From e3240e9c9b955e1cc1bb1f6a8b9e8d58c0e57e5c Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 11:02:29 -0500 Subject: [PATCH 1/6] [Sphinx] Fix links after website update --- doc/sphinx/yaml/reactions.rst | 26 +++++++++++++------------- interfaces/cython/cantera/ck2cti.py | 2 +- interfaces/cython/cantera/ck2yaml.py | 18 +++++++++--------- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index 8c5e0aa11f..8def6fdd46 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -47,7 +47,7 @@ The fields common to all ``reaction`` entries are: 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 `__ + `Reaction orders `__ for additional information. ``negative-orders`` @@ -102,7 +102,7 @@ Reaction types A homogeneous reaction with a pressure-independent rate coefficient and mass action kinetics, as -`described here `__. +`described here `__. Additional fields are: @@ -126,7 +126,7 @@ Example:: -------------- A three body reaction as -`described here `__. +`described here `__. The reaction equation should include the third body collision partner ``M``. @@ -147,7 +147,7 @@ Example:: ----------- A falloff reaction as -`described here `__. +`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 @@ -165,13 +165,13 @@ as: ``Troe`` Parameters for the - `Troe `__ + `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 `__ + `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. @@ -191,7 +191,7 @@ Example:: ------------------------ A chemically activated reaction as -`described here `__. +`described here `__. The parameters are the same as for :ref:`sec-yaml-falloff` reactions. @@ -208,7 +208,7 @@ Example:: -------------------------------- A pressure-dependent reaction using multiple Arrhenius expressions as -`described here `__. +`described here `__. The only additional field in this reaction type is: @@ -233,7 +233,7 @@ Example:: ------------- A reaction parameterized as a bivariate Chebyshev polynomial as -`described here `__. +`described here `__. Additional fields are: @@ -267,7 +267,7 @@ Example:: ----------------- A reaction with parameters to calculate rate constant based on Blowers Masel -approximation as `described here `__. +approximation as `described here `__. Additional fields are: @@ -293,7 +293,7 @@ Example:: -------------------------- A reaction involving an electron as one of the reactants, where the electron temperature -may differ from the gas temperature as `described here `__. +may differ from the gas temperature as `described here `__. Includes the fields of an :ref:`sec-yaml-elementary` reaction, except that the ``rate-constant`` field is a mapping with the fields: @@ -315,7 +315,7 @@ Includes the fields of an :ref:`sec-yaml-elementary` reaction, except that the A reaction occurring on a surface between two bulk phases, or along an edge at the intersection of two surfaces, as -`described here `__. +`described here `__. Includes the fields of an :ref:`sec-yaml-elementary` reaction plus: @@ -395,7 +395,7 @@ Example:: A reaction occurring on a surface between two bulk phases, or along an edge at the intersection of two surfaces, which the rate constant can be calculated by Blowers Masel Approximation with Arrhenius expression as -`described here `__. +`described here `__. Includes the fields of a :ref:`sec-yaml-Blowers-Masel` reaction and the fields of an :ref:`sec-yaml-interface-reaction` reaction. diff --git a/interfaces/cython/cantera/ck2cti.py b/interfaces/cython/cantera/ck2cti.py index db263eed7a..30a96c27a7 100644 --- a/interfaces/cython/cantera/ck2cti.py +++ b/interfaces/cython/cantera/ck2cti.py @@ -835,7 +835,7 @@ class Sri(object): A kinetic model of a phenomenological rate coefficient :math:`k(T, P)` using the "SRI" formulation of the blending function :math:`F` using either 3 or 5 parameters. See `The SRI Falloff Function - `__. + `__. The attributes are: diff --git a/interfaces/cython/cantera/ck2yaml.py b/interfaces/cython/cantera/ck2yaml.py index 69a67076b0..3c79dc4323 100644 --- a/interfaces/cython/cantera/ck2yaml.py +++ b/interfaces/cython/cantera/ck2yaml.py @@ -403,7 +403,7 @@ def as_yaml(self, extra=()): class ElementaryRate(KineticsModel): """ A reaction rate described by a single Arrhenius expression. - See https://cantera.org/science/reactions.html#reactions-with-a-pressure-independent-rate + See https://cantera.org/science/kinetics.html#reactions-with-a-pressure-independent-rate :param rate: The Arrhenius expression describing this reaction rate. @@ -422,7 +422,7 @@ def reduce(self, output): class SurfaceRate(KineticsModel): """ An Arrhenius-like reaction occurring on a surface - See https://cantera.org/science/reactions.html#surface-reactions + See https://cantera.org/science/kinetics.html#surface-reactions :param rate: The Arrhenius expression describing this reaction rate. @@ -470,7 +470,7 @@ class PDepArrhenius(KineticsModel): """ A rate calculated by interpolating between Arrhenius expressions at various pressures. - See https://cantera.org/science/reactions.html#pressure-dependent-arrhenius-rate-expressions-p-log + See https://cantera.org/science/kinetics.html#pressure-dependent-arrhenius-rate-expressions-p-log :param pressures: A list of pressures at which Arrhenius expressions are given. @@ -499,7 +499,7 @@ def reduce(self, output): class Chebyshev(KineticsModel): """ A rate calculated in terms of a bivariate Chebyshev polynomial. - See https://cantera.org/science/reactions.html#chebyshev-reaction-rate-expressions + See https://cantera.org/science/kinetics.html#chebyshev-reaction-rate-expressions :param coeffs: Matrix of Chebyshev coefficients, dimension N_T by N_P @@ -541,7 +541,7 @@ def reduce(self, output): class ThreeBody(KineticsModel): """ A rate calculated for a reaction which includes a third-body collider. - See https://cantera.org/science/reactions.html#three-body-reactions + See https://cantera.org/science/kinetics.html#three-body-reactions :param high_rate: The Arrhenius kinetics (high-pressure limit) @@ -570,7 +570,7 @@ def reduce(self, output): class Falloff(ThreeBody): """ A rate for a pressure-dependent falloff reaction. - See https://cantera.org/science/reactions.html#falloff-reactions + See https://cantera.org/science/kinetics.html#falloff-reactions :param low_rate: The Arrhenius kinetics at the low-pressure limit @@ -604,7 +604,7 @@ def reduce(self, output): class ChemicallyActivated(ThreeBody): """ A rate for a chemically-activated reaction. - See https://cantera.org/science/reactions.html#chemically-activated-reactions + See https://cantera.org/science/kinetics.html#chemically-activated-reactions :param low_rate: The Arrhenius kinetics at the low-pressure limit @@ -638,7 +638,7 @@ def reduce(self, output): class Troe: """ The Troe falloff function, described with either 3 or 4 parameters. - See https://cantera.org/science/reactions.html#the-troe-falloff-function + See https://cantera.org/science/kinetics.html#the-troe-falloff-function """ def __init__(self, A=0.0, T3=0.0, T1=0.0, T2=None): self.A = A @@ -656,7 +656,7 @@ def reduce(self, output): class Sri: """ The SRI falloff function, described with either 3 or 5 parameters. - See https://cantera.org/science/reactions.html#the-sri-falloff-function + See https://cantera.org/science/kinetics.html#the-sri-falloff-function """ def __init__(self, *, A, B, C, D=None, E=None): self.A = A From 09869d39a06b9ce821f7cee016721829fbb6de51 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 11:11:04 -0500 Subject: [PATCH 2/6] [Sphinx] Add Tsang to YAML documentation --- doc/sphinx/yaml/reactions.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index 8def6fdd46..24190d1154 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -176,6 +176,12 @@ as: 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) From 358eacc2e1963dca834968d0bc04a53b3c0fa552 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 13:08:00 -0500 Subject: [PATCH 3/6] [Sphinx] Update YAML documentation for surface reactions --- doc/sphinx/yaml/reactions.rst | 94 ++++++++++++++++++++++------------- 1 file changed, 59 insertions(+), 35 deletions(-) diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index 24190d1154..a42efa0fd9 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -314,10 +314,10 @@ Includes the fields of an :ref:`sec-yaml-elementary` reaction, except that the The activation energy term :math:`E_{a,e}` that is related to the electron temperature -.. _sec-yaml-interface-reaction: +.. _sec-yaml-interface-Arrhenius: -``interface`` -------------- +``interface-Arrhenius`` +----------------------- A reaction occurring on a surface between two bulk phases, or along an edge at the intersection of two surfaces, as @@ -325,18 +325,6 @@ at the intersection of two surfaces, as Includes the fields of an :ref:`sec-yaml-elementary` reaction plus: -``sticking-coefficient`` - An :ref:`Arrhenius-type ` expression for the sticking coefficient - -``Motz-Wise`` - A boolean applicable to sticking reactions, 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 for sticking reactions only if - the reaction includes multiple non-surface species. - ``coverage-dependencies`` A mapping of species names to coverage dependence parameters, where these parameters are contained in either a mapping with the fields: @@ -370,6 +358,62 @@ 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 `, +while using the :ref:`Blowers-Masel ` rate parameterization. + +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}} + +.. _sec-yaml-sticking-Arrhenius: + +``sticking-Arrhenius`` +----------------------- + +A sticking reaction occurring on a surface adjacent to a bulk phase, as +`described here `__. + +Includes the fields of an :ref:`sec-yaml-interface-Arrhenius` reaction plus: + +``sticking-coefficient`` + An :ref:`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} + +.. _sec-yaml-sticking-Blowers-Masel: + +``sticking-Blowers-Masel`` +--------------------------- + +Includes the same fields as :ref:`sticking-Arrhenius `, +while using the :ref:`Blowers-Masel ` rate parameterization. + +Example:: + + equation: OH + PT(S) => OH(S) + type: Blowers-Masel + sticking-coefficient: {A: 1.0, b: 0, Ea0: 0, w: 100000} + Motz-Wise: true + .. _sec-yaml-electrochemical-reaction: ``electrochemical`` @@ -392,23 +436,3 @@ Example:: equation: LiC6 <=> Li+(e) + C6 rate-constant: [5.74, 0.0, 0.0] beta: 0.4 - -.. _sec-yaml-surface-Blowers-Masel: - -``surface-Blowers-Masel`` -------------------------- - -A reaction occurring on a surface between two bulk phases, or along an edge -at the intersection of two surfaces, which the rate constant can be calculated -by Blowers Masel Approximation with Arrhenius expression as -`described here `__. - -Includes the fields of a :ref:`sec-yaml-Blowers-Masel` reaction and -the fields of an :ref:`sec-yaml-interface-reaction` reaction. - -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}} From 043620e0b0418abe0a698ee7a8b92d56401cd90b Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 13:52:20 -0500 Subject: [PATCH 4/6] [Sphinx] Update YAML documentation for 'type' entry --- doc/sphinx/yaml/reactions.rst | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index a42efa0fd9..c26e594de4 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -28,16 +28,17 @@ The fields common to all ``reaction`` entries are: - :ref:`Chebyshev ` - :ref:`two-temperature-plasma ` - :ref:`Blowers-Masel ` - - :ref:`surface-Blowers-Masel ` Reactions without a specified ``type`` on surfaces or edges are - automatically treated as :ref:`interface ` - reactions, and reactions that involve charge transfer between phases are - automatically treated as :ref:`electrochemical ` - reactions. Reactions on surfaces or edges specifying ``type`` as - ``Blowers-Masel`` are treated as - :ref:`surface-Blowers-Masel `. + automatically treated as :ref:`interface-Arrhenius ` + reactions, unless a ``sticking-coefficient`` implies a + :ref:`sticking-Arrhenius ` reaction. Interface + reactions that involve charge transfer between phases are automatically treated as + :ref:`electrochemical ` reactions. + Reactions on surfaces or edges specifying ``type`` as ``Blowers-Masel`` are treated + as :ref:`interface-Blowers-Masel ` or + :ref:`sticking-Blowers-Masel `. ``duplicate`` Boolean indicating whether the reaction is a known duplicate of another @@ -422,7 +423,7 @@ Example:: Interface reactions involving charge transfer between phases, as `described here `__. -Includes the fields of an :ref:`sec-yaml-interface-reaction` reaction, plus: +Includes the fields of an :ref:`sec-yaml-interface-Arrhenius` reaction, plus: ``beta`` The symmetry factor for the reaction. Default is 0.5. From 87ccdee90dbeac3f9986df1a65c90be3dd3692ee Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 18:26:09 -0500 Subject: [PATCH 5/6] [Sphinx] Make reaction rate documentation consistent --- doc/sphinx/yaml/reactions.rst | 185 ++++++++++++++++++++++------------ 1 file changed, 121 insertions(+), 64 deletions(-) diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index c26e594de4..3fbfa36455 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -22,12 +22,12 @@ The fields common to all ``reaction`` entries are: - :ref:`elementary ` - :ref:`three-body ` + - :ref:`Blowers-Masel ` + - :ref:`two-temperature-plasma ` - :ref:`falloff ` - :ref:`chemically-activated ` - :ref:`pressure-dependent-Arrhenius ` - :ref:`Chebyshev ` - - :ref:`two-temperature-plasma ` - - :ref:`Blowers-Masel ` Reactions without a specified ``type`` on surfaces or edges are automatically treated as :ref:`interface-Arrhenius ` @@ -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 +========================= -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:: +.. _sec-yaml-Arrhenius-rate: + +Arrhenius +--------- + +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 `__. +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^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] + + +.. _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 `__. +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 @@ -108,7 +170,7 @@ action kinetics, as Additional fields are: ``rate-constant`` - An :ref:`Arrhenius-type ` list or mapping. + An :ref:`Arrhenius-type ` list or mapping. ``negative-A`` A boolean indicating whether a negative value for the pre-exponential factor @@ -142,6 +204,39 @@ Example:: efficiencies: {AR: 0.83, H2O: 5} +.. _sec-yaml-Blowers-Masel: + +``Blowers-Masel`` +----------------- + +Includes the fields of an :ref:`elemntary ` reaction, except that +the ``rate-constant`` field is a +:ref:`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} + + +.. _sec-yaml-two-temperature-plasma: + +``two-temperature-plasma`` +-------------------------- + +Includes the fields of an :ref:`elementary ` reaction, except that +the ``rate-constant`` field is a +:ref:`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} + + .. _sec-yaml-falloff: ``falloff`` @@ -159,10 +254,10 @@ Includes field for specifying :ref:`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 @@ -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`` @@ -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:: @@ -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 `__. - -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 `__. - -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: @@ -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 `, -while using the :ref:`Blowers-Masel ` rate parameterization. +while using the :ref:`Blowers-Masel ` parameterization +for the rate constant. Example:: @@ -374,10 +426,11 @@ 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`` ------------------------ +---------------------- A sticking reaction occurring on a surface adjacent to a bulk phase, as `described here `__. @@ -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 ` expression for the sticking coefficient + An :ref:`Arrhenius-type ` expression for the sticking + coefficient ``Motz-Wise`` A boolean indicating whether to use the Motz-Wise correction factor for sticking @@ -400,13 +454,15 @@ 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 `, -while using the :ref:`Blowers-Masel ` rate parameterization. +while using the :ref:`Blowers-Masel ` parameterization +for the sticking coefficient. Example:: @@ -415,6 +471,7 @@ Example:: sticking-coefficient: {A: 1.0, b: 0, Ea0: 0, w: 100000} Motz-Wise: true + .. _sec-yaml-electrochemical-reaction: ``electrochemical`` From 02fb55db9bbee1d450efcf23a40363b3edc101c8 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 24 Apr 2022 19:58:29 -0500 Subject: [PATCH 6/6] [Sphinx] Add link to phases documentation --- doc/sphinx/yaml/phases.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/sphinx/yaml/phases.rst b/doc/sphinx/yaml/phases.rst index 4b7781a6a5..5759d4c62e 100644 --- a/doc/sphinx/yaml/phases.rst +++ b/doc/sphinx/yaml/phases.rst @@ -1,5 +1,7 @@ .. highlight:: yaml +.. _sec-yaml-phases: + ***************** Phase Definitions *****************