Reactions#

The fields common to all reaction entries are:

equation

The stoichiometric equation for the reaction. Each term (that is, stoichiometric coefficient, species name, + or <=>) in the equation must be separated by a space.

Reversible reactions may be written using <=> or = to separate reactants and products. Irreversible reactions are written using =>.

type

A string specifying the type of reaction or rate coefficient parameterization. The default is elementary. Reaction types are:

elementary
three-body
Blowers-Masel
two-temperature-plasma
electron-collision-plasma
falloff
chemically-activated
pressure-dependent-Arrhenius
Chebyshev
linear-Burke

Reactions without a specified type on surfaces or edges are automatically treated as interface-Arrhenius reactions, unless a sticking-coefficient implies a sticking-Arrhenius reaction. Interface reactions that involve charge transfer between phases are automatically treated as electrochemical reactions.

Reactions on surfaces or edges specifying type as Blowers-Masel are treated as interface-Blowers-Masel or sticking-Blowers-Masel.

duplicate

Boolean indicating whether the reaction is a known duplicate of another reaction. The default is false.

orders

An optional mapping of species to explicit reaction orders to use. Reaction orders for reactant species not explicitly mentioned are taken to be their respective stoichiometric coefficients. See Reaction Orders for additional information.

negative-orders

Boolean indicating whether negative reaction orders are allowed. The default is false.

nonreactant-orders

Boolean indicating whether orders for non-reactant species are allowed. The default is false.

Depending on the reaction type, other fields may be necessary to specify the rate of the reaction.

Reaction rate expressions#

Arrhenius#

Arrhenius rate expressions are specified as a mapping with fields:

A: The pre-exponential factor \(A\)
b: The temperature exponent \(b\)
Ea: The activation energy \(E_a\)

or a corresponding three-element list. The following are equivalent:

{A: 2.70E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
[2.70E+13 cm^3/mol/s, 0, 355 cal/mol]

Blowers-Masel#

Blowers-Masel rate expressions calculate the rate constant based on the Blowers Masel approximation as described here. The rate parameters are specified as a mapping with fields:

A: The pre-exponential factor \(A\)
b: The temperature exponent \(b\)
Ea0: The intrinsic activation energy \(E_{a0}\)
w: The average of the bond dissociation energy of the bond breaking and that being formed in the reaction \(w\)

or a corresponding four-element list. The following are equivalent:

{A: 3.87e+04 cm^3/mol/s, b: 2.7, Ea0: 6260.0 cal/mol, w: 1e9 cal/mol}
[3.87e+04 cm^3/mol/s, 2.7, 6260.0 cal/mol, 1e9 cal/mol]

Two-Temperature Plasma#

Two-temperature plasma reactions involve an electron as one of the reactants, where the electron temperature may differ from the gas temperature as described here. The rate parameters are specified as a mapping with fields:

A: The pre-exponential factor
b: The temperature exponent, which is applied to the electron temperature
Ea-gas: The activation energy term \(E_{a,g}\) that is related to the gas temperature
Ea-electron: The activation energy term \(E_{a,e}\) that is related to the electron temperature

or a corresponding four-element list. The following are equivalent:

{A: 17283, b: -3.1, Ea-gas: -5820 J/mol, Ea-electron: 1081 J/mol}
[17283, -3.1, -5820 J/mol, 1081 J/mol]

Efficiencies#

Some reaction types include parameters for the “efficiency” of different species as third-body colliders. For these reactions, the following additional fields are supported:

efficiencies: A mapping of species names to efficiency values
default-efficiency: The efficiency for use for species not included in the efficiencies mapping. Defaults to 1.0.

Examples:

- equation: O + H + M <=> OH + M
  rate-constant: {A: 5.0e+5, b: -1.0, Ea: 0.0}
  default-efficiency: 0.0
  efficiencies: {H2: 2.0, H2O: 6.0, AR: 0.7}
- equation: O + H + M <=> OH + M
  rate-constant: {A: 3.0e+5, b: 0.0, Ea: 123.0}
  # Efficiencies for the species in the previous reaction must be explicitly zero
  # to avoid double counting and being considered a duplicate reaction
  efficiencies: {H2: 0.0, H2O: 0.0, AR: 0.0, CO: 3.0}

Reaction types#

`elementary`#

A homogeneous reaction with a pressure-independent rate coefficient and mass action kinetics, as described here.

Additional fields are:

rate-constant: An Arrhenius-type list or mapping.
negative-A: A boolean indicating whether a negative value for the pre-exponential factor is allowed. The default is false.

Example:

- equation: N + NO <=> N2 + O
  rate-constant: {A: -2.70000E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
  negative-A: true

`three-body`#

A three body reaction as described here.

The reaction equation must include a third body collision partner, which may be either a specific species or the generic third body M.

Includes the fields of an elementary reaction, plus the fields for specifying efficiencies.

Example:

- equation: 2 O + M = O2 + M
  type: three-body
  rate-constant: [1.20000E+17 cm^6/mol^2/s, -1, 0]
  efficiencies: {AR: 0.83, H2O: 5}

The type field of the YAML entry may be omitted. Reactions containing the generic third body M are automatically identified as three-body reactions. Reactions are also identified as three-body reactions if all of the following conditions are met:

There is exactly one species appearing as both a reactant and product
All reactants and products have integral stoichiometric coefficients
The sum of the stoichiometric coefficients for either the reactants or products is 3.

Examples:

- equation: H + 2 O2 <=> HO2 + O2  # Reaction 34
  rate-constant: {A: 2.08e+19, b: -1.24, Ea: 0.0}
- equation: H + O2 + N2 <=> HO2 + N2  # Reaction 36
  rate-constant: {A: 2.6e+19, b: -1.24, Ea: 0.0}

Caution

If a corresponding reaction with the generic third body M also appears in the mechanism, such as:

- equation: H + O2 + M <=> HO2 + M  # Reaction 33
  rate-constant: {A: 2.8e+18, b: -0.86, Ea: 0.0}
  efficiencies: {O2: 0.0, H2O: 0.0, CO: 0.75, CO2: 1.5, C2H6: 1.5, N2: 0.0, AR: 0.0}

then the third body efficiency for any third bodies that are given in the explicit form of Reaction 34 or Reaction 35 above must be set to zero, as shown here for O2 and N2, or the reactions must be marked as duplicate.

Changed in version 3.0: Three body reactions are detected automatically and the the type field may be omitted. Reactions with explicit third bodies are required to be marked as duplicates of reactions with the generic third body if the corresponding efficiency is not zero.

Added in version 3.1: Reactions with explicit third bodies and the corresponding reaction with “M” issue warnings instead of raising errors by default. The explicit-third-body-duplicates field of the phase entry can be used to control how these reactions are handled.

`Blowers-Masel`#

Includes the fields of an elementary reaction, except that the rate-constant field is a Blowers-Masel-type list or mapping.

Example:

- equation: O + H2 <=> H + OH
  type: Blowers-Masel
  rate-constant: {A: 3.87e+04 cm^2/mol/s, b: 2.7, Ea0: 6260.0 cal/mol, w: 1e9 cal/mol}

`two-temperature-plasma`#

Includes the fields of an elementary reaction, except that the rate-constant field is a two-temperature-plasma list or mapping.

Example:

- equation: O + H => O + H
  type: two-temperature-plasma
  rate-constant: {A: 17283, b: -3.1, Ea-gas: -5820 J/mol, Ea-electron: 1081 J/mol}

`electron-collision-plasma`#

Electron collision plasma reactions involve an electron as one of the reactants, and are parameterized by the collision cross section as a function of the electron energy. The rate calculation is described here. The rate parameters are specified using the following additional fields in the reaction entry:

energy-levels: A list of electron energy levels [V]
cross-sections: A list of collision cross sections [m²] for the reaction at the specified energy levels.

Example:

- equation: O2 + e => e + e + O2+
  type: electron-collision-plasma
  energy-levels: [13.0, 15.5, 18, 23]
  cross-sections: [1.17e-22, 7.3e-22, 1.64e-21, 3.66e-21]

Added in version 3.1.

`falloff`#

A falloff reaction as described here.

The reaction equation should include the pressure-dependent third body collision partner (+M) or (+name) where name is the name of a species. The latter case is equivalent to setting the efficiency for name to 1 and the efficiency for all other species to 0.

Includes field for specifying efficiencies as well as:

high-P-rate-constant: An Arrhenius expression for the high-pressure limit
low-P-rate-constant: An Arrhenius expression for the low-pressure limit
Troe: Parameters for the Troe falloff function. A mapping containing the keys A, T3, T1 and optionally T2. The default value for T2 is 0.
SRI: Parameters for the SRI falloff function. A mapping containing the keys A, B, C, and optionally D and E. The default values for D and E are 1.0 and 0.0, respectively.
Tsang: Parameters for the Tsang falloff function. A mapping containing the keys A and B. The default value for B is 0.0.

Examples:

- equation: H + CH2 (+ N2) <=> CH3 (+N2)
  type: falloff
  high-P-rate-constant: [6.00000E+14 cm^3/mol/s, 0, 0]
  low-P-rate-constant: {A: 1.04000E+26 cm^6/mol^2/s, b: -2.76, Ea: 1600}
  Troe: {A: 0.562, T3: 91, T1: 5836}
- equation: O + CO (+M) <=> CO2 (+M)
  type: falloff  # Lindemann form since no additional falloff function parameters given
  low-P-rate-constant: {A: 6.02e+14, b: 0.0, Ea: 3000.0}
  high-P-rate-constant: {A: 1.8e+10, b: 0.0, Ea: 2385.0}
  efficiencies: {H2: 2.0, O2: 6.0, H2O: 6.0, CH4: 2.0, CO: 1.5, CO2: 3.5,
    C2H6: 3.0, AR: 0.5}

`chemically-activated`#

A chemically activated reaction as described here.

The parameters are the same as for falloff reactions.

Example:

- equation: CH3 + OH (+M) <=> CH2O + H2 (+M)
  type: chemically-activated
  high-P-rate-constant: [5.88E-14, 6.721, -3022.227]
  low-P-rate-constant: [282320.078, 1.46878, -3270.56495]

`pressure-dependent-Arrhenius`#

A pressure-dependent reaction using multiple Arrhenius expressions as described here.

The only additional field in this reaction type is:

rate-constants: A list of mappings, where each mapping is the mapping form of an Arrhenius expression with the addition of a pressure P.

Example:

- equation: H + CH4 <=> H2 + CH3
  type: pressure-dependent-Arrhenius
  rate-constants:
  - {P: 0.039474 atm, A: 2.720000e+09 cm^3/mol/s, b: 1.2, Ea: 6834.0}
  - {P: 1.0 atm, A: 1.260000e+20, b: -1.83, Ea: 15003.0}
  - {P: 1.0 atm, A: 1.230000e+04, b: 2.68, Ea: 6335.0}
  - {P: 1.01325 MPa, A: 1.680000e+16, b: -0.6, Ea: 14754.0}

`Chebyshev`#

A reaction parameterized as a bivariate Chebyshev polynomial as described here.

Additional fields are:

temperature-range: A list of two values specifying the minimum and maximum temperatures at which the rate constant is valid
pressure-range: A list of two values specifying the minimum and maximum pressures at which the rate constant is valid
data: A list of lists containing the Chebyshev coefficients

Example:

- equation: CH4 <=> CH3 + H
  type: Chebyshev
  temperature-range: [290, 3000]
  pressure-range: [0.0098692326671601278 atm, 98.692326671601279 atm]
  data: [[-1.44280e+01,  2.59970e-01, -2.24320e-02, -2.78700e-03],
         [ 2.20630e+01,  4.88090e-01, -3.96430e-02, -5.48110e-03],
         [-2.32940e-01,  4.01900e-01, -2.60730e-02, -5.04860e-03],
         [-2.93660e-01,  2.85680e-01, -9.33730e-03, -4.01020e-03],
         [-2.26210e-01,  1.69190e-01,  4.85810e-03, -2.38030e-03],
         [-1.43220e-01,  7.71110e-02,  1.27080e-02, -6.41540e-04]]

`linear-Burke`#

A complex-forming reaction (one that depends on both P and X) parameterized according to the reduced-pressure linear mixture rule as described here.

efficiency and eig0 comprise the two acceptable ways to represent the contribution of each bath gas component (collider) to the reduced pressure. All explicitly defined colliders must include either efficiency or eig0, but the choice must remain consistent throughout a single reaction (either all colliders are defined with efficiency, or all are defined with eig0).

The pressure-dependent aspect of each collider rate constant can be parameterized in the user’s choice of Troe, pressure-dependent-Arrhenius, or Chebyshev representations. The same parameters used for a standalone Troe, PLOG, or Chebyshev reaction are then inserted directly below efficiency or eig0 for a given collider. At minimum, this treatment must be applied to M. However, additional colliders may also be given their own Troe, PLOG, or Chebyshev parameterization if so desired. Mixing and matching of types within the same reaction is allowed (e.g., a PLOG table for M, Troe parameters for H2, and Chebyshev data for NH3).

A mathematical description of this YAML implementation can be found in Eq. 8 of Singal et al. [2024].

Additional fields are:

colliders

A list of dictionaries, where each entry contains parameters corresponding to individual colliders (species in the bath gas). Each entry within the colliders list may contain the following fields:

name: The name of the collider species (e.g., H2O). The first collider defined must be M, which represents the generic reference collider (often Ar or N2) that represents all species lacking their own explicit parameterization.
eig0: The absolute value of the least negative chemically significant eigenvalue of the master equation for the \(i^{th}\) collider (when pure), evaluated at the low-pressure limit, \(\Lambda_{0,i}(T)[M]\). The user must explicitly assign an eig0 for M. This parameter is entered in modified Arrhenius format to enable consideration of temperature dependence.
efficiency: The third-body efficiency of the collider relative to that of the reference collider M, defined as \(\epsilon_{0,i}(T)=\Lambda_{0,i}(T)/\Lambda_{0,\text{M}}(T)\). The user does not need to assign an efficiency for M, as it is always equal to 1 by definition. However, they are free to do so, as long as it takes the form efficiency: {A: 1, b: 0, Ea: 0} (no variations are permitted). This parameter is entered in modified Arrhenius format to enable consideration of temperature dependence. If the user wishes to specify a temperature-independent value, then A can be set to this value and b and Ea can be set to 0 (such as H2O: {A: 10, b: 0, Ea: 0}).

A Troe implementation also requires: high-P-rate-constant, low-P-rate-constant, Troe (do not use the Troe efficiencies key).

A pressure-dependent-Arrhenius implementation also requires: rate-constants.

A Chebyshev implementation also requires: temperature-range, pressure-range, data.

Examples:

linear-Burke rate with Troe format for the reference collider (N2):

- equation: H + OH <=> H2O
  type: linear-Burke
  colliders:
  - name: M
    type: falloff
    low-P-rate-constant: {A: 4.530000e+21, b: -1.820309e+00, Ea: 4.987000e+02}
    high-P-rate-constant: {A: 2.510000e+13, b: 2.329303e-01, Ea: -1.142000e+02}
    Troe: {A: 9.995044e-01, T3: 1.0e-30, T1: 1.0e+30}
  - name: AR
    efficiency: {A: 2.20621e-02, b: 4.74036e-01, Ea: -1.13148e+02}
  - name: H2O
    efficiency: {A: 1.04529e-01, b: 5.50787e-01, Ea: -2.32675e+02}

linear-Burke rate with PLOG format for the reference collider (Ar):

- equation: H + O2 (+M) <=> HO2 (+M) # Adding '(+M)' is optional
  type: linear-Burke
  colliders:
  - name: M
    type: pressure-dependent-Arrhenius
    rate-constants:
    - {P: 1.316e-02 atm, A: 9.39968e+14, b: -2.14348e+00, Ea: 7.72730e+01}
    - {P: 1.316e-01 atm, A: 1.07254e+16, b: -2.15999e+00, Ea: 1.30239e+02}
    - {P: 3.947e-01 atm, A: 3.17830e+16, b: -2.15813e+00, Ea: 1.66994e+02}
    - {P: 1.000e+00 atm, A: 7.72584e+16, b: -2.15195e+00, Ea: 2.13473e+02}
    - {P: 3.000e+00 atm, A: 2.11688e+17, b: -2.14062e+00, Ea: 2.79031e+02}
    - {P: 1.000e+01 atm, A: 6.53093e+17, b: -2.13213e+00, Ea: 3.87493e+02}
    - {P: 3.000e+01 atm, A: 1.49784e+18, b: -2.10026e+00, Ea: 4.87579e+02}
    - {P: 1.000e+02 atm, A: 3.82218e+18, b: -2.07057e+00, Ea: 6.65984e+02}
  - name: HE
    efficiency: {A: 3.37601e-01, b: 1.82568e-01, Ea: 3.62408e+01}
  - name: N2
    efficiency: {A: 1.24932e+02, b: -5.93263e-01, Ea: 5.40921e+02}
  - name: H2
    efficiency: {A: 3.13717e+04, b: -1.25419e+00, Ea: 1.12924e+03}
  - name: CO2
    efficiency: {A: 1.62413e+08, b: -2.27622e+00, Ea: 1.97023e+03}
  - name: NH3
    efficiency: {A: 4.97750e+00, b: 1.64855e-01, Ea: -2.80351e+02}
  - name: H2O
    efficiency: {A: 3.69146e+01, b: -7.12902e-02, Ea: 3.19087e+01}

linear-Burke rate with Chebyshev format for the reference collider (Ar):

- equation: H2O2 <=> 2 OH
  type: linear-Burke
  colliders:
  - name: M
    type: Chebyshev
    temperature-range: [200.0, 2000.0]
    pressure-range: [1.000e-01 atm, 1.000e+02 atm]
    data:
    - [-1.58e+01, 8.71e-01, -9.44e-02, -2.81e-03, -4.48e-04, 1.58e-03, -2.51e-04]
    - [2.32e+01, 5.27e-01, 2.89e-02, -5.46e-03, 7.08e-04, -3.03e-03, 7.81e-04]
    - [-3.80e-01, 8.63e-02, 4.03e-02, -7.23e-03, 5.76e-04, 2.79e-03, -1.49e-03]
    - [-1.48e-01, -7.18e-03, 2.21e-02, 6.23e-03, -5.98e-03, -8.22e-06, 1.92e-03]
    - [-6.06e-02, -1.42e-02, 1.34e-03, 9.62e-03, 1.70e-03, -3.65e-03, -4.32e-04]
    - [-2.46e-02, -9.71e-03, -5.88e-03, 3.05e-03, 5.87e-03, 1.50e-03, -2.01e-03]
    - [-1.54e-02, -5.24e-03, -6.91e-03, -5.94e-03, -1.22e-03, 2.17e-03, 1.59e-03]
  - name: N2
    efficiency: {A: 1.14813e+00, b: 4.60090e-02, Ea: -2.92413e+00}
  - name: CO2
    efficiency: {A: 8.98839e+01, b: -4.27974e-01, Ea: 2.41392e+02}
  - name: H2O2
    efficiency: {A: 6.45295e-01, b: 4.26266e-01, Ea: 4.28932e+01}
  - name: H2O
    efficiency: {A: 1.36377e+00, b: 3.06592e-01, Ea: 2.10079e+02}

`interface-Arrhenius`#

A reaction occurring on a surface between two bulk phases, or along an edge at the intersection of two surfaces, as described here.

Includes the fields of an elementary reaction plus:

coverage-dependencies

A mapping of species names to coverage dependence parameters, where these parameters are contained in either a mapping with the fields:

a: Coefficient for exponential dependence on the coverage
m: Power-law exponent of coverage dependence
E: Activation energy dependence on coverage, which uses the same sign convention as the leading-order activation energy term. This can be a scalar value for the linear dependency or a list of four values for the polynomial dependency given in the order of 1st, 2nd, 3rd, and 4th-order coefficients

or a list containing the three elements above, in the given order.

Note that parameters a, m and E correspond to parameters \(\eta_{ki}\), \(\mu_{ki}\) and \(\epsilon_{ki}\) in Eq 11.113 of Kee et al. [2003], respectively.

Examples:

- equation: 2 H(s) => H2 + 2 Pt(s)
  rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea: 67400 J/mol}
  coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}

- equation: 2 O(S) => O2 + 2 Pt(S)
  rate-constant: {A: 3.7e+21, b: 0, Ea: 213200 J/mol}
  coverage-dependencies: {O(S): {a: 0.0, m: 0.0,
    E: [1.0e3 J/mol, 3.0e3 J/mol , -7.0e4 J/mol , 5.0e3 J/mol]}}

- equation: CH4 + PT(S) + O(S) => CH3(S) + OH(S)
  rate-constant: {A: 5.0e+18, b: 0.7, Ea: 4.2e+04}
  coverage-dependencies:
    O(S): [0, 0, 8000]
    PT(S): [0, -1.0, 0]

- equation: 2 O(S) => O2 + 2 Pt(S)
  rate-constant: {A: 3.7e+21, b: 0, Ea: 213200 J/mol}
  coverage-dependencies:
    O(S): [0, 0, [1.0e6, 3.0e6, -7.0e7, 5.0e6]]

`interface-Blowers-Masel`#

Includes the same fields as interface-Arrhenius, while using the Blowers-Masel parameterization for the rate constant.

Example:

- equation: 2 H(s) => H2 + 2 Pt(s)
  type: Blowers-Masel
  rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea0: 67400 J/mol, w: 1000000 J/mol}
  coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}

`sticking-Arrhenius`#

A sticking reaction occurring on a surface adjacent to a bulk phase, as described here.

Includes the fields of an interface-Arrhenius reaction plus:

sticking-coefficient: An Arrhenius-type expression for the sticking coefficient
Motz-Wise: A boolean indicating whether to use the Motz-Wise correction factor for sticking coefficients near unity. Defaults to false.
sticking-species: The name of the sticking species. Required if the reaction includes multiple non-surface species.

Example:

- equation: OH + PT(S) => OH(S)
  sticking-coefficient: {A: 1.0, b: 0, Ea: 0}

`sticking-Blowers-Masel`#

Includes the same fields as sticking-Arrhenius, while using the Blowers-Masel parameterization for the sticking coefficient.

Example:

- equation: OH + PT(S) => OH(S)
  type: Blowers-Masel
  sticking-coefficient: {A: 1.0, b: 0, Ea0: 0, w: 100000}
  Motz-Wise: true

`electrochemical`#

Interface reactions involving charge transfer between phases.

Includes the fields of an interface-Arrhenius reaction, plus:

beta: The symmetry factor for the reaction. Default is 0.5.
exchange-current-density-formulation: Set to true if the rate constant parameterizes the exchange current density. Default is false.

Example:

- equation: LiC6 <=> Li+(e) + C6
  rate-constant: [5.74, 0.0, 0.0]
  beta: 0.4

Reactions#

Reaction rate expressions#

Arrhenius#

Blowers-Masel#

Two-Temperature Plasma#

Efficiencies#

Reaction types#

elementary#

three-body#

Blowers-Masel#

two-temperature-plasma#

electron-collision-plasma#

falloff#

chemically-activated#

pressure-dependent-Arrhenius#

Chebyshev#

linear-Burke#

interface-Arrhenius#

interface-Blowers-Masel#

sticking-Arrhenius#

sticking-Blowers-Masel#

electrochemical#

`elementary`#

`three-body`#

`Blowers-Masel`#

`two-temperature-plasma`#

`electron-collision-plasma`#

`falloff`#

`chemically-activated`#

`pressure-dependent-Arrhenius`#

`Chebyshev`#

`linear-Burke`#

`interface-Arrhenius`#

`interface-Blowers-Masel`#

`sticking-Arrhenius`#

`sticking-Blowers-Masel`#

`electrochemical`#