OX(15) + CHX(23)
    X(1) + CC=[Ni](86) <=> CH3X(16) + CHX(23)
    CH3X(16) + CX(21) <=> CH2X(22) + CHX(23)
    CX(21) + CH2X(22) <=> CHX(23) + CHX(23)

After model enlargement:
    The model core has 23 species and 26 reactions
    The model edge has 67 species and 173 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 9 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 9 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 42 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 42 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:28
    Memory used: 613.87 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 1.2120e-13 s, species CX(21) at rate ratio 0.000129060470291 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species CX(21) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CX(21)
Created 0 new edge species
Moved 4 reactions from edge to core
    X(1) + CHX(23) <=> HX(14) + CX(21)
    H2(6) + CX(21) <=> CH2X(22)
    CH3X(16) + CX(21) <=> CH2X(22) + CHX(23)
    CX(21) + CH2X(22) <=> CHX(23) + CHX(23)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 24 species and 30 reactions
    The model edge has 66 species and 169 reactions


Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 1 new edge species
    CC#[Ni](87)
Added 0 new core reactions
Created 1 new edge reactions
    X(1) + CC#[Ni](87) <=> CH3X(16) + CX(21)

After model enlargement:
    The model core has 24 species and 30 reactions
    The model edge has 67 species and 170 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 13 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 13 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 43 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 43 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:32
    Memory used: 621.52 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 2.7155e-10 s, species HOX(17) at rate ratio 0.000107886789363 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species HOX(17) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    HOX(17)
Created 0 new edge species
Moved 8 reactions from edge to core
    X(1) + CH4(2) + OX(15) <=> CH3X(16) + HOX(17)
    HX(14) + OX(15) <=> X(1) + HOX(17)
    X(1) + X(1) + H2O(5) <=> HX(14) + HOX(17)
    X(1) + X(1) + CH3OH(11) <=> CH3X(16) + HOX(17)
    X(1) + OH(13) <=> HOX(17)
    HOX(17) + CH2X(22) <=> OX(15) + CH3X(16)
    HOX(17) + CHX(23) <=> OX(15) + CH2X(22)
    HOX(17) + CX(21) <=> OX(15) + CHX(23)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 25 species and 38 reactions
    The model edge has 66 species and 162 reactions


Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 3 new edge species
    OO[Ni](88)
    OC=[Ni](89)
    OC#[Ni](90)
Added 0 new core reactions
Created 5 new edge reactions
    X(1) + OO[Ni](88) <=> OX(15) + HOX(17)
    X(1) + OC[Ni](36) <=> HOX(17) + CH2X(22)
    X(1) + OC=[Ni](89) <=> HOX(17) + CHX(23)
    X(1) + OC#[Ni](90) <=> HOX(17) + CX(21)
    X(1) + X(1) + OO(84) <=> HOX(17) + HOX(17)

After model enlargement:
    The model core has 25 species and 38 reactions
    The model edge has 69 species and 167 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 21 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 21 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 48 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 48 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:36
    Memory used: 631.48 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 1.5111e-09 s, species OCX(20) at rate ratio 0.0001000098486 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species OCX(20) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    OCX(20)
Created 0 new edge species
Moved 2 reactions from edge to core
    X(1) + CO(7) <=> OCX(20)
    OX(15) + CX(21) <=> X(1) + OCX(20)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 26 species and 40 reactions
    The model edge has 68 species and 165 reactions


Species with SMILES of CC(=O)[Ni] named acetylX based on thermo library name
Species with SMILES of O=C(O)[Ni] named HOCOX based on thermo library name
Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 2 new edge species
    acetylX(91)
    HOCOX(92)
Added 0 new core reactions
Created 7 new edge reactions
    CH2X(22) + O=C[Ni](33) <=> CH3X(16) + OCX(20)
    X(1) + acetylX(91) <=> CH3X(16) + OCX(20)
    X(1) + O=C[Ni](33) <=> HX(14) + OCX(20)
    CHX(23) + O=C[Ni](33) <=> OCX(20) + CH2X(22)
    CX(21) + O=C[Ni](33) <=> OCX(20) + CHX(23)
    OX(15) + O=C[Ni](33) <=> HOX(17) + OCX(20)
    X(1) + HOCOX(92) <=> HOX(17) + OCX(20)

After model enlargement:
    The model core has 26 species and 40 reactions
    The model edge has 70 species and 172 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 23 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 23 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 55 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 55 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:40
    Memory used: 647.19 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 5.2490e-09 s, species H2OX(18) at rate ratio 0.000103100595156 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species H2OX(18) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    H2OX(18)
Created 0 new edge species
Moved 4 reactions from edge to core
    X(1) + CH4(2) + HOX(17) <=> CH3X(16) + H2OX(18)
    X(1) + H2O(5) <=> H2OX(18)
    OX(15) + H2OX(18) <=> HOX(17) + HOX(17)
    HX(14) + HOX(17) <=> X(1) + H2OX(18)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 27 species and 44 reactions
    The model edge has 69 species and 168 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 27 species and 44 reactions
    The model edge has 69 species and 168 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 27 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 27 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 55 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 55 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:45
    Memory used: 664.20 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 2.0590e-08 s, species O=C[Ni](33) at rate ratio 0.00010000776539 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species O=C[Ni](33) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    O=C[Ni](33)
Created 0 new edge species
Moved 7 reactions from edge to core
    X(1) + X(1) + CH2O(8) <=> HX(14) + O=C[Ni](33)
    X(1) + HCO(12) <=> O=C[Ni](33)
    CH2X(22) + O=C[Ni](33) <=> CH3X(16) + OCX(20)
    X(1) + O=C[Ni](33) <=> HX(14) + OCX(20)
    CHX(23) + O=C[Ni](33) <=> OCX(20) + CH2X(22)
    CX(21) + O=C[Ni](33) <=> OCX(20) + CHX(23)
    OX(15) + O=C[Ni](33) <=> HOX(17) + OCX(20)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 28 species and 51 reactions
    The model edge has 68 species and 161 reactions


Species with SMILES of O=CO[Ni] named formyloxyX based on thermo library name
Species with SMILES of O=CC[Ni] named vinoxyX based on thermo library name
Species with SMILES of O=CC=[Ni] named ketene(T)X based on thermo library name
Species with SMILES of O=CC(=O)[Ni] named OCHCOX based on thermo library name
Generating kinetics for new reactions...

Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 5 new edge species
    formyloxyX(93)
    vinoxyX(94)
    ketene(T)X(95)
    O=CC#[Ni](96)
    OCHCOX(97)
Added 0 new core reactions
Created 8 new edge reactions
    X(1) + formyloxyX(93) <=> OX(15) + O=C[Ni](33)
    X(1) + X(1) + CH3CHO(43) <=> CH3X(16) + O=C[Ni](33)
    X(1) + vinoxyX(94) <=> CH2X(22) + O=C[Ni](33)
    X(1) + ketene(T)X(95) <=> CHX(23) + O=C[Ni](33)
    X(1) + O=CC#[Ni](96) <=> CX(21) + O=C[Ni](33)
    X(1) + X(1) + formic_acid(55) <=> HOX(17) + O=C[Ni](33)
    X(1) + OCHCOX(97) <=> OCX(20) + O=C[Ni](33)
    X(1) + X(1) + O=CC=O(83) <=> O=C[Ni](33) + O=C[Ni](33)

After model enlargement:
    The model core has 28 species and 51 reactions
    The model edge has 73 species and 169 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 34 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 34 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:50
    Memory used: 682.84 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 9.1489e-08 s, species CO2X(19) at rate ratio 0.000100026507073 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species CO2X(19) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    CO2X(19)
Created 0 new edge species
Moved 3 reactions from edge to core
    X(1) + CO2(4) <=> CO2X(19)
    OX(15) + OCX(20) <=> X(1) + CO2X(19)
    HX(14) + CO2X(19) <=> HOX(17) + OCX(20)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 29 species and 54 reactions
    The model edge has 72 species and 166 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 29 species and 54 reactions
    The model edge has 72 species and 166 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 37 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 37 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:03:57
    Memory used: 703.30 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 3.4173e-06 s, species COX(32) at rate ratio 0.000100076088221 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species COX(32) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    COX(32)
Created 0 new edge species
Moved 1 reactions from edge to core
    X(1) + CO(7) <=> COX(32)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 30 species and 55 reactions
    The model edge has 71 species and 165 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 30 species and 55 reactions
    The model edge has 71 species and 165 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 38 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 38 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:04:03
    Memory used: 700.67 MB

Conducting simulation of reaction system 1...
Reached max number of objects...preparing to terminate
At time 5.7878e-06 s, species [H][H].[Ni](31) at rate ratio 0.000100588614249 exceeded the minimum rate for moving to model core of 0.0001
terminating simulation due to interrupt...


Adding species [H][H].[Ni](31) to model core

Summary of Model Enlargement
---------------------------------
Added 1 new core species
    [H][H].[Ni](31)
Created 0 new edge species
Moved 1 reactions from edge to core
    X(1) + H2(6) <=> [H][H].[Ni](31)
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 31 species and 56 reactions
    The model edge has 70 species and 164 reactions



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 31 species and 56 reactions
    The model edge has 70 species and 164 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 39 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 39 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:04:08
    Memory used: 722.63 MB

Conducting simulation of reaction system 1...
At time 2.1835e-05 s, reached target termination conversion: 0.950000 of O2(3)
    O2(3) conversion: 0.9505    



Summary of Secondary Model Edge Enlargement
---------------------------------
Added 0 new core species
Created 0 new edge species
Added 0 new core reactions
Created 0 new edge reactions

After model enlargement:
    The model core has 31 species and 56 reactions
    The model edge has 70 species and 164 reactions


Saving current model core to Chemkin file...
Chemkin file contains 17 reactions.
Chemkin file contains 39 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 17 reactions.
Chemkin file contains 39 reactions.
Saving current model core and edge to Chemkin file...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving annotated version of Chemkin files...
Chemkin file contains 157 reactions.
Chemkin file contains 63 reactions.
Saving current model core to HTML file...
Saving current model edge to HTML file...
Updating RMG execution statistics...
    Execution time (DD:HH:MM:SS): 00:00:04:10
    Memory used: 731.77 MB

Making seed mechanism...
Performing final model checks...
No collision rate violators found.

MODEL GENERATION COMPLETED

The final model core has 31 species and 56 reactions
The final model edge has 70 species and 164 reactions

RMG execution terminated at Tue Dec  4 16:46:23 2018
================================================================================
                                 Profiling Data                                 
================================================================================
Sorted by internal time
Tue Dec  4 16:46:25 2018    /Users/rwest/Code/Cat/cpox-methane/RMG.profile

         166971795 function calls (158091842 primitive calls) in 250.684 seconds

   Ordered by: internal time
   List reduced from 3207 to 25 due to restriction <25>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
2544335/2181394   43.875    0.000   48.831    0.000 base.py:908(matchNodeToStructure)
     7516   21.534    0.003   33.532    0.004 common.py:153(ensure_species)
1586467/54   18.384    0.000   40.634    0.752 rules.py:456(fillRulesByAveragingUp)
6558721/1546789   11.810    0.000   49.084    0.000 copy.py:145(deepcopy)
   398323    9.330    0.000   25.804    0.000 family.py:1786(__generateReactions)
  6158249    6.722    0.000    8.249    0.000 copy.py:267(_keep_alive)
  1365498    6.261    0.000    6.261    0.000 base.py:1249(getAllCombinations)
  1587251    5.176    0.000    9.118    0.000 rules.py:432(getAllRules)
     4325    4.902    0.001   19.661    0.005 common.py:190(ensure_independent_atom_ids)
    16305    4.733    0.000   13.342    0.001 adjlist.py:420(fromAdjacencyList)
 13401218    3.516    0.000    3.530    0.000 {isinstance}
   175132    3.057    0.000    3.987    0.000 {eval}
325539/77323    3.006    0.000   28.260    0.000 copy.py:306(_reconstruct)
  1125806    2.835    0.000    5.479    0.000 Graph.py:81(add_edge)
1474853/1474827    2.501    0.000   15.708    0.000 copy.py:253(_deepcopy_dict)
     3810    2.312    0.001    3.871    0.001 family.py:1206(applyRecipe)
    50928    2.249    0.000    2.626    0.000 family.py:1582(__matchReactantToTemplate)
       15    2.160    0.144   11.203    0.747 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
1522571/1522502    2.144    0.000    2.465    0.000 {method 'format' of 'str' objects}
  1587251    2.097    0.000   11.462    0.000 rules.py:412(getRule)
  1587261    2.067    0.000    3.150    0.000 posixpath.py:82(split)
288533/142906    1.998    0.000   50.986    0.000 base.py:989(descendTree)
325524/77308    1.954    0.000   10.493    0.000 copy.py:234(_deepcopy_tuple)
       54    1.910    0.035   91.870    1.701 family.py:1058(addKineticsRulesFromTrainingSet)
      184    1.740    0.009    6.446    0.035 base.py:183(load)


   Ordered by: internal time
   List reduced from 3207 to 25 due to restriction <25>

Function                                                           was called by...
                                                                       ncalls  tottime  cumtime
base.py:908(matchNodeToStructure)                                  <- 2181394   39.629   48.831  base.py:989(descendTree)
                                                                    362941/232802    4.246    5.294  base.py:1104(matchToStructure)
common.py:153(ensure_species)                                      <-    4325    4.534    9.625  common.py:190(ensure_independent_atom_ids)
                                                                         2650   16.048   22.015  common.py:230(find_degenerate_reactions)
                                                                          541    0.952    1.892  family.py:1786(__generateReactions)
rules.py:456(fillRulesByAveragingUp)                               <-      54    0.004   40.634  family.py:1198(fillKineticsRulesByAveragingUp)
                                                                    1586413/442   18.380   40.627  rules.py:456(fillRulesByAveragingUp)
copy.py:145(deepcopy)                                              <-     316    0.000    0.004  base.py:273(getSpecies)
                                                                        12429    0.022    0.141  base.py:1320(loadEntry)
                                                                       502431    1.066    7.219  common.py:153(ensure_species)
                                                                       206857    0.388    2.524  common.py:190(ensure_independent_atom_ids)
                                                                    240758/28430    0.467    3.586  copy.py:226(_deepcopy_list)
                                                                    1495623/455575    2.347    9.849  copy.py:234(_deepcopy_tuple)
                                                                      2946206    5.027   12.175  copy.py:253(_deepcopy_dict)
                                                                         3795    0.006    0.625  copy.py:283(_deepcopy_inst)
                                                                    325550/77308    0.708   10.809  copy.py:306(_reconstruct)
                                                                          508    0.001    0.009  draw.py:133(draw)
                                                                        68363    0.163    2.830  family.py:1058(addKineticsRulesFromTrainingSet)
                                                                        61532    0.119    0.812  family.py:1206(applyRecipe)
                                                                       253959    0.458    3.198  family.py:1786(__generateReactions)
                                                                          149    0.001    0.037  family.py:2341(getKineticsFromDepository)
                                                                       203884    0.390    2.639  filtration.py:342(mark_unreactive_structures)
                                                                        11266    0.018    0.127  model.py:236(checkForExistingSpecies)
                                                                        11750    0.021    0.139  model.py:305(makeNewSpecies)
                                                                       107880    0.379   26.238  react.py:66(reactSpecies)
                                                                         6243    0.036    1.478  rules.py:456(fillRulesByAveragingUp)
                                                                         1087    0.004    0.082  rules.py:618(estimateKinetics)
                                                                           14    0.000    0.004  thermo.py:242(averageThermoData)
                                                                        30906    0.060    0.732  thermo.py:346(convertRingToSubMolecule)
                                                                          232    0.000    0.002  thermo.py:371(combineTwoRingsIntoSubMolecule)
                                                                          140    0.000    0.001  thermo.py:440(bicyclicDecompositionForPolyring)
                                                                         4268    0.007    0.054  thermo.py:511(splitBicyclicIntoSingleRings)
                                                                         1186    0.002    0.013  thermo.py:521(saturate_ring_bonds)
                                                                        22250    0.045    0.201  thermo.py:1102(getThermoData)
                                                                         2393    0.004    0.025  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                                         1203    0.004    0.032  thermo.py:1416(getThermoDataFromLibraries)
                                                                          256    0.002    0.094  thermo.py:1525(getThermoDataFromLibrary)
                                                                        23109    0.042    0.296  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                                        12163    0.021    0.142  thermoengine.py:160(evaluator)
                                                                           15    0.000    0.011  transport.py:377(getTransportPropertiesFromLibrary)
family.py:1786(__generateReactions)                                <-  397782    1.261    4.092  family.py:1609(generateReactions)
                                                                           61    0.007    0.285  family.py:1643(addReverseAttribute)
                                                                          480    8.062   21.428  family.py:1716(calculateDegeneracy)
copy.py:267(_keep_alive)                                           <- 6158249    6.722    8.249  copy.py:145(deepcopy)
base.py:1249(getAllCombinations)                                   <-      46    0.000    0.000  family.py:945(generateProductTemplate)
                                                                      1365452    6.261    6.261  rules.py:456(fillRulesByAveragingUp)
rules.py:432(getAllRules)                                          <- 1587251    5.176    9.118  rules.py:412(getRule)
common.py:190(ensure_independent_atom_ids)                         <-    4059    4.523   17.346  database.py:457(generate_reactions_from_families)
                                                                          266    0.379    2.315  family.py:1716(calculateDegeneracy)
adjlist.py:420(fromAdjacencyList)                                  <-    6959    3.192   11.259  base.py:273(getSpecies)
                                                                          233    0.027    0.037  base.py:1320(loadEntry)
                                                                         4916    0.839    0.982  groups.py:75(loadEntry)
                                                                            2    0.000    0.002  input.py:161(adjacencyList)
                                                                            2    0.000    0.000  main.py:399(initialize)
                                                                            2    0.000    0.000  solvation.py:335(loadEntry)
                                                                          102    0.008    0.010  solvation.py:402(loadEntry)
                                                                           51    0.003    0.003  statmech.py:216(loadEntry)
                                                                          465    0.063    0.252  thermo.py:591(loadEntry)
                                                                         3265    0.569    0.676  thermo.py:656(loadEntry)
                                                                          264    0.029    0.116  transport.py:132(loadEntry)
                                                                           44    0.002    0.003  transport.py:183(loadEntry)
{isinstance}                                                       <-     112    0.000    0.000  BIFFRecords.py:66(get_biff_record)
                                                                           16    0.000    0.000  BIFFRecords.py:266(__init__)
                                                                         1176    0.000    0.000  Cell.py:172(_get_cells_biff_data_mul)
                                                                          152    0.000    0.000  Row.py:41(__init__)
                                                                         2968    0.001    0.001  Row.py:234(write)
                                                                          160    0.000    0.000  UnicodeUtils.py:45(upack2)
                                                                          144    0.000    0.000  UnicodeUtils.py:105(upack1)
                                                                           16    0.000    0.000  Workbook.py:344(add_sheet)
                                                                            6    0.000    0.000  __init__.py:49(normalize_encoding)
                                                                           15    0.000    0.000  __init__.py:70(process_projection_requirements)
                                                                            6    0.000    0.000  __init__.py:71(search_function)
                                                                         3120    0.001    0.001  __init__.py:312(getMessage)
                                                                           16    0.000    0.000  __init__.py:383(_init)
                                                                         3120    0.001    0.001  __init__.py:849(emit)
                                                                       116129    0.013    0.013  __init__.py:1216(log)
                                                                          284    0.000    0.002  _abcoll.py:548(update)
                                                                           15    0.000    0.000  _base.py:432(__init__)
                                                                           45    0.000    0.000  _base.py:866(set_position)
                                                                          315    0.000    0.000  _base.py:3790(get_tightbbox)
                                                                           32    0.000    0.000  _compat.py:79(encode_filename)
                                                                          492    0.000    0.000  _distn_infrastructure.py:524(argsreduce)
                                                                          251    0.000    0.000  _distn_infrastructure.py:3404(get_distribution_names)
                                                                          131    0.000    0.000  _methods.py:43(_count_reduce_items)
                                                                            5    0.000    0.000  _methods.py:53(_mean)
                                                                          252    0.000    0.000  _methods.py:76(_var)
                                                                          126    0.000    0.000  _methods.py:122(_std)
                                                                           15    0.000    0.000  _subplots.py:23(__init__)
                                                                          164    0.000    0.000  _util.py:14(_valarray)
                                                                            8    0.000    0.000  _version.py:114(_compare)
                                                                            2    0.000    0.000  abc.py:105(register)
                                                                        28093    0.004    0.004  adjlist.py:725(toAdjacencyList)
                                                                            1    0.000    0.000  api.py:48(__init__)
                                                                            1    0.000    0.000  api.py:112(_cdef)
                                                                            2    0.000    0.000  api.py:130(dlopen)
                                                                            3    0.000    0.000  api.py:144(_typeof_locked)
                                                                            8    0.000    0.000  api.py:195(sizeof)
                                                                         6828    0.002    0.002  api.py:224(new)
                                                                            1    0.000    0.000  api.py:275(cast)
                                                                            1    0.000    0.000  api.py:766(_make_ffi_library)
                                                                          470    0.000    0.000  api.py:801(update_accessors)
                                                                         3758    0.002    0.002  artist.py:353(get_transform)
                                                                         2160    0.001    0.001  artist.py:667(set_clip_path)
                                                                          880    0.000    0.000  ast.py:243(generic_visit)
                                                                         8556    0.002    0.002  base.py:464(__loadTree)
                                                                        26106    0.007    0.007  base.py:843(ancestors)
                                                                      7930322    2.080    2.080  base.py:908(matchNodeToStructure)
                                                                       362941    0.107    0.107  base.py:1104(matchToStructure)
                                                                         4082    0.002    0.002  base.py:1111(isspmatrix)
                                                                       346871    0.060    0.060  base.py:1132(getPossibleStructures)
                                                                       231284    0.052    0.052  base.py:1273(isMoleculeForbidden)
                                                                         2041    0.000    0.000  blas.py:226(_get_funcs)
                                                                         1125    0.000    0.000  c_parser.py:250(_type_modify_decl)
                                                                         5586    0.001    0.001  c_parser.py:305(_fix_decl_name_type)
                                                                         5511    0.002    0.002  c_parser.py:367(_build_declarations)
                                                                            1    0.000    0.000  c_parser.py:620(p_decl_body)
                                                                        18414    0.007    0.007  cbook.py:687(is_string_like)
                                                                          300    0.000    0.003  cbook.py:2554(safe_first_element)
                                                                           32    0.000    0.000  ck2cti.py:894(get_index)
                                                                         1019    0.000    0.000  ck2cti.py:909(contains)
                                                                           85    0.000    0.000  collections.py:305(namedtuple)
                                                                         5584    0.002    0.002  colors.py:107(_is_nth_color)
                                                                          310    0.000    0.000  colors.py:151(_to_rgba_no_colorcycle)
                                                                          660    0.000    0.000  common.py:47(saveEntry)
                                                                        30163    0.013    0.013  common.py:153(ensure_species)
                                                                           12    0.000    0.000  commontypes.py:24(resolve_common_type)
                                                                           32    0.000    0.000  compiler.py:74(generate)
                                                                         5344    0.001    0.001  compiler.py:1184(visit_Output)
                                                                         1696    0.001    0.001  compiler.py:1376(visit_Const)
                                                                          288    0.000    0.000  compiler.py:1492(visit_Getitem)
                                                                         4271    0.002    0.002  constraints.py:36(failsSpeciesConstraints)
                                                                       651093    0.151    0.151  copy.py:306(_reconstruct)
                                                                          510    0.000    0.000  core.py:599(filled)
                                                                        31778    0.014    0.014  core.py:6048(isMaskedArray)
                                                                          629    0.000    0.000  cparser.py:303(_internal_parse)
                                                                          729    0.000    0.000  cparser.py:399(_parse_decl)
                                                                            3    0.000    0.000  cparser.py:452(parse_type_and_quals)
                                                                         1975    0.000    0.000  cparser.py:474(_extract_quals)
                                                                         1678    0.000    0.000  cparser.py:486(_get_type_pointer)
                                                                         9192    0.001    0.001  cparser.py:495(_get_type_and_quals)
                                                                          501    0.000    0.000  cparser.py:589(_parse_function_type)
                                                                         1680    0.000    0.000  cparser.py:624(_as_func_arg)
                                                                           86    0.000    0.000  cparser.py:632(_get_struct_union_enum_type)
                                                                           21    0.000    0.000  cparser.py:757(_parse_constant)
                                                                          780    0.001    0.001  data.py:49(__init__)
                                                                            1    0.000    0.000  database.py:146(loadFamilies)
                                                                         4059    0.001    0.001  database.py:457(generate_reactions_from_families)
                                                                        85467    0.011    0.011  dimensionality.py:15(assert_isinstance)
                                                                          101    0.000    0.000  draw.py:133(draw)
                                                                            6    0.000    0.000  dyld.py:31(ensure_utf8)
                                                                            2    0.000    0.000  encoder.py:186(encode)
                                                                           32    0.000    0.000  environment.py:553(compile)
                                                                         3810    0.002    0.002  family.py:260(__apply)
                                                                          136    0.000    0.000  family.py:945(generateProductTemplate)
                                                                         8073    0.001    0.001  family.py:1058(addKineticsRulesFromTrainingSet)
                                                                         9382    0.003    0.003  family.py:1206(applyRecipe)
                                                                       128975    0.036    0.036  family.py:1582(__matchReactantToTemplate)
                                                                      1151943    0.252    0.252  family.py:1786(__generateReactions)
                                                                           15    0.000    0.000  figure.py:111(add)
                                                                           15    0.000    0.000  figure.py:427(set_tight_layout)
                                                                           30    0.000    0.000  figure.py:940(add_subplot)
                                                                       166581    0.030    0.030  filtration.py:95(get_octet_deviation)
                                                                         3624    0.003    0.013  font_manager.py:970(_normalize_font_family)
                                                                           28    0.000    0.000  font_manager.py:1107(score_family)
                                                                         3696    0.001    0.001  font_manager.py:1228(findfont)
                                                                         3674    0.000    0.000  fonts.py:18(_encode_string)
                                                                         2558    0.001    0.001  fromnumeric.py:1383(ravel)
                                                                        27534    0.016    0.016  fromnumeric.py:1743(sum)
                                                                          492    0.000    0.000  function_base.py:1963(place)
                                                                          432    0.000    0.000  function_base.py:2162(__init__)
                                                                           30    0.000    0.000  gridspec.py:139(__getitem__)
                                                                        58813    0.017    0.017  groups.py:98(getReactionTemplate)
                                                                          630    0.000    0.000  image.py:130(<genexpr>)
                                                                            8    0.000    0.000  input.py:56(database)
                                                                            1    0.000    0.000  input.py:111(convertBindingEnergies)
                                                                           10    0.000    0.000  input.py:334(surfaceReactor)
                                                                          146    0.000    0.000  inspect.py:51(ismodule)
                                                                          324    0.000    0.000  inspect.py:67(ismethod)
                                                                          324    0.000    0.000  inspect.py:142(isfunction)
                                                                          324    0.000    0.000  inspect.py:208(iscode)
                                                                           15    0.000    0.000  legend.py:149(__init__)
                                                                           15    0.000    0.000  legend.py:855(set_bbox_to_anchor)
                                                                            1    0.000    0.000  lex.py:211(readtab)
                                                                            4    0.000    0.000  lex.py:251(input)
                                                                            1    0.000    0.000  lex.py:584(get_tokens)
                                                                            5    0.000    0.000  lex.py:632(get_states)
                                                                           48    0.000    0.000  lex.py:663(get_rules)
                                                                        26080    0.009    0.009  lexer.py:597(tokeniter)
                                                                           84    0.000    0.000  main.py:1168(processToSpeciesNetworks)
                                                                           14    0.000    0.000  main.py:1183(<setcomp>)
                                                                           28    0.000    0.000  main.py:1190(processPdepNetworks)
                                                                           28    0.000    0.000  main.py:1208(processReactionsToSpecies)
                                                                            4    0.000    0.000  main.py:1760(__init__)
                                                                        12852    0.008    0.008  markers.py:248(set_marker)
                                                                         2217    0.000    0.000  model.py:305(makeNewSpecies)
                                                                         3279    0.000    0.000  model.py:404(checkForExistingReaction)
                                                                          256    0.000    0.000  model.py:486(makeNewReaction)
                                                                            1    0.000    0.000  model.py:572(global_cache)
                                                                          466    0.000    0.000  model.py:579(enlarge)
                                                                           14    0.000    0.000  model.py:764(<setcomp>)
                                                                           28    0.000    0.000  model.py:770(<setcomp>)
                                                                          202    0.000    0.000  model.py:903(generateKinetics)
                                                                           36    0.000    0.000  model.py:1547(addReactionLibraryToEdge)
                                                                          276    0.000    0.000  model.py:1869(searchRetrieveReactions)
                                                                         2745    0.001    0.001  model.py:1954(getSpecies)
                                                                          479    0.000    0.000  model.py:1968(retrieveNewSpecies)
                                                                       509664    0.113    0.113  nodes.py:164(iter_child_nodes)
                                                                        52192    0.011    0.011  nodes.py:184(find_all)
                                                                       328794    0.137    0.137  numeric.py:2064(isscalar)
                                                                         3274    0.001    0.001  output.py:45(saveOutputHTML)
                                                                         5544    0.001    0.001  output.py:96(visit_Tuple)
                                                                          416    0.000    0.000  parser.py:846(subparse)
                                                                           30    0.000    0.000  patches.py:2510(set_boxstyle)
                                                                           15    0.000    0.000  plot.py:148(__init__)
                                                                            4    0.000    0.000  polynomial.py:1045(__init__)
                                                                           34    0.000    0.000  posixpath.py:329(normpath)
                                                                            1    0.000    0.000  posixpath.py:358(abspath)
                                                                        50251    0.010    0.010  quantity.py:19(validate_unit_quantity)
                                                                       114305    0.061    0.061  quantity.py:31(validate_dimensionality)
                                                                        14340    0.007    0.007  quantity.py:118(__new__)
                                                                        48103    0.009    0.009  quantity.py:200(astype)
                                                                       161389    0.090    0.090  quantity.py:217(__array_prepare__)
                                                                       161389    0.023    0.023  quantity.py:240(__array_wrap__)
                                                                           15    0.000    0.000  rcsetup.py:77(f)
                                                                           81    0.000    0.000  re.py:230(_compile)
                                                                           74    0.000    0.000  rules.py:65(loadEntry)
                                                                           72    0.000    0.000  rules.py:384(getEntries)
                                                                       117088    0.047    0.047  runtime.py:231(call)
                                                                           15    0.000    0.000  shape_base.py:785(tile)
                                                                           60    0.000    0.000  spines.py:44(__init__)
                                                                          168    0.000    0.000  sre_compile.py:546(isstring)
                                                                         3095    0.001    0.001  sre_parse.py:141(__getitem__)
                                                                            2    0.000    0.000  subprocess.py:330(__init__)
                                                                            2    0.000    0.000  subprocess.py:880(_execute_child)
                                                                          101    0.000    0.000  surfaces.py:49(_encode_filename)
                                                                         1464    0.001    0.001  text.py:64(get_rotation)
                                                                         1691    0.000    0.000  textwrap.py:146(_munge_whitespace)
                                                                         1691    0.001    0.001  textwrap.py:163(_split)
                                                                          368    0.000    0.000  thermo.py:1072(recordPolycylicGenericNodes)
                                                                          187    0.000    0.000  thermo.py:1087(recordRingGenericNodes)
                                                                           54    0.000    0.000  thermo.py:1277(correctBindingEnergy)
                                                                           10    0.000    0.000  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                                          659    0.000    0.000  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                                         1725    0.001    0.001  thermo.py:1990(__addRingCorrectionThermoDataFromTree)
                                                                        68602    0.022    0.022  thermo.py:2085(__addGroupThermoData)
                                                                        23336    0.006    0.006  thermo.py:2136(__removeGroupThermoData)
                                                                          321    0.000    0.000  thermoengine.py:43(processThermoData)
                                                                          360    0.000    0.000  ticker.py:191(_divmod)
                                                                           60    0.000    0.000  transforms.py:546(anchored)
                                                                          540    0.000    0.000  transforms.py:1066(__init__)
                                                                         3543    0.001    0.001  transforms.py:1173(__add__)
                                                                           30    0.000    0.000  transforms.py:1550(__init__)
                                                                         3449    0.003    0.003  transforms.py:1763(transform_affine)
                                                                          150    0.000    0.000  transforms.py:2233(__eq__)
                                                                          225    0.000    0.000  transforms.py:2266(blended_transform_factory)
                                                                          480    0.000    0.000  transforms.py:2337(__eq__)
                                                                        10734    0.003    0.003  transforms.py:2471(composite_transform_factory)
                                                                         1502    0.000    0.000  transforms.py:2685(__init__)
                                                                         4440    0.004    0.004  units.py:125(get_converter)
                                                                       102336    0.026    0.026  visitor.py:58(generic_visit)
                                                                           22    0.000    0.000  warnings.py:96(simplefilter)
                                                                        27329    0.007    0.007  yacc.py:240(__getitem__)
                                                                            1    0.000    0.000  yacc.py:1960(read_table)
                                                                            1    0.000    0.000  yacc.py:3035(get_tokens)
                                                                          146    0.000    0.000  yacc.py:3104(get_pfunctions)
{eval}                                                             <-  175132    3.057    3.987  registry.py:19(__getitem__)
copy.py:306(_reconstruct)                                          <-      15    0.000    0.000  copy.py:66(copy)
                                                                    325524/77308    3.006   28.260  copy.py:145(deepcopy)
Graph.py:81(add_edge)                                              <- 1125806    2.835    5.479  Graph.py:45(from_edges)
copy.py:253(_deepcopy_dict)                                        <- 1474853/1474827    2.501   15.708  copy.py:145(deepcopy)
family.py:1206(applyRecipe)                                        <-     297    0.206    0.232  family.py:945(generateProductTemplate)
                                                                         3513    2.105    3.640  family.py:1489(__generateProductStructures)
family.py:1582(__matchReactantToTemplate)                          <-   50928    2.249    2.626  family.py:1786(__generateReactions)
{method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}  <-      15    2.160   11.203  main.py:596(execute)
{method 'format' of 'str' objects}                                 <- 1228270    0.455    0.455  adjlist.py:725(toAdjacencyList)
                                                                          752    0.001    0.001  base.py:111(__repr__)
                                                                       124352    0.252    0.284  base.py:908(matchNodeToStructure)
                                                                          218    0.000    0.000  ck2cti.py:116(to_cti)
                                                                          136    0.000    0.000  ck2cti.py:118(<genexpr>)
                                                                         1364    0.001    0.001  ck2cti.py:191(to_cti)
                                                                          124    0.000    0.000  ck2cti.py:221(to_cti)
                                                                          112    0.000    0.000  ck2cti.py:298(to_cti)
                                                                          224    0.000    0.000  ck2cti.py:437(rateStr)
                                                                           34    0.000    0.000  ck2cti.py:456(to_cti)
                                                                           32    0.000    0.000  ck2cti.py:471(rateStr)
                                                                           78    0.000    0.000  ck2cti.py:492(to_cti)
                                                                          128    0.000    0.000  ck2cti.py:867(to_cti)
                                                                            2    0.000    0.000  ck2cti.py:1507(loadChemkinFile)
                                                                           62    0.000    0.000  ck2cti.py:1958(getSpeciesString)
                                                                          258    0.000    0.000  ck2cti.py:1983(writeCTI)
                                                                           85    0.001    0.001  collections.py:305(namedtuple)
                                                                          271    0.000    0.000  collections.py:373(<genexpr>)
                                                                          271    0.000    0.000  collections.py:375(<genexpr>)
                                                                          882    0.001    0.001  common.py:47(saveEntry)
                                                                           37    0.019    0.021  common.py:348(reduce_same_reactant_degeneracy)
                                                                            1    0.000    0.000  database.py:222(loadLibraries)
                                                                           25    0.000    0.000  draw.py:893(__generateAtomLabels)
                                                                          324    0.000    0.000  family.py:621(load)
                                                                          434    0.001    0.002  family.py:945(generateProductTemplate)
                                                                        24185    0.030    0.030  family.py:1058(addKineticsRulesFromTrainingSet)
                                                                          447    0.000    0.000  family.py:2341(getKineticsFromDepository)
                                                                            2    0.000    0.000  family.py:2640(getTrainingDepository)
                                                                          154    0.000    0.000  groups.py:72(__repr__)
                                                                          616    0.000    0.000  groups.py:98(getReactionTemplate)
                                                                           14    0.000    0.000  input.py:137(species)
                                                                            1    0.000    0.000  input.py:619(readInputFile)
                                                                            6    0.000    0.000  library.py:498(save)
                                                                           15    0.000    0.000  listener.py:65(update)
                                                                           30    0.000    0.000  listener.py:125(update)
                                                                            1    0.000    0.000  main.py:596(execute)
                                                                            1    0.000    0.000  main.py:1396(logHeader)
                                                                          133    0.000    0.000  model.py:305(makeNewSpecies)
                                                                          220    0.011    0.012  model.py:486(makeNewReaction)
                                                                           31    0.000    0.000  model.py:579(enlarge)
                                                                           34    0.000    0.000  model.py:903(generateKinetics)
                                                                          676    0.005    0.005  model.py:998(printEnlargeSummary)
                                                                           67    0.001    0.001  model.py:1048(addSpeciesToCore)
                                                                            1    0.000    0.000  model.py:1547(addReactionLibraryToEdge)
                                                                         1501    0.004    0.004  output.py:45(saveOutputHTML)
                                                                         2960    0.001    0.001  output.py:51(visit_Call)
                                                                         1848    0.001    0.001  output.py:96(visit_Tuple)
                                                                         2400    0.002    0.002  output.py:151(visit_Num)
                                                                           15    0.000    0.000  plot.py:159(plot)
                                                                           14    0.000    0.000  rmg.py:237(getDB)
                                                                        24151    0.030    0.030  rules.py:456(fillRulesByAveragingUp)
                                                                          378    0.001    0.001  rules.py:618(estimateKinetics)
                                                                          316    0.000    0.000  rules.py:765(getTemplateLabel)
                                                                            1    0.000    0.000  solvation.py:510(loadGroups)
                                                                            1    0.000    0.000  statmech.py:521(loadGroups)
                                                                           16    0.000    0.000  stats.py:87(update_execution)
                                                                         8038    0.005    0.005  thermo.py:190(addThermoData)
                                                                          268    0.000    0.000  thermo.py:220(removeThermoData)
                                                                           14    0.000    0.000  thermo.py:242(averageThermoData)
                                                                            4    0.000    0.000  thermo.py:816(loadLibraries)
                                                                            1    0.000    0.000  thermo.py:852(loadGroups)
                                                                          256    0.001    0.001  thermo.py:1102(getThermoData)
                                                                           30    0.000    0.000  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                                         1466    0.003    0.003  thermo.py:1990(__addRingCorrectionThermoDataFromTree)
                                                                        70442    1.300    1.585  thermo.py:2085(__addGroupThermoData)
                                                                        23336    0.016    0.016  thermo.py:2136(__removeGroupThermoData)
                                                                            3    0.000    0.000  transport.py:270(loadLibraries)
                                                                            1    0.000    0.000  transport.py:289(loadGroups)
                                                                            1    0.000    0.000  transport.py:513(__addCriticalPointContribution)
rules.py:412(getRule)                                              <- 1586467    2.096   11.452  rules.py:456(fillRulesByAveragingUp)
                                                                          784    0.001    0.010  rules.py:618(estimateKinetics)
posixpath.py:82(split)                                             <-       2    0.000    0.000  library.py:498(save)
                                                                            8    0.000    0.000  os.py:136(makedirs)
                                                                      1587251    2.067    3.150  rules.py:432(getAllRules)
base.py:989(descendTree)                                           <- 145627/42960    1.034   18.937  base.py:989(descendTree)
                                                                        32501    0.139   12.952  groups.py:98(getReactionTemplate)
                                                                        16626    0.397   24.542  thermo.py:1990(__addRingCorrectionThermoDataFromTree)
                                                                        70442    0.327   11.389  thermo.py:2085(__addGroupThermoData)
                                                                        23336    0.101    2.103  thermo.py:2136(__removeGroupThermoData)
                                                                            1    0.000    0.000  transport.py:513(__addCriticalPointContribution)
copy.py:234(_deepcopy_tuple)                                       <- 325524/77308    1.954   10.493  copy.py:145(deepcopy)
family.py:1058(addKineticsRulesFromTrainingSet)                    <-      54    1.910   91.870  main.py:322(loadDatabase)
base.py:183(load)                                                  <-      52    0.911    1.143  depository.py:126(load)
                                                                          108    0.390    1.709  family.py:621(load)
                                                                            1    0.002    0.787  rmg.py:130(loadForbiddenStructures)
                                                                            1    0.006    0.007  solvation.py:304(load)
                                                                            1    0.012    0.135  solvation.py:366(load)
                                                                            3    0.014    0.030  solvation.py:510(loadGroups)
                                                                            1    0.007    0.012  statmech.py:521(loadGroups)
                                                                            4    0.086    0.525  thermo.py:816(loadLibraries)
                                                                            8    0.276    1.209  thermo.py:869(<dictcomp>)
                                                                            3    0.030    0.878  transport.py:270(loadLibraries)
                                                                            2    0.007    0.013  transport.py:289(loadGroups)


Sorted by cumulative time
Tue Dec  4 16:46:25 2018    /Users/rwest/Code/Cat/cpox-methane/RMG.profile

         166971795 function calls (158091842 primitive calls) in 250.684 seconds

   Ordered by: cumulative time
   List reduced from 3207 to 25 due to restriction <25>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.005    0.005  251.267  251.267 main.py:596(execute)
        1    0.005    0.005  155.222  155.222 main.py:399(initialize)
        1    0.001    0.001  153.487  153.487 main.py:322(loadDatabase)
       54    1.910    0.035   91.870    1.701 family.py:1058(addKineticsRulesFromTrainingSet)
       47    0.013    0.000   75.214    1.600 model.py:579(enlarge)
    17224    0.221    0.000   71.039    0.004 {map}
       16    0.017    0.001   70.849    4.428 react.py:116(reactAll)
       16    0.000    0.000   70.832    4.427 react.py:40(react)
       16    0.000    0.000   70.832    4.427 util.py:153(map_)
       16    0.000    0.000   70.831    4.427 fallbacks.py:30(wrapper)
     4059    0.059    0.000   70.816    0.017 util.py:110(__call__)
     4059    0.675    0.000   70.757    0.017 react.py:66(reactSpecies)
288533/142906    1.998    0.000   50.986    0.000 base.py:989(descendTree)
  542/532    0.671    0.001   49.332    0.093 thermo.py:1102(getThermoData)
6558721/1546789   11.810    0.000   49.084    0.000 copy.py:145(deepcopy)
2544335/2181394   43.875    0.000   48.831    0.000 base.py:908(matchNodeToStructure)
      276    0.082    0.000   46.829    0.170 thermo.py:1553(getThermoDataFromGroups)
      828    0.018    0.000   46.600    0.056 thermo.py:1704(estimateThermoViaGroupAdditivity)
     4059    0.187    0.000   43.777    0.011 database.py:457(generate_reactions_from_families)
       54    0.116    0.002   40.750    0.755 family.py:1198(fillKineticsRulesByAveragingUp)
1586467/54   18.384    0.000   40.634    0.752 rules.py:456(fillRulesByAveragingUp)
     1312    0.474    0.000   39.479    0.030 thermo.py:1613(estimateRadicalThermoViaHBI)
      828    0.321    0.000   38.275    0.046 thermo.py:1726(computeGroupAdditivityThermo)
     7516   21.534    0.003   33.532    0.004 common.py:153(ensure_species)
325539/77323    3.006    0.000   28.260    0.000 copy.py:306(_reconstruct)


   Ordered by: cumulative time
   List reduced from 3207 to 25 due to restriction <25>

Function                                           was called by...
                                                       ncalls  tottime  cumtime
main.py:596(execute)                               <-       1    0.005  251.267  <string>:1(<module>)
main.py:399(initialize)                            <-       1    0.005  155.222  main.py:596(execute)
main.py:322(loadDatabase)                          <-       1    0.001  153.487  main.py:399(initialize)
family.py:1058(addKineticsRulesFromTrainingSet)    <-      54    1.910   91.870  main.py:322(loadDatabase)
model.py:579(enlarge)                              <-      17    0.000    0.100  main.py:399(initialize)
                                                           30    0.013   75.113  main.py:596(execute)
{map}                                              <-     328    0.001    0.002  _distn_infrastructure.py:1875(ppf)
                                                            4    0.000    0.000  ck2cti.py:1124(setupKinetics)
                                                           85    0.000    0.000  collections.py:305(namedtuple)
                                                           16    0.015   70.831  fallbacks.py:30(wrapper)
                                                            2    0.000    0.000  sre_compile.py:256(_optimize_charset)
                                                        16787    0.205    0.205  urllib.py:1262(quote)
                                                            2    0.000    0.000  utils.py:10(<module>)
react.py:116(reactAll)                             <-      16    0.017   70.849  model.py:579(enlarge)
react.py:40(react)                                 <-      16    0.000   70.832  react.py:116(reactAll)
util.py:153(map_)                                  <-      16    0.000   70.832  react.py:40(react)
fallbacks.py:30(wrapper)                           <-      16    0.000   70.831  util.py:153(map_)
util.py:110(__call__)                              <-    4059    0.059   70.816  {map}
react.py:66(reactSpecies)                          <-    4059    0.675   70.757  util.py:110(__call__)
base.py:989(descendTree)                           <- 145627/42960    1.034   18.937  base.py:989(descendTree)
                                                        32501    0.139   12.952  groups.py:98(getReactionTemplate)
                                                        16626    0.397   24.542  thermo.py:1990(__addRingCorrectionThermoDataFromTree)
                                                        70442    0.327   11.389  thermo.py:2085(__addGroupThermoData)
                                                        23336    0.101    2.103  thermo.py:2136(__removeGroupThermoData)
                                                            1    0.000    0.000  transport.py:513(__addCriticalPointContribution)
thermo.py:1102(getThermoData)                      <-     418    0.465   48.687  family.py:1058(addKineticsRulesFromTrainingSet)
                                                           10    0.000    0.017  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                          114    0.206    0.644  thermoengine.py:118(generateThermoData)
copy.py:145(deepcopy)                              <-     316    0.000    0.004  base.py:273(getSpecies)
                                                        12429    0.022    0.141  base.py:1320(loadEntry)
                                                       502431    1.066    7.219  common.py:153(ensure_species)
                                                       206857    0.388    2.524  common.py:190(ensure_independent_atom_ids)
                                                    240758/28430    0.467    3.586  copy.py:226(_deepcopy_list)
                                                    1495623/455575    2.347    9.849  copy.py:234(_deepcopy_tuple)
                                                      2946206    5.027   12.175  copy.py:253(_deepcopy_dict)
                                                         3795    0.006    0.625  copy.py:283(_deepcopy_inst)
                                                    325550/77308    0.708   10.809  copy.py:306(_reconstruct)
                                                          508    0.001    0.009  draw.py:133(draw)
                                                        68363    0.163    2.830  family.py:1058(addKineticsRulesFromTrainingSet)
                                                        61532    0.119    0.812  family.py:1206(applyRecipe)
                                                       253959    0.458    3.198  family.py:1786(__generateReactions)
                                                          149    0.001    0.037  family.py:2341(getKineticsFromDepository)
                                                       203884    0.390    2.639  filtration.py:342(mark_unreactive_structures)
                                                        11266    0.018    0.127  model.py:236(checkForExistingSpecies)
                                                        11750    0.021    0.139  model.py:305(makeNewSpecies)
                                                       107880    0.379   26.238  react.py:66(reactSpecies)
                                                         6243    0.036    1.478  rules.py:456(fillRulesByAveragingUp)
                                                         1087    0.004    0.082  rules.py:618(estimateKinetics)
                                                           14    0.000    0.004  thermo.py:242(averageThermoData)
                                                        30906    0.060    0.732  thermo.py:346(convertRingToSubMolecule)
                                                          232    0.000    0.002  thermo.py:371(combineTwoRingsIntoSubMolecule)
                                                          140    0.000    0.001  thermo.py:440(bicyclicDecompositionForPolyring)
                                                         4268    0.007    0.054  thermo.py:511(splitBicyclicIntoSingleRings)
                                                         1186    0.002    0.013  thermo.py:521(saturate_ring_bonds)
                                                        22250    0.045    0.201  thermo.py:1102(getThermoData)
                                                         2393    0.004    0.025  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                         1203    0.004    0.032  thermo.py:1416(getThermoDataFromLibraries)
                                                          256    0.002    0.094  thermo.py:1525(getThermoDataFromLibrary)
                                                        23109    0.042    0.296  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                        12163    0.021    0.142  thermoengine.py:160(evaluator)
                                                           15    0.000    0.011  transport.py:377(getTransportPropertiesFromLibrary)
base.py:908(matchNodeToStructure)                  <- 2181394   39.629   48.831  base.py:989(descendTree)
                                                    362941/232802    4.246    5.294  base.py:1104(matchToStructure)
thermo.py:1553(getThermoDataFromGroups)            <-     276    0.082   46.829  thermo.py:1102(getThermoData)
thermo.py:1704(estimateThermoViaGroupAdditivity)   <-     828    0.018   46.600  thermo.py:1553(getThermoDataFromGroups)
database.py:457(generate_reactions_from_families)  <-    4059    0.187   43.777  react.py:66(reactSpecies)
family.py:1198(fillKineticsRulesByAveragingUp)     <-      54    0.116   40.750  main.py:322(loadDatabase)
rules.py:456(fillRulesByAveragingUp)               <-      54    0.004   40.634  family.py:1198(fillKineticsRulesByAveragingUp)
                                                    1586413/442   18.380   40.627  rules.py:456(fillRulesByAveragingUp)
thermo.py:1613(estimateRadicalThermoViaHBI)        <-     661    0.117    0.824  thermo.py:1102(getThermoData)
                                                          651    0.357   38.655  thermo.py:1704(estimateThermoViaGroupAdditivity)
thermo.py:1726(computeGroupAdditivityThermo)       <-     651    0.258   30.348  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                          177    0.062    7.927  thermo.py:1704(estimateThermoViaGroupAdditivity)
common.py:153(ensure_species)                      <-    4325    4.534    9.625  common.py:190(ensure_independent_atom_ids)
                                                         2650   16.048   22.015  common.py:230(find_degenerate_reactions)
                                                          541    0.952    1.892  family.py:1786(__generateReactions)
copy.py:306(_reconstruct)                          <-      15    0.000    0.000  copy.py:66(copy)
                                                    325524/77308    3.006   28.260  copy.py:145(deepcopy)


   Ordered by: cumulative time
   List reduced from 3207 to 25 due to restriction <25>

Function                                           called...
                                                       ncalls  tottime  cumtime
main.py:596(execute)                               ->      54    0.000    0.011  __init__.py:1623(info)
                                                            1    0.005  155.222  main.py:399(initialize)
                                                            1    0.000    0.026  main.py:566(register_listeners)
                                                            1    0.014    0.019  main.py:951(check_model)
                                                            1    0.001    0.148  main.py:1031(makeSeedMech)
                                                           14    0.000    0.001  main.py:1168(processToSpeciesNetworks)
                                                            2    0.000    0.055  main.py:1226(generateCanteraFiles)
                                                           15    0.006    0.007  main.py:1271(updateReactionThresholdAndReactFlags)
                                                           16    0.000    9.455  main.py:1353(saveEverything)
                                                            1    0.000    0.000  main.py:1376(finish)
                                                            1    0.000    0.000  main.py:1760(__init__)
                                                           15    0.000    0.000  main.py:1795(add_t_conv_N)
                                                           15    0.000    0.000  main.py:1805(get_cond)
                                                           16    0.000    0.000  main.py:1846(generate_cond)
                                                           16    0.000    0.000  main.py:1896(log_conditions)
                                                           30    0.013   75.113  model.py:579(enlarge)
                                                           15    0.000    0.000  model.py:748(addNewSurfaceObjects)
                                                           15    0.000    0.000  model.py:781(adjustSurface)
                                                            1    0.000    0.000  model.py:1408(getModelSize)
                                                            4    0.000    0.000  posixpath.py:61(join)
                                                            1    0.000    0.000  {any}
                                                           99    0.000    0.000  {len}
                                                            1    0.000    0.000  {max}
                                                            1    0.000    0.000  {method 'append' of 'list' objects}
                                                            1    0.000    0.000  {method 'format' of 'str' objects}
                                                           15    0.000    0.000  {method 'reset_max_edge_species_rate_ratios' of 'rmgpy.solver.base.ReactionSystem' objects}
                                                           15    2.160   11.203  {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
                                                            1    0.000    0.000  {min}
main.py:399(initialize)                            ->       5    0.000    0.000  Graph.py:45(from_edges)
                                                            5    0.000    0.000  Graph.py:174(get_nof_nodes)
                                                            5    0.000    0.000  Graph.py:180(get_edges)
                                                            1    0.006    0.027  __init__.py:10(<module>)
                                                            2    0.000    0.000  __init__.py:23(find_module)
                                                            1    0.000    0.000  __init__.py:1623(info)
                                                            2    0.000    0.000  adjlist.py:420(fromAdjacencyList)
                                                           17    0.001    0.001  base.py:1273(isMoleculeForbidden)
                                                           17    0.000    0.000  constraints.py:36(failsSpeciesConstraints)
                                                            1    0.005    1.319  main.py:216(loadInput)
                                                            1    0.000    0.000  main.py:255(checkInput)
                                                            1    0.001  153.487  main.py:322(loadDatabase)
                                                            1    0.000    0.000  main.py:1253(initializeReactionThresholdAndReactFlags)
                                                            1    0.000    0.059  main.py:1396(logHeader)
                                                            4    0.000    0.012  model.py:305(makeNewSpecies)
                                                           17    0.000    0.100  model.py:579(enlarge)
                                                            1    0.000    0.135  model.py:1547(addReactionLibraryToEdge)
                                                            1    0.000    0.000  model.py:1900(initializeIndexSpeciesDict)
                                                            3    0.000    0.000  openbabel.py:1689(__init__)
                                                            3    0.000    0.000  openbabel.py:2270(__init__)
                                                            6    0.000    0.000  openbabel.py:5008(__init__)
                                                            6    0.000    0.000  openbabel.py:5014(__iter__)
                                                           13    0.000    0.000  openbabel.py:5020(next)
                                                            4    0.000    0.000  six.py:184(find_module)
                                                           17    0.000    0.075  thermoengine.py:178(submit)
                                                            3    0.000    0.001  util.py:112(makeOutputSubdirectory)
                                                            2    0.000    0.000  {len}
                                                            3    0.000    0.000  {method 'append' of 'list' objects}
                                                            2    0.000    0.000  {method 'extend' of 'list' objects}
                                                            1    0.000    0.000  {method 'split' of 'str' objects}
                                                            1    0.000    0.000  {time.asctime}
                                                            1    0.000    0.000  {time.time}
main.py:322(loadDatabase)                          ->       3    0.000    0.001  __init__.py:1623(info)
                                                            1    0.000    0.000  copy.py:66(copy)
                                                           54    1.910   91.870  family.py:1058(addKineticsRulesFromTrainingSet)
                                                           54    0.116   40.750  family.py:1198(fillKineticsRulesByAveragingUp)
                                                            1    0.000    0.000  main.py:279(checkLibraries)
                                                            1    0.000    0.000  rmg.py:58(__init__)
                                                            1    0.000   20.866  rmg.py:75(load)
                                                            1    0.000    0.000  thermo.py:1251(setDeltaAtomicAdsorptionEnergies)
                                                            8    0.000    0.000  {len}
                                                            1    0.000    0.000  {method 'itervalues' of 'dict' objects}
                                                            2    0.000    0.000  {method 'values' of 'dict' objects}
family.py:1058(addKineticsRulesFromTrainingSet)    ->    4328    0.012    0.012  Cycle.py:27(__init__)
                                                         3130    0.027    0.272  Graph.py:45(from_edges)
                                                        24075    0.004    0.004  Graph.py:150(get_node_for_index)
                                                         3130    0.001    0.002  Graph.py:174(get_nof_nodes)
                                                         3130    0.001    0.001  Graph.py:180(get_edges)
                                                            5    0.000    0.000  __init__.py:23(find_module)
                                                            1    0.011    0.163  __init__.py:345(<module>)
                                                            4    0.000    0.002  __init__.py:1623(info)
                                                          154    0.008    0.048  _distn_infrastructure.py:1875(ppf)
                                                         8061    0.040    0.040  base.py:81(__init__)
                                                         8061    0.003    0.003  base.py:114(longDesc)
                                                         8061    0.004    0.004  base.py:123(shortDesc)
                                                         7398    0.023    0.023  collections.py:71(__setitem__)
                                                           52    0.002    0.004  collections.py:121(values)
                                                        68363    0.163    2.830  copy.py:145(deepcopy)
                                                          154    0.001    0.001  family.py:82(__init__)
                                                          154    0.012   25.219  family.py:1716(calculateDegeneracy)
                                                         8215    0.017   11.639  family.py:2313(getReactionTemplate)
                                                          154    0.000    0.288  family.py:2483(getReactionTemplateLabels)
                                                           54    0.000    0.000  family.py:2640(getTrainingDepository)
                                                          418    0.003    0.209  filtration.py:53(filter_structures)
                                                          767    0.003    0.030  filtration.py:84(get_octet_deviation_list)
                                                         2225    0.041    0.043  filtration.py:95(get_octet_deviation)
                                                          767    0.007    0.008  filtration.py:171(get_charge_span_list)
                                                          154    0.000    0.001  fromnumeric.py:2200(amax)
                                                          154    0.001    0.002  fromnumeric.py:2300(amin)
                                                          154    0.005    0.009  linalg.py:458(inv)
                                                          154    0.016    0.148  linalg.py:1785(lstsq)
                                                          154    0.001    0.002  numeric.py:86(zeros_like)
                                                          154    0.001    0.002  numeric.py:194(ones_like)
                                                           52    0.000    0.001  rules.py:384(getEntries)
                                                           10    0.000    0.000  six.py:184(find_module)
                                                          418    0.465   48.687  thermo.py:1102(getThermoData)
                                                         8073    0.001    0.001  {isinstance}
                                                           52    0.000    0.000  {max}
                                                          817    0.000    0.000  {method 'append' of 'list' objects}
                                                         8061    0.005    0.005  {method 'changeT0' of 'rmgpy.kinetics.arrhenius.Arrhenius' objects}
                                                        24185    0.030    0.030  {method 'format' of 'str' objects}
                                                        16122    0.006    0.006  {method 'join' of 'str' objects}
                                                           52    0.002    0.004  {method 'sort' of 'list' objects}
                                                         8055    0.217    0.217  {method 'toArrheniusEP' of 'rmgpy.kinetics.arrhenius.Arrhenius' objects}
model.py:579(enlarge)                              ->     102    0.000    0.018  __init__.py:1623(info)
                                                           27    0.000    0.000  display.py:45(display)
                                                          258    0.004    2.226  model.py:802(processNewReactions)
                                                          202    0.002    1.776  model.py:881(applyKineticsToReaction)
                                                           47    0.002    0.306  model.py:998(printEnlargeSummary)
                                                           31    0.007    0.014  model.py:1048(addSpeciesToCore)
                                                          516    0.002    0.004  model.py:1927(inflate)
                                                          258    0.000    0.001  model.py:1968(retrieveNewSpecies)
                                                           16    0.017   70.849  react.py:116(reactAll)
                                                          466    0.000    0.000  {isinstance}
                                                          216    0.000    0.000  {len}
                                                          241    0.001    0.001  {method 'append' of 'list' objects}
                                                           31    0.000    0.000  {method 'format' of 'str' objects}
                                                          241    0.006    0.006  {rmgpy.chemkin.markDuplicateReaction}
                                                           16    0.000    0.000  {zip}
{map}                                              ->     656    0.000    0.001  numeric.py:414(asarray)
                                                            9    0.000    0.000  re.py:208(escape)
                                                           16    0.000    0.000  sre_compile.py:101(fixup)
                                                         4059    0.059   70.816  util.py:110(__call__)
react.py:116(reactAll)                             ->      16    0.000   70.832  react.py:40(react)
                                                         4032    0.000    0.000  {method 'append' of 'list' objects}
react.py:40(react)                                 ->      16    0.000   70.832  util.py:153(map_)
                                                           16    0.000    0.000  {built-in method from_iterable}
util.py:153(map_)                                  ->      16    0.000   70.831  fallbacks.py:30(wrapper)
                                                           16    0.000    0.000  util.py:107(__init__)
fallbacks.py:30(wrapper)                           ->       1    0.000    0.000  {_warnings.warn}
                                                           16    0.000    0.000  {hasattr}
                                                           16    0.015   70.831  {map}
                                                           16    0.000    0.000  {method 'get' of 'dict' objects}
util.py:110(__call__)                              ->    4059    0.675   70.757  react.py:66(reactSpecies)
react.py:66(reactSpecies)                          ->  107880    0.379   26.238  copy.py:145(deepcopy)
                                                         4059    0.187   43.777  database.py:457(generate_reactions_from_families)
                                                         4059    0.034    0.043  react.py:84(deflate)
                                                         4059    0.024    0.024  rmg.py:237(getDB)
base.py:989(descendTree)                           -> 2181394   39.629   48.831  base.py:908(matchNodeToStructure)
                                                    145627/42960    1.034   18.937  base.py:989(descendTree)
                                                       534574    0.058    0.058  {len}
                                                       146084    0.031    0.031  {method 'append' of 'list' objects}
                                                        99550    0.069    0.069  {method 'startswith' of 'str' objects}
thermo.py:1102(getThermoData)                      ->     649    0.002    0.002  Cycle.py:27(__init__)
                                                          529    0.005    0.046  Graph.py:45(from_edges)
                                                         3501    0.001    0.001  Graph.py:150(get_node_for_index)
                                                          529    0.000    0.000  Graph.py:174(get_nof_nodes)
                                                          529    0.000    0.000  Graph.py:180(get_edges)
                                                            1    0.000    0.000  __init__.py:23(find_module)
                                                          256    0.001    0.002  __init__.py:1631(debug)
                                                        22250    0.045    0.201  copy.py:145(deepcopy)
                                                           87    0.001    0.053  filtration.py:53(filter_structures)
                                                          118    0.000    0.003  filtration.py:84(get_octet_deviation_list)
                                                          322    0.004    0.005  filtration.py:95(get_octet_deviation)
                                                          118    0.001    0.001  filtration.py:171(get_charge_span_list)
                                                          284    0.001    0.001  input.py:913(getInput)
                                                            2    0.000    0.000  six.py:184(find_module)
                                                           54    0.001    0.005  thermo.py:1277(correctBindingEnergy)
                                                           10    0.044    0.097  thermo.py:1329(getThermoDataForSurfaceSpecies)
                                                          542    0.007    0.607  thermo.py:1416(getThermoDataFromLibraries)
                                                          276    0.082   46.829  thermo.py:1553(getThermoDataFromGroups)
                                                          661    0.117    0.824  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                          284    0.000    0.000  thermo.py:2397(findCp0andCpInf)
                                                          264    0.000    0.000  {len}
                                                          284    0.000    0.000  {math.log}
                                                            8    0.000    0.000  {method 'append' of 'list' objects}
                                                            2    0.000    0.000  {method 'extend' of 'list' objects}
                                                          256    0.001    0.001  {method 'format' of 'str' objects}
                                                            8    0.000    0.000  {method 'getEnthalpy' of 'rmgpy.thermo.thermodata.ThermoData' objects}
                                                          248    0.000    0.000  {method 'lower' of 'str' objects}
                                                            8    0.000    0.000  {method 'sort' of 'list' objects}
                                                            8    0.000    0.000  {sorted}
copy.py:145(deepcopy)                              -> 3978597    0.466    0.466  copy.py:198(_deepcopy_atomic)
                                                    48362/24770    0.188    3.643  copy.py:226(_deepcopy_list)
                                                    325524/77308    1.954   10.493  copy.py:234(_deepcopy_tuple)
                                                    1474853/1474827    2.501   15.708  copy.py:253(_deepcopy_dict)
                                                      6158249    6.722    8.249  copy.py:267(_keep_alive)
                                                         3795    0.023    0.675  copy.py:283(_deepcopy_inst)
                                                    325524/77308    3.006   28.260  copy.py:306(_reconstruct)
                                                       652642    0.358    0.358  {getattr}
                                                      6558721    0.512    0.512  {id}
                                                       327118    0.105    0.105  {issubclass}
                                                         1594    0.002    0.002  {method '__deepcopy__' of 'numpy.ndarray' objects}
                                                       325524    0.839    0.839  {method '__reduce_ex__' of 'object' objects}
                                                     13042494    1.580    1.580  {method 'get' of 'dict' objects}
base.py:908(matchNodeToStructure)                  ->   11252    0.032    0.032  Cycle.py:27(__init__)
                                                         8771    0.124    0.901  Graph.py:45(from_edges)
                                                        63572    0.011    0.011  Graph.py:150(get_node_for_index)
                                                         8771    0.005    0.006  Graph.py:174(get_nof_nodes)
                                                         8771    0.002    0.002  Graph.py:180(get_edges)
                                                         8787    0.024    0.057  __init__.py:1631(debug)
                                                       115565    0.116    0.270  __init__.py:1639(log)
                                                    107623/64548    0.371    5.609  base.py:1104(matchToStructure)
                                                           16    0.000    0.000  openbabel.py:1689(__init__)
                                                           16    0.000    0.000  openbabel.py:2270(__init__)
                                                      7930322    2.080    2.080  {isinstance}
                                                       124352    0.252    0.284  {method 'format' of 'str' objects}
                                                      3251851    0.394    0.394  {method 'iteritems' of 'dict' objects}
                                                      2436712    0.442    0.442  {method 'keys' of 'dict' objects}
thermo.py:1553(getThermoDataFromGroups)            ->     276    0.008    0.057  thermo.py:1582(prioritizeThermo)
                                                          828    0.018   46.600  thermo.py:1704(estimateThermoViaGroupAdditivity)
                                                          276    0.090    0.090  thermo.py:2397(findCp0andCpInf)
                                                          828    0.000    0.000  {method 'append' of 'list' objects}
thermo.py:1704(estimateThermoViaGroupAdditivity)   ->     651    0.357   38.655  thermo.py:1613(estimateRadicalThermoViaHBI)
                                                          177    0.062    7.927  thermo.py:1726(computeGroupAdditivityThermo)
database.py:457(generate_reactions_from_families)  ->    4059    0.017    0.018  common.py:174(generate_molecule_combos)
                                                         4059    4.523   17.346  common.py:190(ensure_independent_atom_ids)
                                                         4059    0.097   20.636  common.py:230(find_degenerate_reactions)
                                                         4059    0.312    5.121  database.py:537(react_molecules)
                                                           61    0.001    0.466  family.py:1643(addReverseAttribute)
                                                         4059    0.001    0.001  {isinstance}
                                                         7740    0.001    0.001  {len}
                                                         4059    0.000    0.000  {method 'extend' of 'list' objects}
family.py:1198(fillKineticsRulesByAveragingUp)     ->      54    0.000    0.000  family.py:1186(getRootTemplate)
                                                           54    0.004   40.634  rules.py:456(fillRulesByAveragingUp)
rules.py:456(fillRulesByAveragingUp)               ->   24151    0.105    0.105  base.py:81(__init__)
                                                      1365452    6.261    6.261  base.py:1249(getAllCombinations)
                                                        24151    0.062    0.062  collections.py:71(__setitem__)
                                                         6243    0.036    1.478  copy.py:145(deepcopy)
                                                      1586467    2.096   11.452  rules.py:412(getRule)
                                                    1586413/442   18.380   40.627  rules.py:456(fillRulesByAveragingUp)
                                                        17908    0.465    0.483  rules.py:557(__getAverageKinetics)
                                                      2602856    0.211    0.211  {len}
                                                        68171    0.011    0.011  {method 'append' of 'list' objects}
                                                      2730904    0.536    0.536  {method 'extend' of 'list' objects}
                                                        24151    0.030    0.030  {method 'format' of 'str' objects}
                                                      6010699    1.049    1.269  {method 'join' of 'str' objects}
                                                       999292    0.352    0.352  {min}
thermo.py:1613(estimateRadicalThermoViaHBI)        ->     953    0.002    0.002  Cycle.py:27(__init__)
                                                          718    0.007    0.069  Graph.py:45(from_edges)
                                                         5284    0.001    0.001  Graph.py:150(get_node_for_index)
                                                          718    0.000    0.000  Graph.py:174(get_nof_nodes)
                                                          718    0.000    0.000  Graph.py:180(get_edges)
                                                        23109    0.042    0.296  copy.py:145(deepcopy)
                                                          661    0.009    0.552  thermo.py:1416(getThermoDataFromLibraries)
                                                          651    0.258   30.348  thermo.py:1726(computeGroupAdditivityThermo)
                                                        24054    0.086    4.545  thermo.py:2085(__addGroupThermoData)
                                                        23336    0.070    2.938  thermo.py:2136(__removeGroupThermoData)
                                                          659    0.000    0.000  {isinstance}
                                                            8    0.000    0.000  {len}
                                                            8    0.000    0.000  {math.log}
                                                         1202    0.116    0.242  {method 'getSmallestSetOfSmallestRings' of 'rmgpy.molecule.graph.Graph' objects}
                                                          659    0.010    0.010  {method 'isCyclic' of 'rmgpy.molecule.graph.Graph' objects}
thermo.py:1726(computeGroupAdditivityThermo)       ->    1656    0.007    0.034  numeric.py:86(zeros_like)
                                                          311    0.005   22.925  thermo.py:1830(__addPolycyclicCorrectionThermoData)
                                                          484    0.035    4.165  thermo.py:1990(__addRingCorrectionThermoDataFromTree)
                                                        46378    0.229   10.484  thermo.py:2085(__addGroupThermoData)
                                                          773    0.086    0.168  {method 'getDisparateRings' of 'rmgpy.molecule.graph.Graph' objects}
                                                          773    0.082    0.166  {method 'getSmallestSetOfSmallestRings' of 'rmgpy.molecule.graph.Graph' objects}
                                                          828    0.013    0.013  {method 'isCyclic' of 'rmgpy.molecule.graph.Graph' objects}
common.py:153(ensure_species)                      ->    9083    0.029    0.029  Cycle.py:27(__init__)
                                                        20296    0.123    0.915  Graph.py:45(from_edges)
                                                        50098    0.010    0.010  Graph.py:150(get_node_for_index)
                                                        20296    0.013    0.017  Graph.py:174(get_nof_nodes)
                                                        20296    0.006    0.006  Graph.py:180(get_edges)
                                                       502431    1.066    7.219  copy.py:145(deepcopy)
                                                        14892    0.086    3.063  filtration.py:53(filter_structures)
                                                        15624    0.033    0.227  filtration.py:84(get_octet_deviation_list)
                                                        36737    0.418    0.440  filtration.py:95(get_octet_deviation)
                                                        15624    0.054    0.056  filtration.py:171(get_charge_span_list)
                                                        15074    0.003    0.003  {any}
                                                        30163    0.013    0.013  {isinstance}
copy.py:306(_reconstruct)                          -> 325550/77308    0.708   10.809  copy.py:145(deepcopy)
                                                           15    0.000    0.000  copy_reg.py:92(__newobj__)
                                                        11745    0.096    0.520  dimensionality.py:55(__hash__)
                                                        11745    0.009    1.106  dimensionality.py:203(__eq__)
                                                        11745    0.063    1.789  quantity.py:118(__new__)
                                                        11745    0.007    0.013  quantity.py:130(dimensionality)
                                                        11745    0.344   12.321  quantity.py:146(simplified)
                                                           41    0.000    0.000  {hasattr}
                                                       325539    0.030    0.030  {id}
                                                       651093    0.151    0.151  {isinstance}
                                                       325539    0.041    0.041  {len}
                                                           15    0.000    0.000  {method 'update' of 'dict' objects}


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