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[Sphinx] Make reaction rate information consistent
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ischoegl committed Apr 24, 2022
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181 changes: 119 additions & 62 deletions doc/sphinx/yaml/reactions.rst
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Expand Up @@ -22,12 +22,12 @@ The fields common to all ``reaction`` entries are:

- :ref:`elementary <sec-yaml-elementary>`
- :ref:`three-body <sec-yaml-three-body>`
- :ref:`Blowers-Masel <sec-yaml-Blowers-Masel>`
- :ref:`two-temperature-plasma <sec-yaml-two-temperature-plasma>`
- :ref:`falloff <sec-yaml-falloff>`
- :ref:`chemically-activated <sec-yaml-chemically-activated>`
- :ref:`pressure-dependent-Arrhenius <sec-yaml-pressure-dependent-Arrhenius>`
- :ref:`Chebyshev <sec-yaml-Chebyshev>`
- :ref:`two-temperature-plasma <sec-yaml-two-temperature-plasma>`
- :ref:`Blowers-Masel <sec-yaml-Blowers-Masel>`

Reactions without a specified ``type`` on surfaces or edges are
automatically treated as :ref:`interface-Arrhenius <sec-yaml-interface-Arrhenius>`
Expand Down Expand Up @@ -62,20 +62,82 @@ The fields common to all ``reaction`` entries are:
Depending on the reaction ``type``, other fields may be necessary to specify
the rate of the reaction.

.. _sec-yaml-arrhenius:

Arrhenius expression
====================
Reaction rate expressions
=========================

.. _sec-yaml-Arrhenius-rate:

Arrhenius
---------

Arrhenius expressions can be specified as either a three-element list containing
the pre-exponential factor :math:`A`, the temperature exponent :math:`b`, and
the activation energy :math:`E_a`, or a mapping containing the fields ``A``,
``b``, and ``Ea``. The following are equivalent::
Arrhenius rate expressions are specified as a mapping with fields:

``A``
The pre-exponential factor :math:`A`
``b``
The temperature exponent :math:`b`
``Ea``
The activation energy :math:`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]


.. _sec-yaml-Blowers-Masel-rate:

Blowers-Masel
-------------

Blowers-Masel rate expressions calculate the rate constant based on the Blowers Masel
approximation as
`described here <https://cantera.org/science/kinetics.html#sec-blowers-masel>`__.
The rate parameters are specified as a mapping with fields:

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

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

{A: 3.87e+04 cm^2/mol/s, b: 2.7, Ea0: 6260.0 cal/mol, w: 1e9 cal/mol}
[3.87e+04 cm^2/mol/s, 2.7, 6260.0 cal/mol, 1e9 cal/mol]


.. _sec-yaml-two-temperature-plasma-rate:

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 <https://cantera.org/science/kinetics.html#two-temperature-plasma-reactions>`__.
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 :math:`E_{a,g}` that is related to the gas temperature
``Ea-electron``
The activation energy term :math:`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}


.. _sec-yaml-efficiencies:

Efficiencies
Expand Down Expand Up @@ -108,7 +170,7 @@ action kinetics, as
Additional fields are:

``rate-constant``
An :ref:`Arrhenius-type <sec-yaml-arrhenius>` list or mapping.
An :ref:`Arrhenius-type <sec-yaml-Arrhenius-rate>` list or mapping.

``negative-A``
A boolean indicating whether a negative value for the pre-exponential factor
Expand Down Expand Up @@ -142,6 +204,39 @@ Example::
efficiencies: {AR: 0.83, H2O: 5}


.. _sec-yaml-Blowers-Masel:

``Blowers-Masel``
-----------------

Includes the fields of an :ref:`elemntary <sec-yaml-elementary>` reaction, except that
the ``rate-constant`` field is a
:ref:`Blowers-Masel-type <sec-yaml-Blowers-Masel-rate>` 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}


.. _sec-yaml-two-temperature-plasma:

``two-temperature-plasma``
--------------------------

Includes the fields of an :ref:`elementary <sec-yaml-elementary>` reaction, except that
the ``rate-constant`` field is a
:ref:`Two-temperature-plasma-type <sec-yaml-two-temperature-plasma-rate>` 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}


.. _sec-yaml-falloff:

``falloff``
Expand All @@ -159,10 +254,10 @@ Includes field for specifying :ref:`efficiencies <sec-yaml-efficiencies>` as wel
as:

``high-P-rate-constant``
An :ref:`sec-yaml-arrhenius` expression for the high-pressure limit
An :ref:`sec-yaml-Arrhenius-rate` expression for the high-pressure limit

``low-P-rate-constant``
An :ref:`sec-yaml-arrhenius` expression for the low-pressure limit
An :ref:`sec-yaml-Arrhenius-rate` expression for the low-pressure limit

``Troe``
Parameters for the
Expand Down Expand Up @@ -209,6 +304,7 @@ Example::
high-P-rate-constant: [5.88E-14, 6.721, -3022.227]
low-P-rate-constant: [282320.078, 1.46878, -3270.56495]


.. _sec-yaml-pressure-dependent-Arrhenius:

``pressure-dependent-Arrhenius``
Expand All @@ -221,7 +317,7 @@ The only additional field in this reaction type is:

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

Example::

Expand Down Expand Up @@ -268,52 +364,6 @@ Example::
[-2.26210e-01, 1.69190e-01, 4.85810e-03, -2.38030e-03],
[-1.43220e-01, 7.71110e-02, 1.27080e-02, -6.41540e-04]]

.. _sec-yaml-Blowers-Masel:

``Blowers-Masel``
-----------------

A reaction with parameters to calculate rate constant based on Blowers Masel
approximation as `described here <https://cantera.org/science/kinetics.html#sec-blowers-masel>`__.

Additional fields are:

``rate-constant``
A list of values containing the pre-exponential factor :math:`A`, the
temperature exponent :math:`b`, the intrinsic activation energy :math:`E_{a0}`,
and the average of the bond dissociation energy of the bond breaking and that
being formed in the reaction :math:`w`.

``negative-A``
A boolean indicating whether a negative value for the pre-exponential factor
is allowed. The default is ``false``.

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}

.. _sec-yaml-two-temperature-plasma:

``two-temperature-plasma``
--------------------------

A reaction involving an electron as one of the reactants, where the electron temperature
may differ from the gas temperature as `described here <https://cantera.org/science/kinetics.html#two-temperature-plasma-reactions>`__.

Includes the fields of an :ref:`sec-yaml-elementary` reaction, except that the
``rate-constant`` field is a mapping with the fields:

``A``
The pre-exponential factor
``b``
The temperature exponent, which is applied to the electron temperature
``Ea_T``
The activation energy term :math:`E_{a,g}` that is related to the gas temperature
``Ea_Te``
The activation energy term :math:`E_{a,e}` that is related to the electron
temperature

.. _sec-yaml-interface-Arrhenius:

Expand Down Expand Up @@ -359,13 +409,15 @@ Examples::
O(S): [0, 0, 8000]
PT(S): [0, -1.0, 0]


.. _sec-yaml-interface-Blowers-Masel:

``interface-Blowers-Masel``
---------------------------

Includes the same fields as :ref:`interface-Arrhenius <sec-yaml-interface-Arrhenius>`,
while using the :ref:`Blowers-Masel <sec-yaml-Blowers-Masel>` rate parameterization.
while using the :ref:`Blowers-Masel <sec-yaml-Blowers-Masel-rate>` parameterization
for the rate constant.

Example::

Expand All @@ -374,6 +426,7 @@ Example::
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}}


.. _sec-yaml-sticking-Arrhenius:

``sticking-Arrhenius``
Expand All @@ -385,7 +438,8 @@ A sticking reaction occurring on a surface adjacent to a bulk phase, as
Includes the fields of an :ref:`sec-yaml-interface-Arrhenius` reaction plus:

``sticking-coefficient``
An :ref:`Arrhenius-type <sec-yaml-arrhenius>` expression for the sticking coefficient
An :ref:`Arrhenius-type <sec-yaml-Arrhenius-rate>` expression for the sticking
coefficient

``Motz-Wise``
A boolean applicable to sticking reactions, indicating whether to use the
Expand All @@ -401,13 +455,15 @@ Example::
equation: OH + PT(S) => OH(S)
sticking-coefficient: {A: 1.0, b: 0, Ea: 0}


.. _sec-yaml-sticking-Blowers-Masel:

``sticking-Blowers-Masel``
---------------------------

Includes the same fields as :ref:`sticking-Arrhenius <sec-yaml-sticking-Arrhenius>`,
while using the :ref:`Blowers-Masel <sec-yaml-Blowers-Masel>` rate parameterization.
while using the :ref:`Blowers-Masel <sec-yaml-Blowers-Masel-rate>` parameterization
for the sticking coefficient.

Example::

Expand All @@ -416,6 +472,7 @@ Example::
sticking-coefficient: {A: 1.0, b: 0, Ea0: 0, w: 100000}
Motz-Wise: true


.. _sec-yaml-electrochemical-reaction:

``electrochemical``
Expand Down

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