sphinx/yaml/species.rst

.. highlight:: yaml

.. _sec-yaml-species:

*******
Species
*******

The fields of a ``species`` entry are:

``name``
    String identifier used for the species. Required.

``composition``
    Mapping that 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``
    A mapping or list of mappings. Each mapping contains an equation of state
    model specification for the species, any parameters for that model, and any
    parameters for interactions with other species. See
    :ref:`sec-yaml-species-eos`. If this field is absent and a model is
    required, 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 is 1.

``Debye-Huckel``
    Additional model parameters used in the Debye-Hückel model. See
    :ref:`sec-yaml-Debye-Huckel` for more information.


.. _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 giving the temperature intervals on which the 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, intermediate, 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. Note that this is different from the standard CHEMKIN
    formulation that uses two temperature regions listed in descending 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 giving the temperature intervals on which the 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 giving the temperature intervals on which the 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, intermediate, 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.

``T-min``
    The minimum temperature at which this thermo data should be used.
    Defaults to 0.0.

``T-max``
    The maximum temperature at which this thermo data should be used.
    Defaults to infinity.

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.

``T-min``
    The minimum temperature at which this thermo data should be used.
    Defaults to 0.0.

``T-max``
    The maximum temperature at which this thermo data should be used.
    Defaults to infinity.

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:`liquid-water-IAPWS95 <sec-yaml-eos-liquid-water-iapws95>`
    - :ref:`molar-volume-temperature-polynomial <sec-yaml-eos-molar-volume-temperature-polynomial>`
    - :ref:`Redlich-Kwong <sec-yaml-eos-redlich-kwong>`


.. _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-liquid-water-iapws95:

Liquid 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-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 values 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-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