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[Doc] Fix minor issues in linear-Burke rate docs
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pjsingal authored and speth committed Oct 23, 2024
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Showing 1 changed file with 22 additions and 14 deletions.
36 changes: 22 additions & 14 deletions doc/sphinx/yaml/reactions.rst
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@ The fields common to all ``reaction`` entries are:
- ``chemically-activated`` (:ref:`details <sec-yaml-chemically-activated>`)
- ``pressure-dependent-Arrhenius`` (:ref:`details <sec-yaml-pressure-dependent-Arrhenius>`)
- ``Chebyshev`` (:ref:`details <sec-yaml-Chebyshev>`)
- ``linear-Burke`` (:ref:`details <sec-yaml-linear-Burke>`)


Reactions without a specified ``type`` on surfaces or edges are
automatically treated as :ref:`interface-Arrhenius <sec-yaml-interface-Arrhenius>`
Expand Down Expand Up @@ -412,7 +414,7 @@ choice must remain consistent throughout a single reaction (either all colliders
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 :ref:`Troe <sec-yaml-falloff>`, :ref:`pressure-dependent-arrhenius <sec-yaml-pressure-dependent-Arrhenius>`,
user's choice of :ref:`Troe <sec-yaml-falloff>`, :ref:`pressure-dependent-Arrhenius <sec-yaml-pressure-dependent-Arrhenius>`,
or :ref:`Chebyshev <sec-yaml-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
Expand All @@ -421,6 +423,9 @@ or Chebyshev parameterization if so desired. Mixing and matching of types within
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
:cite:t:`singal2024`.

Additional fields are:

``colliders``
Expand All @@ -436,30 +441,30 @@ Additional fields are:
``eig0``
The absolute value of the least negative chemically significant eigenvalue of
the master equation for the :math:`i^{th}` collider (when pure), evaluated at
the low-pressure limit, :math:`\Lambda_{0,i}(T)[M]`. This parameter is entered
in modified Arrhenius format to enable consideration of temperature dependence.
the low-pressure limit, :math:`\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 :math:`\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. 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.

A :ref:`Troe <sec-yaml-falloff>` implementation alse requires: ``high-P-rate-constant``,
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 other 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 :ref:`Troe <sec-yaml-falloff>` implementation also requires: ``high-P-rate-constant``,
``low-P-rate-constant``, ``Troe`` (do not use the Troe ``efficiencies`` key).

A :ref:`pressure-dependent-arrhenius<sec-yaml-pressure-dependent-Arrhenius>` implementation
A :ref:`pressure-dependent-Arrhenius <sec-yaml-pressure-dependent-Arrhenius>` implementation
also requires: ``rate-constants``.

A :ref:`Chebyshev <sec-yaml-Chebyshev>` implementation also requires: ``temperature-range``,
``pressure-range``, ``data``.

A mathematical description of this YAML implementation can be found in Eq. 8 of
:cite:t:`singal2024`.

Examples:

*`linear-Burke` rate with Troe format for the reference collider (N2)*:
Expand All @@ -468,6 +473,7 @@ Examples:
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}
Expand All @@ -478,10 +484,11 @@ Examples:

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

equation: H + O2 (+M) <=> HO2 (+M)
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}
Expand Down Expand Up @@ -510,6 +517,7 @@ Examples:
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:
Expand Down

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