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# 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

  - falloff

  - chemically-activated

  - pressure-dependent-Arrhenius

  - Chebyshev

  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: -2.70000E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
    [-2.70000E+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.

## 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 should include the third body collision partner `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}

### `Blowers-Masel`

Includes the fields of an elemntary 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-type 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}

### `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.

Example:

    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}

### `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]]

### `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

  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, R. J., Coltrin, M. E., & Glarborg, P.(2003). Chemically reacting flow: theory and practice. John Wiley & Sons], 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: 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]

### `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, as described here.

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