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[Doc] Add API documentation for the YAML input format

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.. toctree::
:maxdepth: 2
yaml/index
cti/classes
cython/index
matlab/index

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.. highlight:: yaml
.. _sec-yaml-elements:
********
Elements
********
``element`` entries are needed only when defining custom elements which are not
standard chemical elements, or defining specific isotopes.
The fields of an ``element`` entry are:
``symbol``
The symbol used for the element, as used when specifying the composition of
species.
``atomic-weight``
The atomic weight of the element, in unified atomic mass units (dalton).
``atomic-number``
The atomic number of the element. Optional.
``entropy298``
The standard molar entropy of the element at 298.15 K. Optional.

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.. highlight:: yaml
*****************
General Structure
*****************
Sections
--------
The top level of a Cantera `YAML <https://yaml.org/spec/1.2/spec.html#Introduction>`_
input file is a mapping which defines different input file sections. Each
section consists of a list of mappings which define objects of the same type,
e.g. reactions, species, phases, or elements. The ``phases`` section of an input
file contains all of the phase definitions. Multiple sections containing
reaction, species, or element definitions can be used. The specific names
``reactions``, ``species``, and ``elements`` are used as defaults when looking
for :ref:`sec-yaml-reactions`, :ref:`sec-yaml-species`, and
:ref:`sec-yaml-elements` to add to a phase. A simple input file has the
following structure::
phases:
- name: gas
thermo: ideal-gas
additional: fields
- name: solid
thermo: model-name
additional: fields
species:
- name: A
additional: fields
- name: B
additional: fields
- name: C
additional: fields
reactions:
- equation: A + B <=> C + D
additional: fields
- equation: A + C <=> 2 D
additional: fields
Units
-----
While Cantera generally works internally in SI units, input values can be
provided using a number of different units.
Compound units are written using the asterisk (``*``) to indicate
multiplication, the forward slash (``/``) to indicate division, and the caret
(``^``) to indicate exponentiation. Exponents can include negative and decimal
values. Standard one-letter metric prefixes can be applied to any unit.
Supported base units are:
- Mass: ``g``
- Length: ``m``, ``micron``, ``angstrom``, ``Å``
- Time: ``s``, ``min``, ``hr``
- Temperature: ``K``, ``C``
- Current: ``A``
- Quantity: ``mol`` (gram mole), ``gmol``, ``mole``, ``kmol``, ``kgmol``, ``molec``
Supported compound units are:
- Energy: ``J``, ``cal``, ``erg``, ``eV``
- Activation Energy: ``K``, or any unit of energy per quantity (``J/kmol``,
``cal/mol``, etc.)
- Force: ``N``, ``dyn``
- Pressure: ``Pa``, ``atm``, ``bar``, ``dyn/cm^2``
- Volume: ``m^3``, ``liter``, ``L``, ``l``, ``cc``
- Other electrical units: ``ohm``, ``V``, ``coulomb``
Units can be specified on individual input values by placing them after the
value, separated by a space::
{A: 1.45e9 cm^3/kmol, b: 0.4, Ea: 21033 kJ/kmol}
or by using a ``units`` mapping::
units: {mass: g, quantity: mol, pressure: atm, activation-energy: cal/mol}
A ``units`` mapping will set the default units for all values within the same
YAML list or mapping, including any nested lists and mappings. Units not
specified by a mapping use the values from higher level mappings, or the Cantera
defaults if no ``units`` mapping specifies applicable units. If a ``units``
mapping appears in a list, it must be the first item in that list.
Default units may be set for ``mass``, ``length``, ``time``, ``temperature``,
``current``, ``quantity``, ``pressure``, ``energy``, and ``activation-energy``.
The units ``pressure`` and ``energy`` are used when these units appear
explicitly in the units that a value is being converted to within Cantera. For
example, a conversion to ``N/m^2`` will use the default units for mass, length,
and time, while a conversion to ``Pa`` will use the default units for pressure.
Conversions of activation energies implicitly include scaling by the gas
constant where necessary. Setting default units for ``energy`` and ``quantity``
will determine the default units of ``activation-energy``, which can be
overridden by explicitly giving the desired units of ``activation-energy``.

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*************************
YAML Input File Reference
*************************
.. toctree::
:maxdepth: 2
general
phases
elements
species
reactions

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.. highlight:: yaml
*****************
Phase Definitions
*****************
The fields of a ``phase`` entry are:
``name``
String identifier used for the phase. Required.
``elements``
Specification for the elements present in the phase. This can be:
- Omitted, in which case the standard elements will be added as needed by
the species included in the phase.
- A list of element symbols, which can be either defined in the ``elements``
section of the file, or taken from the standard elements.
- A list of single-element mappings of section names to lists of element
symbols. These sections can be in the same file as the phase definition,
or from another file if written as ``file-path/sectionname``. If a
relative path is specified, the directory containing the current file is
searched first, followed by the Cantera data path. Standard elements can
be included by referencing the fictitious section ``default``.
``species``
Specification for the species present in the phase. This can be:
- a list of species which appear in the ``species`` section of the file.
- The string ``all``, to indicate that all species in the ``species``
section should be included. This is the default if no ``species`` entry is
present.
- A list of single-element mappings of section names to either the string
``all`` or a list of species names. These sections can be in the same file
as the phase definition, or from another file if written as
``file-path/sectionname``. If a relative path is specified, the directory
containing the current file is searched first, followed by the Cantera
data path.
Species may be skipped depending on the setting of the
``skip-undeclared-elements`` option.
``skip-undeclared-elements``
If set to ``true``, do not add species which contain elements that are not
explicitly included in the phase. The default is ``false``, where the
presence of such species is considered an error.
``state``
A mapping specifying the thermodynamic state. See
:ref:`sec-yaml-setting-state`.
``thermo``
String specifying the phase thermodynamic model to be used. Supported model
strings are:
- :ref:`compound-lattice <sec-yaml-compound-lattice>`
- :ref:`constant-density <sec-yaml-constant-density>`
- :ref:`Debye-Huckel <sec-yaml-Debye-Huckel>`
- :ref:`edge <sec-yaml-edge>`
- :ref:`fixed-chemical-potential <sec-yaml-fixed-chemical-potential>`
- :ref:`fixed-stoichiometry <sec-yaml-fixed-stoichiometry>`
- :ref:`HMW-electrolyte <sec-yaml-HMW-electrolyte>`
- :ref:`ideal-gas <sec-yaml-ideal-gas>`
- :ref:`ideal-gas-VPSS <sec-yaml-ideal-gas-VPSS>`
- :ref:`ideal-molal-solution <sec-yaml-ideal-molal-solution>`
- :ref:`ideal-condensed <sec-yaml-ideal-condensed>`
- :ref:`ideal-solution-VPSS <sec-yaml-ideal-solution-VPSS>`
- :ref:`ideal-surface <sec-yaml-ideal-surface>`
- :ref:`ions-from-neutral-molecule <sec-yaml-ions-from-neutral-molecule>`
- :ref:`lattice <sec-yaml-lattice>`
- :ref:`Margules <sec-yaml-Margules>`
- :ref:`Maskell-solid-solution <sec-yaml-Maskell-solid-solution>`
- :ref:`electron-cloud <sec-yaml-electron-cloud>`
- :ref:`pure-fluid <sec-yaml-pure-fluid>`
- :ref:`Redlich-Kister <sec-yaml-Redlich-Kister>`
- :ref:`Redlich-Kwong <sec-yaml-Redlich-Kwong>`
- :ref:`water-IAPWS95 <sec-yaml-water-IAPWS95>`
``kinetics``
String specifying the kinetics model to be used. Supported model strings
are:
- none
- `gas <https://cantera.org/documentation/dev/doxygen/html/de/dae/classCantera_1_1GasKinetics.html#details>`_
- `surface <https://cantera.org/documentation/dev/doxygen/html/d1/d72/classCantera_1_1InterfaceKinetics.html#details>`_
- `edge <https://cantera.org/documentation/dev/doxygen/html/d0/df0/classCantera_1_1EdgeKinetics.html#details>`_
``reactions``
Source of reactions to include in the phase, if a kinetics model has been
specified. This can be:
- The string ``all``, which indicates that all reactions from the
``reactions`` section of the file should be included. This is the default
if no ``reactions`` entry is present.
- The string ``declared-species``, which indicates that all reactions from
the ``reactions`` section involving only species present in the phase
should be included.
- The string ``none``, which indicates that no reactions should be added.
This can be used if reactions will be added programmatically after
the phase is constructed.
- A list of sections from which to include reactions. These sections can be
in the same file as the phase definition, or from another file if written
as ``file-path/sectionname``. If a relative path is specified, the
directory containing the current file is searched first, followed by the
Cantera data path.
- A list of single-item mappings of section names to rules for adding
reactions, where for each section name, that rule is either ``all`` or
``declared-species`` and is applied as described above.
``transport``
String specifying the transport model to be used. Supported model strings
are:
- none
- `high-pressure <https://cantera.org/documentation/dev/doxygen/html/d9/d63/classCantera_1_1HighPressureGasTransport.html#details>`_
- `ionized-gas <https://cantera.org/documentation/dev/doxygen/html/d4/d65/classCantera_1_1IonGasTransport.html#details>`_
- `mixture-averaged <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1MixTransport.html#details>`_
- `mixture-averaged-CK <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1MixTransport.html#details>`_
- `multicomponent <https://cantera.org/documentation/dev/doxygen/html/df/d7c/classCantera_1_1MultiTransport.html#details>`_
- `multicomponent-CK <https://cantera.org/documentation/dev/doxygen/html/df/d7c/classCantera_1_1MultiTransport.html#details>`_
- `unity-Lewis-number <https://cantera.org/documentation/dev/doxygen/html/d3/dd6/classCantera_1_1UnityLewisTransport.html#details>`_
- `water <https://cantera.org/documentation/dev/doxygen/html/df/d1f/classCantera_1_1WaterTransport.html#details>`_
.. _sec-yaml-setting-state:
Setting the state
=================
The state of a ``phase`` can be set using two properties to set the
thermodynamic state, plus the composition.
The composition can be set using one of the following fields, depending on the
phase type. The composition is specified as a mapping of species names to
values. Where necessary, the values will be automatically normalized.
- ``mass-fractions`` or ``Y``
- ``mole-fractions`` or ``X``
- ``coverages``
- ``molalities`` or ``M``
The thermodynamic state can be set using the following property pairs, with some
exceptions for phases where setting that property pair is not implemented. All
properties are on a per unit mass basis where relevant:
- ``T`` and ``P``
- ``T`` and ``D``
- ``T`` and ``V``
- ``H`` and ``P``
- ``U`` and ``V``
- ``S`` and ``V``
- ``S`` and ``P``
- ``S`` and ``T``
- ``P`` and ``V``
- ``U`` and ``P``
- ``V`` and ``H``
- ``T`` and ``H``
- ``S`` and ``H``
- ``D`` and ``P``
The following synonyms are also implemented for use in any of the pairs:
- ``temperature``, ``T``
- ``pressure``, ``P``
- ``enthalpy``, ``H``
- ``entropy``, ``S``
- ``int-energy``, ``internal-energy``, ``U``
- ``specific-volume``, ``V``
- ``density``, ``D``
.. _sec-phase-thermo-models:
Phase thermodynamic models
==========================
.. _sec-yaml-compound-lattice:
``compound-lattice``
--------------------
A phase that is comprised of a fixed additive combination of other lattice
phases, as `described here <https://cantera.org/documentation/dev/doxygen/html/de/de1/classCantera_1_1LatticeSolidPhase.html#details>`_.
Additional fields:
``composition``
A mapping of component phase names to their relative stoichiometries.
Example::
thermo: compound-lattice
composition: {Li7Si3(s): 1.0, Li7Si3-interstitial: 1.0}
.. _sec-yaml-constant-density:
``constant-density``
--------------------
An incompressible phase with constant density, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d9/de4/classCantera_1_1ConstDensityThermo.html#details>`_.
Additional fields:
``density``
The density of the phase
Example::
thermo: constant-density
density: 0.7 g/cm^3
.. _sec-yaml-Debye-Huckel:
``Debye-Huckel``
----------------
The Debye-Hückel model as
`described here <https://cantera.org/documentation/dev/doxygen/html/d8/d9a/classCantera_1_1DebyeHuckel.html#details>`_.
Additional parameters for this model are contained in the ``activity-data``
field:
``activity-data``
The activity data field contains the following fields:
``model``
One of ``dilute-limit``, ``B-dot-with-variable-a``,
``B-dot-with-common-a``, ``beta_ij``, or ``Pitzer-with-beta_ij``
``A_Debye``
The value of the Debye "A" parameter, or the string ``variable`` to use
a calculation based on the water equation of state.
``B_Debye``
The Debye "B" parameter
``max-ionic-strength``
The maximum ionic strength
``use-Helgeson-fixed-form``
Boolean
``default-ionic-radius``
Ionic radius to use for species where the ionic radius has not been
specified.
``B-dot``
The value of B-dot.
``beta``
List of mappings providing values of :math:`\beta_{ij}` for different
species pairs. Each mapping contains a ``species`` key which contains a
list of two species names, and a ``beta`` key which contains the
corresponding value of :math:`\beta_{ij}`.
Example::
thermo: Debye-Huckel
activity-data:
model: beta_ij
max-ionic-strength: 3.0
use-Helgeson-fixed-form: true
default-ionic-radius: 3.042843 angstrom
beta:
- species: [H+, Cl-]
beta: 0.27
- species: [Na+, Cl-]
beta: 0.15
- species: [Na+, OH-]
beta: 0.06
.. _sec-yaml-edge:
``edge``
--------
A one-dimensional edge between two surfaces, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d9/d17/classCantera_1_1EdgePhase.html#details>`_.
Additional fields:
``site-density``
The molar density of sites per unit length along the edge
Example::
thermo: edge
site-density: 5.0e-17 mol/cm
.. _sec-yaml-fixed-chemical-potential:
``fixed-chemical-potential``
----------------------------
A phase defined by a fixed value of the chemical potential, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d6/db0/classCantera_1_1FixedChemPotSSTP.html#details>`_.
Additional fields:
``chemical-potential``
The molar chemical potential of the phase
Example::
thermo: fixed-chemical-potential
chemical-potential: -2.3e7 J/kmol
.. _sec-yaml-fixed-stoichiometry:
``fixed-stoichiometry``
-----------------------
A phase with fixed composition, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d3/d50/classCantera_1_1StoichSubstance.html#details>`_.
.. _sec-yaml-HMW-electrolyte:
``HMW-electrolyte``
-------------------
A dilute or concentrated liquid electrolyte phase which obeys the Pitzer
formulation for nonideality, as
`described here <https://cantera.org/documentation/dev/doxygen/html/de/d1d/classCantera_1_1HMWSoln.html#details>`_.
Additional parameters for this model are contained in the ``activity-data``
field:
``activity-data``
The activity data field contains the following fields:
``temperature-model``
The form of the Pitzer temperature model. One of ``constant``,
``linear`` or ``complex``.
``A_Debye``
The value of the Debye "A" parameter, or the string ``variable`` to use
a calculation based on the water equation of state.
``max-ionic-strength``
The maximum ionic strength
``interactions``
A list of mappings, where each mapping describes a binary or ternary
interaction among species. Fields of this mapping include:
``species``
A list of one to three species names
``beta0``
The :math:`\beta^{(0)}` parameters for an cation/anion interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``beta1``
The :math:`\beta^{(1)}` parameters for an cation/anion interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``beta2``
The :math:`\beta^{(2)}` parameters for an cation/anion interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``Cphi``
The :math:`C^\phi` parameters for an cation/anion interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``alpha1``
The :math:`\alpha^{(1)}` parameter for an cation/anion interaction.
``alpha2``
The :math:`\alpha^{(2)}` parameter for an cation/anion interaction.
``theta``
The :math:`\theta` parameters for a like-charged binary interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``lambda``
The :math:`\lambda` parameters for binary interactions involving at
least one neutral species. 1, 2, or 5 values depending on the value
of ``temperature-model``.
``psi``
The :math:`\Psi` parameters for ternary interactions involving three
charged species. 1, 2, or 5 values depending on the value of
``temperature-model``.
``zeta``
The :math:`\zeta` parameters for ternary interactions involving one
neutral species. 1, 2, or 5 values depending on the value of
``temperature-model``.
``mu``
The :math:`\mu` parameters for a neutral species self-interaction.
1, 2, or 5 values depending on the value of ``temperature-model``.
``cropping-coefficients``
``ln_gamma_k_min``
Default -5.0.
``ln_gamma_k_max``
Default 15.0.
``ln_gamma_o_min``
Default -6.0.
``ln_gamma_o_max``
Default 3.0.
Example::
thermo: HMW-electrolyte
activity-data:
temperature-model: complex
A_Debye: 1.175930 kg^0.5/gmol^0.5
interactions:
- species: [Na+, Cl-]
beta0: [0.0765, 0.008946, -3.3158E-6, -777.03, -4.4706]
beta1: [0.2664, 6.1608E-5, 1.0715E-6, 0.0, 0.0]
beta2: [0.0, 0.0, 0.0, 0.0, 0.0]
Cphi: [0.00127, -4.655E-5, 0.0, 33.317, 0.09421]
alpha1: 2.0
- species: [H+, Cl-]
beta0: [0.1775]
beta1: [0.2945]
beta2: [0.0]
Cphi: [0.0008]
alpha1: 2.0
- species: [Na+, OH-]
beta0: 0.0864
beta1: 0.253
beta2: 0.0
Cphi: 0.0044
alpha1: 2.0
alpha2: 0.0
- {species: [Cl-, OH-], theta: -0.05}
- {species: [Na+, Cl-, OH-], psi: -0.006}
- {species: [Na+, H+], theta: 0.036}
- {species: [Cl-, Na+, H+], psi: [-0.004]}
.. _sec-yaml-ideal-gas:
``ideal-gas``
-------------
The ideal gas model as
`described here <https://cantera.org/documentation/dev/doxygen/html/d7/dfa/classCantera_1_1IdealGasPhase.html#details>`_.
.. _sec-yaml-ideal-gas-VPSS:
``ideal-gas-VPSS``
------------------
The ideal gas model, using variable pressure standard state methods as
`described here <https://cantera.org/documentation/dev/doxygen/html/dc/ddb/classCantera_1_1IdealSolnGasVPSS.html#details>`_.
.. _sec-yaml-ideal-molal-solution:
``ideal-molal-solution``
------------------------
A phase based upon the mixing-rule assumption that all molality-based activity
coefficients are equal to one, as
`described here <https://cantera.org/documentation/dev/doxygen/html/da/d5c/classCantera_1_1IdealMolalSoln.html#details>`_.
Additional fields:
``standard-concentration-basis``
A string specifying the basis for the standard concentration. One of
``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
``cutoff``
Parameters for cutoff treatments of activity coefficients
``model``
``poly`` or ``polyExp``
``gamma_o``
gamma_o value for the cutoff process at the zero solvent point
``gamma_k``
gamma_k minimum for the cutoff process at the zero solvent point
``X_o``
value of the solute mole fraction that centers the cutoff polynomials
for the cutoff = 1 process
``c_0``
Parameter in the polyExp cutoff treatment having to do with rate of
exponential decay
``slope_f``
Parameter in the ``polyExp`` cutoff treatment
``slope_g``
Parameter in the ``polyExp`` cutoff treatment
Example::
thermo: ideal-molal-solution
standard-concentration-basis: solvent-molar-volume
cutoff:
model: polyexp
gamma_o: 0.0001
gamma_k: 10.0
X_o: 0.2
c_0: 0.05
slope_f: 0.6
slope_g: 0.0
.. _sec-yaml-ideal-condensed:
``ideal-condensed``
-------------------
A condensed phase ideal solution as
`described here <https://cantera.org/documentation/dev/doxygen/html/d3/d4c/classCantera_1_1IdealSolidSolnPhase.html#details>`_.
Additional fields:
``standard-concentration-basis``
A string specifying the basis for the standard concentration. One of
``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
.. _sec-yaml-ideal-solution-VPSS:
``ideal-solution-VPSS``
-----------------------
An ideal solution model using variable pressure standard state methods as
`described here <https://cantera.org/documentation/dev/doxygen/html/dc/ddb/classCantera_1_1IdealSolnGasVPSS.html#details>`_.
Additional fields:
``standard-concentration-basis``
A string specifying the basis for the standard concentration. One of
``unity``, ``species-molar-volume``, or ``solvent-molar-volume``.
.. _sec-yaml-ions-from-neutral-molecule:
``ions-from-neutral-molecule``
------------------------------
A model that handles the specification of the chemical potentials for ionic
species, given a specification of the chemical potentials for the same phase
expressed in terms of combinations of the ionic species that represent neutral
molecules, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d7/d4a/classCantera_1_1IonsFromNeutralVPSSTP.html#details>`_.
Additional fields:
``neutral-phase``
The ``name`` of the phase definition for the phase containing the neutral
molecules.
Example::
- name: KCl-ions
thermo: ions-from-neutral-molecule
neutral-phase: KCl-neutral
species: [K+, Cl-]
- name: KCl-neutral
species: [KCl(l)]
thermo: Margules
.. _sec-yaml-lattice:
``lattice``
-----------
A simple thermodynamic model for a bulk phase, assuming a lattice of solid
atoms, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d1/da0/classCantera_1_1LatticePhase.html#details>`_.
Additional fields:
``site-density``
The molar density of lattice sites
.. _sec-yaml-Margules:
``Margules``
------------
A phase employing the Margules approximation for the excess Gibbs free energy, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d7/dfe/classCantera_1_1MargulesVPSSTP.html#details>`_.
Additional fields:
``interactions``
A list of mappings, where each mapping has the following fields:
``species``
A list of two species names
``excess-enthalpy``
A list of two elements specifying the first and second excess enthalpy
coefficients for the interaction of the specified species. Defaults to
[0, 0].
``excess-entropy``
A list of two elements specifying the first and second excess entropy
coefficients for the interaction of the specified species. Defaults to
[0, 0].
``excess-volume-enthalpy``
A list of two elements specifying the first and second enthalpy
coefficients for the excess volume interaction of the specified species.
Defaults to [0, 0].
``excess-volume-entropy``
A list of two elements specifying the first and second entropy
coefficients for the excess volume interaction of the specified species.
Defaults to [0, 0].
Example::
thermo: Margules
interactions:
- species: [KCl(l), LiCl(l)]
excess-enthalpy: [-17570, -377]
excess-entropy: [-7.627, 4.958]
.. _sec-yaml-Maskell-solid-solution:
``Maskell-solid-solution``
--------------------------
A condensed phase non-ideal solution with two species, as
`described here <https://cantera.org/documentation/dev/doxygen/html/dd/d3a/classCantera_1_1MaskellSolidSolnPhase.html#details>`_.
Additional fields:
``excess-enthalpy``
The molar excess enthalpy
``product-species``
String specifying the "product" species
Example::
thermo: Maskell-solid-solution
excess-enthalpy: 5 J/mol
product-species: H(s)
.. _sec-yaml-electron-cloud:
``electron-cloud``
------------------
A phase representing an electron cloud, such as conduction electrons in a metal,
as `described here <https://cantera.org/documentation/dev/doxygen/html/d9/d13/classCantera_1_1MetalPhase.html#details>`_.
Additional fields:
``density``
The density of the bulk metal
.. _sec-yaml-pure-fluid:
``pure-fluid``
--------------
A phase representing a pure fluid equation of state for one of several species,
as `described here <https://cantera.org/documentation/dev/doxygen/html/d1/d29/classCantera_1_1PureFluidPhase.html#details>`_.
Additional fields:
``pure-fluid-name``
Name of the pure fluid model to use:
- ``carbondioxide``
- ``heptane``
- ``hfc134a``
- ``hydrogen``
- ``methane``
- ``nitrogen``
- ``oxygen``
- ``water``
.. _sec-yaml-Redlich-Kister:
``Redlich-Kister``
------------------
A phase employing the Redlich-Kister approximation for the excess Gibbs free
energy, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d23/classCantera_1_1RedlichKisterVPSSTP.html#details>`_.
Additional fields:
``interactions``
A list of mappings, where each mapping has the following fields:
``species``
A list of two species names
``excess-enthalpy``
A list of polynomial coefficients for the excess enthalpy of the
specified binary interaction
``excess-entropy``
A list of polynomial coefficients for the excess entropy of the
specified binary interaction
Example::
thermo: Redlich-Kister
interactions:
- species: [Li(C6), V(C6)]
excess-enthalpy: [-3.268e+06, 3.955e+06, -4.573e+06, 6.147e+06, -3.339e+06,
1.117e+07, 2.997e+05, -4.866e+07, 1.362e+05, 1.373e+08,
-2.129e+07, -1.722e+08, 3.956e+07, 9.302e+07, -3.280e+07]
excess-entropy: [0.0]
.. _sec-yaml-Redlich-Kwong:
``Redlich-Kwong``
-----------------
A multi-species Redlich-Kwong phase as
`described here <https://cantera.org/documentation/dev/doxygen/html/d6/d29/classCantera_1_1RedlichKwongMFTP.html#details>`_.
The parameters for each species are contained in the corresponding species
entries.
.. _sec-yaml-ideal-surface:
``ideal-surface``
-----------------
An ideal surface phase, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d2/d95/classCantera_1_1SurfPhase.html#details>`_.
Additional fields:
``site-density``
The molar density of surface sites
.. _sec-yaml-water-IAPWS95:
``water-IAPWS95``
-----------------
An equation of state for liquid water, as
`described here <https://cantera.org/documentation/dev/doxygen/html/dc/d86/classCantera_1_1WaterSSTP.html#details>`_.

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.. highlight:: yaml
.. _sec-yaml-reactions:
*********
Reactions
*********
The fields of a ``reaction`` entry are:
``equation``
The stoichiometric equation for the reaction. Each term (i.e. stoichiometric
coefficient, species name, ``+`` or ``<=>``) in the equation must be
separated by a space.
Reversible reactions may be written using ``<=>`` or ``=`` to separate
reactants and products. Irreversible reacions are written using ``=>``.
``type``
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>`
Reactions on surfaces or edges are automatically treated as
:ref:`interface <sec-interface-reaction>` reactions, without the need to
specify the ``type``.
``duplicate``
Boolean indicating whether the reaction is a known duplicate of another
reaction. The default is ``false``.
``orders``
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 <https://cantera.org/science/reactions.html#reaction-orders>`_
for additional information.
``negative-orders``
Boolean indicating whether negative reaction orders are allowed. The default
is ``false``.
``nonreactant-orders``
Boolean indicating whether orders for non-reactant species are allowed.
The default is ``false``.
.. _sec-arrhenius:
Arrhenius expression
====================
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::
{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-efficiencies:
Efficiencies
============
Some reaction types include parameters for the "efficiency" of different species
as third-body colliders. For these reactions, the following additional fields
are supported:
``efficiencies``
A mapping of species names to efficiency values
``default-efficiency``
The efficiency for use for species not included in the ``efficiencies``
mapping. Defaults to 1.0.
Reaction types
==============
.. _sec-elementary:
``elementary``
--------------
A homogeneous reaction with a pressure-independent rate coefficient and mass
action kinetics, as
`described here <https://cantera.org/science/reactions.html#reactions-with-a-pressure-independent-rate>`_.
Additional fields are:
``rate-constant``
An :ref:`sec-arrhenius`.
``negative-A``
A boolean indicating whether a negative value for the pre-exponential factor
is allowed. The default is ``false``.
Example::
equation: N + NO <=> N2 + O
rate-constant: {A: -2.70000E+13 cm^3/mol/s, b: 0, Ea: 355 cal/mol}
negative-A: true
.. _sec-three-body:
``three-body``
--------------
A three body reaction as
`described here <https://cantera.org/science/reactions.html#three-body-reactions>`_.
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>`.
Example::
equation: 2 O + M = O2 + M
type: three-body
rate-constant: [1.20000E+17 cm^6/mol^2/s, -1, 0]
efficiencies: {AR: 0.83, H2O: 5}
.. _sec-falloff:
``falloff``
-----------
A falloff reaction as
`described here <https://cantera.org/science/reactions.html#falloff-reactions>`_.
The reaction equation should include the pressure-dependent third body collision
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
efficiency for all other species to 0.
Includes fields for specifying :ref:`efficiencies <sec-efficiencies>` as well
as:
``high-P-rate-constant``
An :ref:`sec-arrhenius` expression for the high-pressure limit
``low-P-rate-constant``
An :ref:`sec-arrhenius` expression for the low-pressure limit
``Troe``
Parameters for the
`Troe <https://cantera.org/science/reactions.html#the-troe-falloff-function>`_
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 <https://cantera.org/science/reactions.html#the-sri-falloff-function>`_
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.
Example::
equation: H + CH2 (+ N2) <=> CH3 (+N2)
type: falloff
high-P-rate-constant: [6.00000E+14 cm^3/mol/s, 0, 0]
low-P-rate-constant: {A: 1.04000E+26 cm^6/mol^2/s, b: -2.76, Ea: 1600}
Troe: {A: 0.562, T3: 91, T1: 5836}
.. _sec-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.
Example::
equation: CH3 + OH (+M) <=> CH2O + H2 (+M)
type: chemically-activated
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:
``pressure-dependent-Arrhenius``
--------------------------------
A pressure-dependent reaction using multiple Arrhenius expressions as
`described here <https://cantera.org/science/reactions.html#pressure-dependent-arrhenius-rate-expressions-p-log>`_.
The additional field 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``.
Example::
equation: H + CH4 <=> H2 + CH3
type: pressure-dependent-Arrhenius
rate-constants:
- {P: 0.039474 atm, A: 2.720000e+09 cm^3/mol/s, b: 1.2, Ea: 6834.0}
- {P: 1.0 atm, A: 1.260000e+20, b: -1.83, Ea: 15003.0}
- {P: 1.0 atm, A: 1.230000e+04, b: 2.68, Ea: 6335.0}
- {P: 1.01325 MPa, A: 1.680000e+16, b: -0.6, Ea: 14754.0}
.. _sec-Chebyshev:
``Chebyshev``
-------------
A reaction parameterized as a bivariate Chebyshev polynomial as
`described here <https://cantera.org/science/reactions.html#chebyshev-reaction-rate-expressions>`_.
Additional fields are:
``temperature-range``
A list of two elements specifying the minimum and maximum temperatures at
which the rate constant is valid
``pressure-range``
A list of two elements specifying the minimum and maximum pressures at
which the rate constant is valid
``data``
A list of lists containing the Chebyshev coefficients
Example::
equation: CH4 <=> CH3 + H
type: Chebyshev
temperature-range: [290, 3000]
pressure-range: [0.0098692326671601278 atm, 98.692326671601279 atm]
data: [[-1.44280e+01, 2.59970e-01, -2.24320e-02, -2.78700e-03],
[ 2.20630e+01, 4.88090e-01, -3.96430e-02, -5.48110e-03],
[-2.32940e-01, 4.01900e-01, -2.60730e-02, -5.04860e-03],
[-2.93660e-01, 2.85680e-01, -9.33730e-03, -4.01020e-03],
[-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-interface-reaction:
``interface``
-------------
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:
``sticking-coefficient``
An :ref:`sec-arrhenius` 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 a mapping with the fields:
``a``
Coefficient for exponential dependence on the coverage
``m``
Power-law exponent of coverage dependence
``E``
Activation energy dependence on coverage
Example::
equation: 2 H(s) => H2 + 2 Pt(s)
rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea: 67400 J/mol}
coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}

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.. highlight:: yaml
.. _sec-yaml-species:
*******
Species
*******
The fields of a ``species`` entry are:
``name``
String identifier used for the species. Required.
``composition``
Mapping which specifies the elemental composition of the species,
e.g. ``{C: 1, H: 4}``. Required.
``thermo``
Mapping containing the reference state thermodynamic model specification
and parameters. See :ref:`sec-yaml-species-thermo`.
``equation-of-state``
Mapping containing the equation of state model specification for the
species, any parameters for that model, and any parameters for interactions
with other species. :ref:`sec-yaml-species-eos`. If this field is absent,
the ``ideal-gas`` model is assumed.
``transport``
Mapping containing the species transport model specification and
parameters. See :ref:`sec-yaml-species-transport`.
``sites``
The number of sites occupied by a surface or edge species. Default 1.
``ionic-radius``
Size of the species. Used in the Debye-Hückel model.
``electrolyte-species-type``
One of ``solvent``, ``charged-species``, ``weak-acid-associated``,
``strong-acid-associated``, ``polar-neutral``, or ``nonpolar-neutral``.
The types ``solvent``, ``charged-species``, and ``nonpolar-neutral`` can be
inferred automatically. Used in the Debye-Hückel model.
``weak-acid-charge``
Charge to use for species can break apart into charged species. Used in the
Debye-Hückel model.
.. _sec-yaml-species-thermo:
Species thermo models
=====================
Fields of a species ``thermo`` entry used by all models are:
``model``
String specifying the model to be used. Required. Supported model strings
are:
- :ref:`NASA7 <sec-yaml-nasa7>`
- :ref:`NASA9 <sec-yaml-nasa9>`
- :ref:`Shomate <sec-yaml-shomate>`
- :ref:`constant-cp <sec-yaml-constcp>`
- :ref:`piecewise-Gibbs <sec-yaml-piecewise-gibbs>`
``reference-pressure``
The reference pressure at which the given thermodynamic properties apply.
Defaults to 1 atm.
.. _sec-yaml-nasa7:
NASA 7-coefficient polynomials
------------------------------
The polynomial form `described here <https://cantera.org/science/science-species.html#the-nasa-7-coefficient-polynomial-parameterization>`_,
given for one or two temperature regions. Additional fields of a ``NASA7``
thermo entry are:
``temperature-ranges``
A list of giving the temperature intervals on which the given polynomials
are valid. For one temperature region, this list contains the minimum and
maximum temperatures for the polynomial. For two temperature regions, this
list contains the minimum temperature, intermediate temperature, and maximum
temperatures.
``data``
A list with one item per temperature region, where that item is a 7 item
list of polynomial coefficients. The temperature regions are arranged in
ascending order.
Example::
thermo:
model: NASA7
temperature-ranges: [300.0, 1000.0, 5000.0]
data:
- [3.298677, 0.0014082404, -3.963222e-06, 5.641515e-09,
-2.444854e-12, -1020.8999, 3.950372]
- [2.92664, 0.0014879768, -5.68476e-07, 1.0097038e-10,
-6.753351e-15, -922.7977, 5.980528]
.. _sec-yaml-nasa9:
NASA 9-coefficient polynomials
------------------------------
The polynomial form `described here <https://cantera.org/science/science-species.html#the-nasa-9-coefficient-polynomial-parameterization>`_,
given for any number of temperature regions. Additional fields of a ``NASA9``
thermo entry are:
``temperature-ranges``
A list of giving the temperature intervals on which the given polynomials
are valid. This list contains the minimum temperature, the intermediate
temperatures between each set pair of regions, and the maximum temperature.
``data``
A list with one item per temperature region, where that item is a 9 item
list of polynomial coefficients. The temperature regions are arranged in
ascending order.
Example::
thermo:
model: NASA9
temperature-ranges: [200.00, 1000.00, 6000.0, 20000]
reference-pressure: 1 bar
data:
- [2.210371497E+04, -3.818461820E+02, 6.082738360E+00, -8.530914410E-03,
1.384646189E-05, -9.625793620E-09, 2.519705809E-12, 7.108460860E+02,
-1.076003744E+01]
- [5.877124060E+05, -2.239249073E+03, 6.066949220E+00, -6.139685500E-04,
1.491806679E-07, -1.923105485E-11, 1.061954386E-15, 1.283210415E+04,
-1.586640027E+01]
- [8.310139160E+08, -6.420733540E+05, 2.020264635E+02, -3.065092046E-02,
2.486903333E-06, -9.705954110E-11, 1.437538881E-15, 4.938707040E+06,
-1.672099740E+03]
.. _sec-yaml-shomate:
Shomate polynomials
-------------------
The polynomial form `described here <https://cantera.org/science/science-species.html#the-shomate-parameterization>`_,
given for one or two temperature regions. Additional fields of a ``Shomate``
thermo entry are:
``temperature-ranges``
A list of giving the temperature intervals on which the given polynomials
are valid. For one temperature region, this list contains the minimum and
maximum temperatures for the polynomial. For two temperature regions, this
list contains the minimum temperature, intermediate temperature, and maximum
temperatures.
``data``
A list with one item per temperature region, where that item is a 7 item
list of polynomial coefficients. The temperature regions are arranged in
ascending order.
Example::
thermo:
model: Shomate
temperature-ranges: [298, 1300, 6000]
data:
- [25.56759, 6.096130, 4.054656, -2.671301, 0.131021,
-118.0089, 227.3665]
- [35.15070, 1.300095, -0.205921, 0.013550, -3.282780,
-127.8375, 231.7120]
.. _sec-yaml-constcp:
Constant heat capacity
----------------------
The constant heat capacity model `described here <https://cantera.org/science/science-species.html#constant-heat-capacity>`_.
Additional fields of a ``constant-cp`` thermo entry are:
``T0``
The reference temperature. Defaults to 298.15 K.
``h0``
The molar enthalpy at the reference temperature. Defaults to 0.0.
``s0``
The molar entropy at the reference temperature. Defaults to 0.0.
``cp0``
The heat capacity at constant pressure. Defaults to 0.0.
Example::
thermo:
model: constant-cp
T0: 1000 K
h0: 9.22 kcal/mol
s0: -3.02 cal/mol/K
cp0: 5.95 cal/mol/K
.. _sec-yaml-piecewise-gibbs:
Piecewise Gibbs
---------------
A model based on piecewise interpolation of the Gibbs free energy as
`described here <https://cantera.org/documentation/dev/doxygen/html/d4/d9e/classCantera_1_1Mu0Poly.html#details>`_
Additional fields of a ``piecewise-Gibbs`` entry are:
``h0``
The molar enthalpy at the reference temperature of 298.15 K. Defaults to
0.0.
``dimensionless``
A boolean flag indicating whether the values of the Gibbs free energy are
given in a dimensionless form, i.e. divided by :math:`RT`. Defaults to
``false``.
``data``
A mapping of temperatures to values of the Gibbs free energy. The Gibbs free
energy can be either in molar units (if ``dimensionless`` is ``false``) or
nondimensionalized by the corresponding temperature (if ``dimensionless`` is
``true``). A value must be provided at :math:`T^\circ = 298.15` K.
Example::
thermo:
model: piecewise-Gibbs
h0: -230.015 kJ/mol
dimensionless: true
data: {298.15: -91.50963, 333.15: -85.0}
.. _sec-yaml-species-eos:
Species equation of state models
================================
``model``
String specifying the model to be used. Required. Supported model strings
are:
- :ref:`constant-volume <sec-yaml-eos-constant-volume>`
- :ref:`density-temperature-polynomial <sec-yaml-eos-density-temperature-polynomial>`
- :ref:`HKFT <sec-yaml-eos-hkft>`
- :ref:`ideal-gas <sec-yaml-eos-ideal-gas>`
- :ref:`ions-from-neutral-molecule <sec-yaml-eos-ions-from-neutral>`
- :ref:`molar-volume-temperature-polynomial <sec-yaml-eos-molar-volume-temperature-polynomial>`
- :ref:`Redlich-Kwong <sec-yaml-eos-redlich-kwong>`
- :ref:`water-IAPWS95 <sec-yaml-eos-water-iapws95>`
.. _sec-yaml-eos-constant-volume:
Constant volume
---------------
A constant volume model as
`described here <https://cantera.org/documentation/dev/doxygen/html/da/d33/classCantera_1_1PDSS__ConstVol.html#details>`_.
Any one of the following may be specified:
``molar-volume``
The molar volume of the species.
``molar-density``
The molar density of the species.
``density``
The mass density of the species.
Example::
equation-of-state:
model: constant-volume
molar-volume: 1.3 cm^3/mol
.. _sec-yaml-eos-density-temperature-polynomial:
Density temperature polynomial
------------------------------
A model in which the density varies with temperature as
`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d2f/classCantera_1_1PDSS__SSVol.html#details>`_.
Additional fields:
``data``
Vector of 4 coefficients for a cubic polynomial in temperature
Example::
equation-of-state:
model: density-temperature-polynomial
units: {mass: g, length: cm}
data: [0.536504, -1.04279e-4, 3.84825e-9, -5.2853e-12]
.. _sec-yaml-eos-hkft:
HKFT
----
The Helgeson-Kirkham-Flowers-Tanger model as
`described here <https://cantera.org/documentation/dev/doxygen/html/d9/d18/classCantera_1_1PDSS__HKFT.html#details>`_.
Additional fields:
``h0``
Enthalpy of formation at the reference temperature and pressure
``s0``
Entropy of formation at the reference temperature and pressure
``a``
4-element vector containing the coefficients :math:`a_1, \ldots a_4`
``c``
2-element vector containing the coefficients :math:`c_1` and :math:`c_2`
``omega``
The :math:`\omega` parameter at the reference temperature and pressure
Example::
equation-of-state:
model: HKFT
h0: -57433. cal/gmol
s0: 13.96 cal/gmol/K
a: [0.1839 cal/gmol/bar, -228.5 cal/gmol,
3.256 cal*K/gmol/bar, -27260. cal*K/gmol]
c: [18.18 cal/gmol/K, -29810. cal*K/gmol]
omega: 33060 cal/gmol
.. _sec-yaml-eos-ideal-gas:
Ideal gas
---------
A species using the ideal gas equation of state, as
`described here <https://cantera.org/documentation/dev/doxygen/html/df/d31/classCantera_1_1PDSS__IdealGas.html#details>`_. This model is the default
if no `equation-of-state` section is included.
.. _sec-yaml-eos-ions-from-neutral:
Ions from neutral molecule
--------------------------
A species equation of state model used with the ``ions-from-neutral-molecule``
phase model, as
`described here <https://cantera.org/documentation/dev/doxygen/html/d5/df4/classCantera_1_1PDSS__IonsFromNeutral.html#details>`_.
Additional fields:
``special-species``
Boolean indicating whether the species is the "special species" in the
phase. Default is ``false``.
``multipliers``
A dictionary mapping species to neutral species multiplier values.
Example::
equation-of-state:
model: ions-from-neutral-molecule
multipliers: {KCl(l): 1.2}
.. _sec-yaml-eos-molar-volume-temperature-polynomial:
Molar volume temperature polynomial
-----------------------------------
A model in which the molar volume varies with temperature as
`described here <https://cantera.org/documentation/dev/doxygen/html/d0/d2f/classCantera_1_1PDSS__SSVol.html#details>`_.
Additional fields:
``data``
Vector of 4 coefficients for a cubic polynomial in temperature
.. _sec-yaml-eos-redlich-kwong:
Redlich-Kwong
-------------
A model where species follow the Redlich-Kwong equation of state as
`described here <https://cantera.org/documentation/dev/doxygen/html/d6/d29/classCantera_1_1RedlichKwongMFTP.html#details>`_.
Additional fields:
``a``
Pure-species ``a`` coefficient. Scalar or list of two elements for a
temperature-dependent expression.
``b``
Pure-species ``b`` coefficient.
``binary-a``
Mapping where the keys are species and the values are the ``a``
coefficients for binary interactions between the two species.
.. _sec-yaml-eos-water-iapws95:
Water IAPWS95
-------------
A detailed equation of state for liquid water as
`described here <https://cantera.org/documentation/dev/doxygen/html/de/d64/classCantera_1_1PDSS__Water.html#details>`_.
.. _sec-yaml-species-transport:
Species transport models
========================
``model``
String specifying the model type. The only model that is specifically
handled is ``gas``.
Gas transport
-------------
Species transport properties are a rare exception to Cantera's use of SI units,
and use the units in which these properties are customarily reported. No
conversions are supported.
The additional fields of a ``gas`` transport entry are:
``geometry``
A string specifying the geometry of the molecule. One of ``atom``,
``linear``, or ``nonlinear``.
``diameter``
The Lennard-Jones collision diameter [Å]
``well-depth``
The Lennard-Jones well depth [K]
``dipole``
The permanent dipole moment [Debye]. Default 0.0.
``polarizability``
The dipole polarizability [Å^3]. Default 0.0.
``rotational-relaxation``
The rotational relaxation collision number at 298 K [-]. Default 0.0.
``acentric-factor``
Pitzer's acentric factor [-]. Default 0.0.
``dispersion-coefficient``
The dispersion coefficient, normalized by :math:`e^2` [Å^5]. Default 0.0.
``quadrupole-polarizability``
The quadrupole polarizability [Å^5]. Default 0.0.
Example::
transport:
model: gas
geometry: linear
well-depth: 107.4
diameter: 3.458
polarizability: 1.6
rotational-relaxation: 3.8