12.3. Kinetics Database

This section describes the general usage of RMG’s kinetic database. See Modifying the Kinetics Database for instructions on modifying the database.

Pressure independent reaction rates in RMG are calculated using a modified Arrhenius equation, designating the reaction coefficient as \(k(T)\) at temperature \(T\).

\[k(T) = A\left(\frac{T}{T_0}\right)^ne^{-(E_0 + \alpha \Delta H_{rxn})/(RT)}\]

\(R\) is the universal gas constant. The kinetic parameters determining the rate coefficient are:

  • \(A\): the pre-exponential A-factor
  • \(T_0\): the reference temperature
  • \(n\): the temperature exponent
  • \(E_0\): the activation energy for a thermoneutral reaction (a barrier height intrinsic to the kinetics family)
  • \(\alpha\): the Evans-Polanyi coefficient (characterizes the position of the transition state along the reaction coordinate, \(0 \le \alpha \le 1\))
  • \(\Delta H_{rxn}\): the enthalpy of reaction

When Evans-Polanyi corrections are used, \(\Delta H_{rxn}\) is calculated using RMG’s thermo database, instead of being specified in the kinetic database. When Evans-Polanyi corrections are not used, \(\Delta H_{rxn}\) and \(\alpha\) are set to zero, and \(E_0\) is the activation energy of the reaction.

12.3.1. Libraries

Kinetic libraries delineate kinetic parameters for specific reactions. RMG always chooses to use kinetics from libraries over families. If multiple libraries contain the same reaction, then precedence is given to whichever library is listed first in the input.py file.

For combustion mechanisms, you should always use at least one small-molecule combustion library, such as the pre-packaged BurkeH2O2 and/or FFCM1 for natural gas. The reactions contained in these libraries are poorly estimated by kinetic families and are universally important to combustion systems.

Kinetic libraries should also be used in the cases where:

  • A set of reaction rates were optimized together
  • You know the reaction rate is not generalizable to similar species (perhaps due to catalysis or aromatic structures)
  • No family exists for the class of reaction
  • You are not confident about the accuracy of kinetic parameters

Below is a list of pre-packaged kinetics library reactions in RMG:

Library Description
1989_Stewart_2CH3_to_C2H5_H Chemically Activated Methyl Recombination to Ethyl (2CH3 -> C2H5 + H)
2001_Tokmakov_H_Toluene_to_CH3_Benzene H + Toluene = CH3 + Benzene
2005_Senosiain_OH_C2H2 pathways on the OH + acetylene surface
2006_Joshi_OH_CO pathways on OH + CO = HOCO = H + CO2 surface
2009_Sharma_C5H5_CH3_highP Cyclopentadienyl + CH3 in high-P limit
2015_Buras_C2H3_C4H6_highP Vinyl + 1,3-Butadiene and other C6H9 reactions in high-P limit
biCPD_H_shift Sigmatropic 1,5-H shifts on biCPD PES
BurkeH2O2inArHe Comprehensive H2/O2 kinetic model in Ar or He atmosphere
BurkeH2O2inN2 Comprehensive H2/O2 kinetic model in N2 atmosphere
C2H4+O_Klipp2017 C2H4 + O intersystem crossing reactions, probably important for all C/H/O combustion
C10H11 Cyclopentadiene pyrolysis in the presence of ethene
C3 Cyclopentadiene pyrolysis in the presence of ethene
C6H5_C4H4_Mebel Formation Mechanism of Naphthalene and Indene
Chernov Soot Formation with C1 and C2 Fuels (aromatic reactions only)
CurranPentane Ignition of pentane isomers
Dooley Methyl formate (contains several mechanisms)
ERC-FoundationFuelv0.9 Small molecule combustio (natural gas)
Ethylamine Ethylamine pyrolysis and oxidation
FFCM1(-) Foundational Fuel Chemistry Model Version 1.0 (excited species removed)
First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP Phenyl + 1,3-Butadiene and other C10H11 reactions in high-P limit
First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP Propargyl + Benzyl and other C10H10 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP C9H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP C10H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP CH3 + Indene in high-P limit
First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP Phenyl + Propene and other C9H11 reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP C10H7 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP C8H7 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP Phenyl + Vinylacetylene and other C10H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP C10H9 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective Effective Phenyl + Diacetylene rates to Benzofulvenyl and 2-Napthyl
Fulvene_H Cyclopentadiene pyrolysis in the presence of ethene
GRI-HCO The HCO <=> H + CO reaction
GRI-Mech3.0 Gas Research Institute natural gas mechanism optimized for 1 atm (discontinued Feb. 2000)
GRI-Mech3.0-N GRI-Mech3.0 including nitrogen chemistry (NOx from N2)
Glarborg Mechanisms by P. Glarborg, assorted by carbon number
JetSurF2.0 Jet Surrogate Fuel model up tp C12 (excited species removed)
Klippenstein_Glarborg2016 Methane oxidation at high pressures and intermediate temperatures
Lai_Hexylbenzene Alkylaromatic reactions for hexylbenzene
Mebel_C6H5_C2H2 Pathways from benzene to naphthalene
Mebel_Naphthyl Reactions of naphthyl-1 and naphthyl-2
Methylformate Methyl formate
Narayanaswamy Oxidation of substituted aromatic species (aromatic reactions only)
Nitrogen_Dean_and_Bozzelli Combustion Chemistry of Nitrogen
Nitrogen_Glarborg_Gimenez_et_al High pressure C2H4 oxidation with nitrogen chemistry
Nitrogen_Glarborg_Lucassen_et_al Fuel-nitrogen conversion in the combustion of small amines
Nitrogen_Glarborg_Zhang_et_al Premixed nitroethane flames at low pressure
NOx important NOx related reactions, e.g., thermal & prompt NO, N2O
NOx/LowT Low temperature kinetics (~<1000K) for selected reactions from the NOx library
OxygenSingTrip Reactions of singlet and triplet oxygen
SOx important SOx related reactions, e.g., H-S, C-S, SOx
Sulfur/DMDS Dimethyl disulfide (CH3SSCH3)
Sulfur/DMS Dimethyl disulfide (CH3SSCH3)
Sulfur/DTBS Di-tert-butyl Sulfide (C4H9SSC4H9)
Sulfur/GlarborgBozzelli SO2 effect on moist CO oxidation with and without NO
Sulfur/GlarborgH2S H2S oxidation at high pressures
Sulfur/GlarborgMarshall OCS chemistry
Sulfur/GlarborgNS Interactions between nitrogen and sulfur species in combustion
Sulfur/Hexanethial_nr Hexyl sulfide (C6H13SC6H13) + hexadecane (C16H34)
Sulfur/Sendt Small sulfur molecule
Sulfur/TP_Song Thiophene (C4H4S, aromatic)
Sulfur/Thial_Hydrolysis Thioformaldehyde (CH2S) and thioacetaldehyde (C2H4S) to COS and CO2
TEOS Organic oxidized silicone
c-C5H5_CH3_Sharma Cyclopentadienyl + CH3
combustion_core Leeds University natural gas mechanism (contains versions 2-5)
fascella Cyclopentadienyl + acetyl
kislovB Formation of indene in combustion
naphthalene_H Cyclopentadiene pyrolysis in the presence of ethene Part 1
vinylCPD_H Cyclopentadiene pyrolysis in the presence of ethene Part 2

12.3.2. Families

Allowable reactions in RMG are divided up into classes called reaction families. All reactions not listed in a kinetic library have their kinetic parameters estimated from the reaction families.

Each reaction family contains the files:

  • groups.py containing the recipe, group definitions, and hierarchical trees
  • training.py containing a training set for the family
  • rules.py containing kinetic parameters for rules

There are currently 58 reaction families in RMG:

1,2-Birad_to_alkene f01
1,2_Insertion_carbene f02
1,2_Insertion_CO f03
1,2_shiftC f04
1,2_shiftS f05
1,3_Insertion_CO2 f06
1,3_Insertion_ROR f07
1,3_Insertion_RSR f08
1,4_Cyclic_birad_scission f09
1,4_Linear_birad_scission f10
1+2_Cycloaddition f11
2+2_cycloaddition_CCO f12
2+2_cycloaddition_Cd f13
2+2_cycloaddition_CO f14
2+2_cycloaddition_CS f15
6_membered_central_C-C_shift f16
Birad_recombination f17
Birad_R_Recombination f18
CO_Disproportionation f19
Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH f20
Cyclic_Ether_Formation f21
Cyclic_Thioether_Formation f22
Cyclopentadiene_scission f23
Diels_alder_addition f24
Disproportionation f25
H_Abstraction f26
HO2_Elimination_from_PeroxyRadical f27
Intra_2+2_cycloaddition_Cd f28
Intra_5_membered_conjugated_C=C_C=C_addition f29
Intra_Diels_alder_monocyclic f30
Intra_Disproportionation f31
Intra_ene_reaction f32
intra_H_migration f33
intra_NO2_ONO_conversion f34
intra_OH_migration f35
Intra_R_Add_Endocyclic f36
Intra_R_Add_Exocyclic f37
Intra_R_Add_Exo_scission f38
Intra_R_Add_ExoTetCyclic f39
Intra_Retro_Diels_alder_bicyclic f40
Intra_RH_Add_Endocyclic f41
Intra_RH_Add_Exocyclic f42
intra_substitutionCS_cyclization f43
intra_substitutionCS_isomerization f44
intra_substitutionS_cyclization f45
intra_substitutionS_isomerization f46
ketoenol f47
Korcek_step1 f48
Korcek_step2 f49
lone_electron_pair_bond f50
R_Addition_COm f51
R_Addition_CSm f52
R_Addition_MultipleBond f53
R_Recombination f54
Singlet_Carbene_Intra_Disproportionation f55
Singlet_Val6_to_triplet f56
Substitution_O f57
SubstitutionS f58

12.3.2.1. Recipe

The recipe can be found near the top of groups.py and describes the changes in bond order and radicals that occur during the reaction. Reacting atoms are labelled with a starred number. Shown below is the recipe for the H-abstraction family.

../../../_images/Recipe.png

The table below shows the possible actions for recipes. The arguments are given in the curly braces as shown above. For the order of bond change in the Change_Bond action, a -1 could represent a triple bond changing to a double bond while a +1 could represent a single bond changing to a double bond.

Action Argument1 Argument2 Argument3
Break_Bond First bonded atom Type of bond Second bonded atom
Form_Bond First bonded atom Type of bond Second bonded atom
Change_Bond First bonded atom Order of bond change Second bonded atom
Gain_Radical Specified atom Number of radicals  
Lose_Radical Specified atom Number of radicals  

Change_Bond order cannot be directly used on benzene bonds. During generation, aromatic species are kekulized to alternating double and single bonds such that reaction families can be applied. However, RMG cannot properly handle benzene bonds written in the kinetic group definitions.

12.3.2.2. Training Set vs Rules

The training set and rules both contain trusted kinetics that are used to fill in templates in a family. The training set contains kinetics for specific reactions, which are then matched to a template. The kinetic rules contain kinetic parameters that do not necessarily correspond to a specific reaction, but have been generalized for a template.

When determining the kinetics for a reaction, a match for the template is searched for in the kinetic database. The three cases in order of decreasing reliability are:

  1. Reaction match from training set
  2. Node template exact match using either training set or rules
  3. Node template estimate averaged from children nodes

Both training sets and reaction libraries use the observed rate, but rules must first be divided by the degeneracy of the reaction. For example, the reaction CH4 + OH –> H2O + CH3 has a reaction degeneracy of 4. If one performed an experiment or obtained this reaction rate using Cantherm (applying the correct symmetry), the resultant rate parameters would be entered into libraries and training sets unmodified. However a kinetic rule created for this reaction must have its A-factor divided by 4 before being entered into the database.

The reaction match from training set is accurate within the documented uncertainty for that reaction. A template exact match is usually accurate within about one order of magnitude. When there is no kinetics available for for the template in either the training set or rules, the kinetics are averaged from the children nodes as an estimate. In these cases, the kinetic parameters are much less reliable. For more information on the estimation algorithm see Kinetics Estimation.

The training set can be modified in training.py and the rules can be modified in rules.py. For more information on modification see Adding Training Reactions and Adding Kinetic Rules.