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[Doc] Make YAML section labels more distinctive #764

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[Doc] Make YAML section labels more distinctive #764

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2 changes: 1 addition & 1 deletion doc/sphinx/yaml/phases.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ The following synonyms are also implemented for use in any of the pairs:
- ``density``, ``D``


.. _sec-phase-thermo-models:
.. _sec-yaml-phase-thermo-models:

Phase thermodynamic models
==========================
Expand Down
56 changes: 28 additions & 28 deletions doc/sphinx/yaml/reactions.rst
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Expand Up @@ -20,17 +20,17 @@ The fields common to all ``reaction`` entries are:
A string specifying the type of reaction or rate coefficient
parameterization. The default is ``elementary``. Reaction types are:

- :ref:`elementary <sec-elementary>`
- :ref:`three-body <sec-three-body>`
- :ref:`falloff <sec-falloff>`
- :ref:`chemically-activated <sec-chemically-activated>`
- :ref:`pressure-dependent-Arrhenius <sec-pressure-dependent-Arrhenius>`
- :ref:`Chebyshev <sec-Chebyshev>`
- :ref:`elementary <sec-yaml-elementary>`
- :ref:`three-body <sec-yaml-three-body>`
- :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>`

Reactions on surfaces or edges are automatically treated as
:ref:`interface <sec-interface-reaction>` reactions, and reactions that
:ref:`interface <sec-yaml-interface-reaction>` reactions, and reactions that
involve charge transfer between phases are automatically treated as
:ref:`electrochemical <sec-electrochemical-reaction>` reactions, without the
:ref:`electrochemical <sec-yaml-electrochemical-reaction>` reactions, without the
need to specify the ``type``.

``duplicate``
Expand All @@ -55,7 +55,7 @@ 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-arrhenius:
.. _sec-yaml-arrhenius:

Arrhenius expression
====================
Expand All @@ -69,7 +69,7 @@ the activation energy :math:`E_a`, or a mapping containing the fields ``A``,
[-2.70000E+13 cm^3/mol/s, 0, 355 cal/mol]


.. _sec-efficiencies:
.. _sec-yaml-efficiencies:

Efficiencies
============
Expand All @@ -89,7 +89,7 @@ are supported:
Reaction types
==============

.. _sec-elementary:
.. _sec-yaml-elementary:

``elementary``
--------------
Expand All @@ -101,7 +101,7 @@ action kinetics, as
Additional fields are:

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

``negative-A``
A boolean indicating whether a negative value for the pre-exponential factor
Expand All @@ -114,7 +114,7 @@ Example::
negative-A: true


.. _sec-three-body:
.. _sec-yaml-three-body:

``three-body``
--------------
Expand All @@ -125,7 +125,7 @@ A three body reaction as
The reaction equation should include the third body collision partner ``M``.

Includes the fields of an ``elementary`` reaction, plus the fields for
specifying :ref:`efficiencies <sec-efficiencies>`.
specifying :ref:`efficiencies <sec-yaml-efficiencies>`.

Example::

Expand All @@ -135,7 +135,7 @@ Example::
efficiencies: {AR: 0.83, H2O: 5}


.. _sec-falloff:
.. _sec-yaml-falloff:

``falloff``
-----------
Expand All @@ -148,14 +148,14 @@ 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 :ref:`efficiencies <sec-efficiencies>` as well
Includes field for specifying :ref:`efficiencies <sec-yaml-efficiencies>` as well
as:

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

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

``Troe``
Parameters for the
Expand All @@ -179,15 +179,15 @@ Example::
Troe: {A: 0.562, T3: 91, T1: 5836}


.. _sec-chemically-activated:
.. _sec-yaml-chemically-activated:

``chemically-activated``
------------------------

A chemically activated reaction as
`described here <https://cantera.org/science/reactions.html#chemically-activated-reactions>`__.

The parameters are the same as for :ref:`sec-falloff` reactions.
The parameters are the same as for :ref:`sec-yaml-falloff` reactions.

Example::

Expand All @@ -196,7 +196,7 @@ Example::
high-P-rate-constant: [5.88E-14, 6.721, -3022.227]
low-P-rate-constant: [282320.078, 1.46878, -3270.56495]

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

``pressure-dependent-Arrhenius``
--------------------------------
Expand All @@ -208,7 +208,7 @@ 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-arrhenius` expression with the addition of a pressure ``P``.
:ref:`sec-yaml-arrhenius` expression with the addition of a pressure ``P``.

Example::

Expand All @@ -221,7 +221,7 @@ Example::
- {P: 1.01325 MPa, A: 1.680000e+16, b: -0.6, Ea: 14754.0}


.. _sec-Chebyshev:
.. _sec-yaml-Chebyshev:

``Chebyshev``
-------------
Expand Down Expand Up @@ -256,7 +256,7 @@ Example::
[-1.43220e-01, 7.71110e-02, 1.27080e-02, -6.41540e-04]]


.. _sec-interface-reaction:
.. _sec-yaml-interface-reaction:

``interface``
-------------
Expand All @@ -265,10 +265,10 @@ A reaction occuring on a surface between two bulk phases, or along an edge
at the intersection of two surfaces, as
`described here <https://cantera.org/science/reactions.html#surface-reactions>`__.

Includes the fields of an :ref:`sec-elementary` reaction plus:
Includes the fields of an :ref:`sec-yaml-elementary` reaction plus:

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

``Motz-Wise``
A boolean applicable to sticking reactions, indicating whether to use the
Expand Down Expand Up @@ -299,15 +299,15 @@ Example::
coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}


.. _sec-electrochemical-reaction:
.. _sec-yaml-electrochemical-reaction:

``electrochemical``
-------------------

Interface reactions involving charge transfer between phases,
as `described here <https://cantera.org/documentation/dev/doxygen/html/d6/ddd/classCantera_1_1ElectrochemicalReaction.html#details>`__.

Includes the fields of an :ref:`sec-interface-reaction` reaction, plus:
Includes the fields of an :ref:`sec-yaml-interface-reaction` reaction, plus:

``beta``
The symmetry factor for the reaction. Default is 0.5.
Expand Down