diff --git a/doc/sphinx/yaml/elements.rst b/doc/sphinx/yaml/elements.rst index 6fd6a35ea..5866b9141 100644 --- a/doc/sphinx/yaml/elements.rst +++ b/doc/sphinx/yaml/elements.rst @@ -6,7 +6,7 @@ Elements ******** -``element`` entries are needed only when defining custom elements which are not +``element`` entries are needed only when defining custom elements that are not standard chemical elements, or defining specific isotopes. The fields of an ``element`` entry are: diff --git a/doc/sphinx/yaml/general.rst b/doc/sphinx/yaml/general.rst index 68ce0ee33..d154c2086 100644 --- a/doc/sphinx/yaml/general.rst +++ b/doc/sphinx/yaml/general.rst @@ -7,10 +7,10 @@ General Structure Sections -------- -The top level of a Cantera `YAML `_ -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 +The top level of a Cantera `YAML `__ +input file is a mapping that defines different input file sections. Each +section consists of a list of mappings that 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 @@ -19,26 +19,26 @@ for :ref:`sec-yaml-reactions`, :ref:`sec-yaml-species`, and following structure:: phases: - - name: gas + - name: spam thermo: ideal-gas - additional: fields - - name: solid + # Additional fields come after this + - name: green-eggs thermo: model-name - additional: fields + # Additional fields come after this species: - name: A - additional: fields + # Additional fields come after this - name: B - additional: fields + # Additional fields come after this - name: C - additional: fields + # Additional fields come after this reactions: - equation: A + B <=> C + D - additional: fields + # Additional fields come after this - equation: A + C <=> 2 D - additional: fields + # Additional fields come after this Units ----- diff --git a/doc/sphinx/yaml/phases.rst b/doc/sphinx/yaml/phases.rst index e3f0cb6b2..0716ab3a5 100644 --- a/doc/sphinx/yaml/phases.rst +++ b/doc/sphinx/yaml/phases.rst @@ -4,7 +4,9 @@ Phase Definitions ***************** -The fields of a ``phase`` entry are: +A ``phase`` is a mapping that contains definitions for the elements, species, +and optionally reactions that can take place in that phase. The fields of a +``phase`` entry are: ``name`` String identifier used for the phase. Required. @@ -15,8 +17,8 @@ The fields of a ``phase`` entry are: - 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 + section of the file or taken from the standard elements. + - A list of single-key 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 @@ -26,13 +28,13 @@ The fields of a ``phase`` entry are: ``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. + - a list of species that 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 + section should be included. This is the default if no ``species`` entry + is present. + - A list of single-key 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. @@ -41,7 +43,7 @@ The fields of a ``phase`` entry are: ``skip-undeclared-elements`` option. ``skip-undeclared-elements`` - If set to ``true``, do not add species which contain elements that are not + If set to ``true``, do not add species that contain elements that are not explicitly included in the phase. The default is ``false``, where the presence of such species is considered an error. @@ -87,9 +89,9 @@ The fields of a ``phase`` entry are: are: - none - - `gas `_ - - `surface `_ - - `edge `_ + - `gas `__ + - `surface `__ + - `edge `__ ``reactions`` Source of reactions to include in the phase, if a kinetics model has been @@ -109,7 +111,7 @@ The fields of a ``phase`` entry are: 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 + - A list of single-key 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. @@ -118,14 +120,14 @@ The fields of a ``phase`` entry are: are: - none - - `high-pressure `_ - - `ionized-gas `_ - - `mixture-averaged `_ - - `mixture-averaged-CK `_ - - `multicomponent `_ - - `multicomponent-CK `_ - - `unity-Lewis-number `_ - - `water `_ + - `high-pressure `__ + - `ionized-gas `__ + - `mixture-averaged `__ + - `mixture-averaged-CK `__ + - `multicomponent `__ + - `multicomponent-CK `__ + - `unity-Lewis-number `__ + - `water `__ @@ -187,7 +189,7 @@ Phase thermodynamic models ----------------------------- A phase implementing tabulated standard state thermodynamics for one species in -a binary solution, as `described here `_. +a binary solution, as `described here `__. Includes the fields of :ref:`sec-yaml-ideal-molal-solution`, plus: @@ -216,7 +218,7 @@ Includes the fields of :ref:`sec-yaml-ideal-molal-solution`, plus: -------------------- A phase that is comprised of a fixed additive combination of other lattice -phases, as `described here `_. +phases, as `described here `__. Additional fields: @@ -235,7 +237,7 @@ Example:: -------------------- An incompressible phase with constant density, as -`described here `_. +`described here `__. Additional fields: @@ -254,7 +256,7 @@ Example:: ---------------- The Debye-Hückel model as -`described here `_. +`described here `__. Additional parameters for this model are contained in the ``activity-data`` field: @@ -277,7 +279,7 @@ field: The maximum ionic strength ``use-Helgeson-fixed-form`` - Boolean + Boolean, ``true`` or ``false`` ``default-ionic-radius`` Ionic radius to use for species where the ionic radius has not been @@ -288,8 +290,8 @@ field: ``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 + species pairs. Each mapping contains a ``species`` key that contains a + list of two species names, and a ``beta`` key that contains the corresponding value of :math:`\beta_{ij}`. Example:: @@ -315,7 +317,7 @@ Example:: -------- A one-dimensional edge between two surfaces, as -`described here `_. +`described here `__. Additional fields: @@ -334,7 +336,7 @@ Example:: ---------------------------- A phase defined by a fixed value of the chemical potential, as -`described here `_. +`described here `__. Additional fields: @@ -353,7 +355,7 @@ Example:: ----------------------- A phase with fixed composition, as -`described here `_. +`described here `__. .. _sec-yaml-HMW-electrolyte: @@ -361,9 +363,9 @@ A phase with fixed composition, as ``HMW-electrolyte`` ------------------- -A dilute or concentrated liquid electrolyte phase which obeys the Pitzer +A dilute or concentrated liquid electrolyte phase that obeys the Pitzer formulation for nonideality, as -`described here `_. +`described here `__. Additional parameters for this model are contained in the ``activity-data`` field: @@ -374,58 +376,77 @@ field: ``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. @@ -467,7 +488,7 @@ Example:: ------------- The ideal gas model as -`described here `_. +`described here `__. .. _sec-yaml-ideal-gas-VPSS: @@ -475,16 +496,17 @@ The ideal gas model as ------------------ The ideal gas model, using variable pressure standard state methods as -`described here `_. +`described here `__. + .. _sec-yaml-ideal-molal-solution: ``ideal-molal-solution`` ------------------------ -A phase based upon the mixing-rule assumption that all molality-based activity +A phase based on the mixing-rule assumption that all molality-based activity coefficients are equal to one, as -`described here `_. +`described here `__. Additional fields: @@ -500,16 +522,21 @@ Additional fields: ``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 @@ -533,7 +560,7 @@ Example:: ------------------- A condensed phase ideal solution as -`described here `_. +`described here `__. Additional fields: @@ -548,7 +575,7 @@ Additional fields: ----------------------- An ideal solution model using variable pressure standard state methods as -`described here `_. +`described here `__. Additional fields: @@ -556,6 +583,7 @@ Additional fields: 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`` @@ -565,7 +593,7 @@ 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 `_. +`described here `__. Additional fields: @@ -591,7 +619,7 @@ Example:: A simple thermodynamic model for a bulk phase, assuming a lattice of solid atoms, as -`described here `_. +`described here `__. Additional fields: @@ -605,7 +633,7 @@ Additional fields: ------------ A phase employing the Margules approximation for the excess Gibbs free energy, as -`described here `_. +`described here `__. Additional fields: @@ -614,20 +642,24 @@ Additional fields: ``species`` A list of two species names + ``excess-enthalpy`` - A list of two elements specifying the first and second excess enthalpy + A list of two values 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 + A list of two values 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 + A list of two values 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 + A list of two values specifying the first and second entropy coefficients for the excess volume interaction of the specified species. Defaults to [0, 0]. @@ -646,12 +678,13 @@ Example:: -------------------------- A condensed phase non-ideal solution with two species, as -`described here `_. +`described here `__. Additional fields: ``excess-enthalpy`` The molar excess enthalpy + ``product-species`` String specifying the "product" species @@ -668,20 +701,21 @@ Example:: ------------------ A phase representing an electron cloud, such as conduction electrons in a metal, -as `described here `_. +as `described here `__. 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 `_. +as `described here `__. Additional fields: @@ -696,6 +730,7 @@ Additional fields: - ``oxygen`` - ``water`` + .. _sec-yaml-Redlich-Kister: ``Redlich-Kister`` @@ -703,7 +738,7 @@ Additional fields: A phase employing the Redlich-Kister approximation for the excess Gibbs free energy, as -`described here `_. +`described here `__. Additional fields: @@ -712,9 +747,11 @@ Additional 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 @@ -736,28 +773,30 @@ Example:: ----------------- A multi-species Redlich-Kwong phase as -`described here `_. +`described here `__. 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 `_. +`described here `__. 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 `_. +`described here `__. diff --git a/doc/sphinx/yaml/reactions.rst b/doc/sphinx/yaml/reactions.rst index fb7513160..389ccedf0 100644 --- a/doc/sphinx/yaml/reactions.rst +++ b/doc/sphinx/yaml/reactions.rst @@ -6,12 +6,12 @@ Reactions ********* -The fields of a ``reaction`` entry are: +The fields common to all ``reaction`` entries 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. + 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 ``=>``. @@ -28,7 +28,7 @@ The fields of a ``reaction`` entry are: - :ref:`Chebyshev ` Reactions on surfaces or edges are automatically treated as - :ref:`interface ` reactions, and reactions which + :ref:`interface ` reactions, and reactions that involve charge transfer between phases are automatically treated as :ref:`electrochemical ` reactions, without the need to specify the ``type``. @@ -41,17 +41,20 @@ The fields of a ``reaction`` entry are: 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 `_ + `Reaction orders `__ for additional information. ``negative-orders`` - Boolean indicating whether negative reaction orders are allowed. The default - is ``false``. + 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``. +Depending on the reaction ``type``, other fields may be necessary to specify +the rate of the reaction. + .. _sec-arrhenius: Arrhenius expression @@ -93,12 +96,12 @@ Reaction types A homogeneous reaction with a pressure-independent rate coefficient and mass action kinetics, as -`described here `_. +`described here `__. Additional fields are: ``rate-constant`` - An :ref:`sec-arrhenius`. + An :ref:`Arrhenius-type ` list or mapping. ``negative-A`` A boolean indicating whether a negative value for the pre-exponential factor @@ -117,7 +120,7 @@ Example:: -------------- A three body reaction as -`described here `_. +`described here `__. The reaction equation should include the third body collision partner ``M``. @@ -138,14 +141,14 @@ Example:: ----------- A falloff reaction as -`described here `_. +`described here `__. 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 +latter case is equivalent to setting the efficiency for ``name`` to 1 and the efficiency for all other species to 0. -Includes fields for specifying :ref:`efficiencies ` as well +Includes field for specifying :ref:`efficiencies ` as well as: ``high-P-rate-constant`` @@ -156,13 +159,13 @@ as: ``Troe`` Parameters for the - `Troe `_ + `Troe `__ 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 `_ + `SRI `__ 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. @@ -182,7 +185,7 @@ Example:: ------------------------ A chemically activated reaction as -`described here `_. +`described here `__. The parameters are the same as for :ref:`sec-falloff` reactions. @@ -199,9 +202,9 @@ Example:: -------------------------------- A pressure-dependent reaction using multiple Arrhenius expressions as -`described here `_. +`described here `__. -The additional field is: +The only additional field in this reaction type is: ``rate-constants`` A list of mappings, where each mapping is the mapping form of an @@ -224,16 +227,16 @@ Example:: ------------- A reaction parameterized as a bivariate Chebyshev polynomial as -`described here `_. +`described here `__. Additional fields are: ``temperature-range`` - A list of two elements specifying the minimum and maximum temperatures at + A list of two values 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 + A list of two values specifying the minimum and maximum pressures at which the rate constant is valid ``data`` @@ -260,12 +263,12 @@ Example:: A reaction occuring on a surface between two bulk phases, or along an edge at the intersection of two surfaces, as -`described here `_. +`described here `__. Includes the fields of an :ref:`sec-elementary` reaction plus: ``sticking-coefficient`` - An :ref:`sec-arrhenius` expression for the sticking coefficient + An :ref:`Arrhenius-type ` expression for the sticking coefficient ``Motz-Wise`` A boolean applicable to sticking reactions, indicating whether to use the @@ -302,7 +305,7 @@ Example:: ------------------- Interface reactions involving charge transfer between phases, -as `described here `_. +as `described here `__. Includes the fields of an :ref:`sec-interface-reaction` reaction, plus: diff --git a/doc/sphinx/yaml/species.rst b/doc/sphinx/yaml/species.rst index 96285a297..097df7bcf 100644 --- a/doc/sphinx/yaml/species.rst +++ b/doc/sphinx/yaml/species.rst @@ -12,8 +12,8 @@ The fields of a ``species`` entry are: String identifier used for the species. Required. ``composition`` - Mapping which specifies the elemental composition of the species, - e.g. ``{C: 1, H: 4}``. Required. + 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 @@ -30,7 +30,7 @@ The fields of a ``species`` entry are: parameters. See :ref:`sec-yaml-species-transport`. ``sites`` - The number of sites occupied by a surface or edge species. Default 1. + The number of sites occupied by a surface or edge species. Default is 1. ``ionic-radius`` Size of the species. Used in the Debye-Hückel model. @@ -67,26 +67,27 @@ Fields of a species ``thermo`` entry used by all models are: 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 `_, +The polynomial form `described here `__, 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. + 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. + ascending order. Note that this is different from the standard CHEMKIN + formulation that uses two temperature regions listed in descending order. Example:: @@ -99,19 +100,20 @@ Example:: - [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 `_, +The polynomial form `described here `__, 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. + 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 @@ -140,16 +142,15 @@ Example:: Shomate polynomials ------------------- -The polynomial form `described here `_, +The polynomial form `described here `__, 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. + 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 @@ -173,15 +174,18 @@ Example:: Constant heat capacity ---------------------- -The constant heat capacity model `described here `_. +The constant heat capacity model `described here `__. 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. @@ -200,16 +204,18 @@ Piecewise Gibbs --------------- A model based on piecewise interpolation of the Gibbs free energy as -`described here `_ +`described here `__ 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 + 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 @@ -250,7 +256,7 @@ Constant volume --------------- A constant volume model as -`described here `_. +`described here `__. Any one of the following may be specified: @@ -276,7 +282,7 @@ Density temperature polynomial ------------------------------ A model in which the density varies with temperature as -`described here `_. +`described here `__. Additional fields: @@ -297,7 +303,7 @@ HKFT ---- The Helgeson-Kirkham-Flowers-Tanger model as -`described here `_. +`described here `__. Additional fields: @@ -308,7 +314,7 @@ Additional fields: Entropy of formation at the reference temperature and pressure ``a`` - 4-element vector containing the coefficients :math:`a_1, \ldots a_4` + 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` @@ -334,8 +340,8 @@ Ideal gas --------- A species using the ideal gas equation of state, as -`described here `_. This model is the default -if no `equation-of-state` section is included. +`described here `__. +This model is the default if no ``equation-of-state`` section is included. .. _sec-yaml-eos-ions-from-neutral: @@ -345,7 +351,7 @@ Ions from neutral molecule A species equation of state model used with the ``ions-from-neutral-molecule`` phase model, as -`described here `_. +`described here `__. Additional fields: @@ -369,7 +375,7 @@ Molar volume temperature polynomial ----------------------------------- A model in which the molar volume varies with temperature as -`described here `_. +`described here `__. Additional fields: @@ -383,12 +389,12 @@ Redlich-Kwong ------------- A model where species follow the Redlich-Kwong equation of state as -`described here `_. +`described here `__. Additional fields: ``a`` - Pure-species ``a`` coefficient. Scalar or list of two elements for a + Pure-species ``a`` coefficient. Scalar or list of two values for a temperature-dependent expression. ``b`` @@ -405,7 +411,7 @@ Water IAPWS95 ------------- A detailed equation of state for liquid water as -`described here `_. +`described here `__. .. _sec-yaml-species-transport: @@ -429,20 +435,28 @@ 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.