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updated yaml description in reactions.rst
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pjsingal committed Oct 9, 2024
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Expand Up @@ -400,44 +400,32 @@ Example::
.. _sec-yaml-linear-Burke:

``linear-Burke``
-------------
----------------

A complex-forming reaction (one that depends on both P and X) parameterized
according to the reduced-pressure linear mixture rule as
:ref:`described here <sec-linear-Burke>`.



Additional fields are:

``colliders``
A list of dictionaries, where each entry contains parameters corresponding
to individual colliders (species in the bath gas).

``name``
The name of the collider species, which must be entered inside quotations (e.g.,
``"H2O"``). The first collider defined must be ``"M"``, which represents the generic
reference collider (often ``Ar`` or ``N2``) that represents all species lacking their
own explicit parameterization.

``eps`` or ``eig0``
The fractional contribution of each bath gas component (collider) to the reduced
pressure. ``eps`` represents the third-body efficiency of the collider relative
to that of the reference collider ``"M"`` (``eps: {A:1, b:0, Ea: 0}`` must be provided for
``"M"`` by necessity). ``eig0`` represents the absolute value of the least negative chemically
significant eigenvalue of the master equation, evaluated for a collider at its low-pressure
limit. All explicitly defined colliders must include either ``eps`` or ``eig0``, but the choice
must remain consistent throughout a single reaction (either all colliders are defined with ``eps``,
or all are defined with ``eig0``). In both cases, the parameters are entered in Arrhenius format to
enable representation of their temperature-dependence.

The pressure-dependent aspect of the 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>`, or
:ref:`Chebyshev <sec-yaml-Chebyshev>` representations. The same parameters used for a standalone
Troe, PLOG, or Chebyshev reaction are then inserted directly below ``eps`` or ``eig0`` for a given collider
(note: Troe cannot be given its own ``efficiencies`` key). At minimum, this treatment must be applied to ``"M"``.
However, additional colliders may also be given their own Troe, PLOG, or Chebyshev
parameterization if so desired. Mixing and matching of types within the same reaction is allowed (e.g., a PLOG
table for ``"M"``, Troe parameters for ``"H2"``, and Chebyshev data for ``"NH3"``).
The name of the collider species (e.g., ``H2O``). The first collider defined must be ``M``, which represents the generic reference collider (often ``Ar`` or ``N2``) that represents all species lacking their own explicit parameterization.

``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.

``eps``
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 must assign ``eps: {A:1, b:0, Ea: 0}`` for ``M``, as this is true 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.

``eps`` and ``eig0`` comprise the two acceptable ways to represent the contribution of each bath gas component (collider) to the reduced pressure. All explicitly defined colliders must include either ``eps`` or ``eig0``, but the choice must remain consistent throughout a single reaction (either all colliders are defined with ``eps``, or all are defined with ``eig0``).

The pressure-dependent aspect of the 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>`, or :ref:`Chebyshev <sec-yaml-Chebyshev>` representations. The same parameters used for a standalone Troe, PLOG, or Chebyshev reaction are then inserted directly below ``eps`` or ``eig0`` for a given collider (note: Troe cannot be given its own ``efficiencies`` key). At minimum, this treatment must be applied to ``M``. However, additional colliders may also be given their own Troe, PLOG, or Chebyshev parameterization if so desired. Mixing and matching of types within the 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`.
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