.. _InputsSpeciesDefs:

Species definitions
===================

The following inputs are defined using the ``species`` prefix.

+--------------------------+------------------------------------------------------------------------+----------+-----------+
|                          | Description                                                            |   Type   | Default   |
+==========================+========================================================================+==========+===========+
| solve                    | Specified name of the species or None to disable the                   | String   |  None     |
|                          | species solver. The name assigned to the species                       |          |           |
|                          | solver is used to specify species inputs.                              |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| diffusivity              | Fluid species diffusivity model.                                       | String   |  None     |
|                          |                                                                        |          |           |
|                          | * ``constant`` a constant diffusion coefficient is used for            |          |           |
|                          |   all fluid species.                                                   |          |           |
|                          |                                                                        |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| diffusivity.constant     | Constant species diffusivity -- required for                           |  Real    |  0        |
|                          | ``constant`` diffusivity model                                         |          |           |
|                          |                                                                        |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| specific_heat            | Species specific heat model. This setting only applies if either       | String   |  None     |
|                          | ``fluid.specific_heat = mixture`` or                                   |          |           |
|                          | ``solids.specific_heat = mixture``                                     |          |           |
|                          |                                                                        |          |           |
|                          | * ``constant`` a constant specific heat is defined for each species    |          |           |
|                          |   and a *mixture* specific heat is computed based on the fluid or      |          |           |
|                          |   particle composition.                                                |          |           |
|                          |                                                                        |          |           |
|                          | * ``NASA7-poly`` the specific heat of each species is defined by two   |          |           |
|                          |   polynomials that are a function of temperature, then a *mixture*     |          |           |
|                          |   specific heat is computed based on the fluid or particle             |          |           |
|                          |   composition. One polynomial defines the specific across the low      |          |           |
|                          |   temperature range while the second defines the specific heat across  |          |           |
|                          |   the high temperature range.                                          |          |           |
|                          |                                                                        |          |           |
|                          |   NASA7 polynomial format:                                             |          |           |
|                          |                                                                        |          |           |
|                          |      :math:`c_p(T) = \sum_{i=0}^5 a_iT^i`                              |          |           |
|                          |                                                                        |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| ignore_discontinuities   | MFIX-Exa asserts that the low and high NASA-7 polynomials are          | int      | 0         |
|                          | continuous at the 1000K temperature split. However, some polynomials   |          |           |
|                          | do not have valid high temperature coefficients, for example, liquid   |          |           |
|                          | water. By setting this keyword to 1, the simulation will only warn     |          |           |
|                          | that the polynomials are discontinuous. Simulations that use           |          |           |
|                          | discontinuous polynomials and cross between the 1000K temperature      |          |           |
|                          | split may fail when computing temperature from enthalpy.               |          |           |
|                          | Therefore, this option should only be used when the simulation is not  |          |           |
|                          | expected to cross over the transition temperature.                     |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+


The following inputs are for each species defined using the ``species.[species name]`` prefix.

+--------------------------+------------------------------------------------------------------------+----------+-----------+
|                          | Description                                                            |   Type   | Default   |
+==========================+========================================================================+==========+===========+
| molecular_weight         | Molecular weight of species. Required for mixture molecular weight     |  Real    |  0        |
|                          | model and when including chemical reactions.                           |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| specific_heat.constant   | Constant species specific heat. Required for all fluid (solids)        |  Real    |  0        |
|                          | species if the fluid (solids) ``specific_heat = mixture`` and the      |          |           |
|                          | specific heat model is ``constant``                                    |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| specific_heat.NASA7.a[i] | Species specific heat polynomial coefficients. Required for all fluid  |  Real    |  0.  0.   |
|                          | (solids) species if the fluid (solids) ``specific_heat = mixture``     |          |           |
|                          | and the specific heat model is ``NASA7-poly``                          |          |           |
|                          |                                                                        |          |           |
|                          | Each polynomial is defined by six coefficients (``a0`` .. ``a5``), and |          |           |
|                          | two values are required for each coefficient. The first value is the   |          |           |
|                          | low temperature polynomial coefficient (T < 1000K) and the second is   |          |           |
|                          | the coefficient for the high temperature polynomial (T > 1000K). A     |          |           |
|                          | total of twelve coefficients are required.                             |          |           |
|                          |                                                                        |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+
| enthalpy_of_formation    | Enthalpy of formation of species. This input is required only when     |  Real    |  0        |
|                          | the specific heat model is ``constant`` and chemical reactions         |          |           |
|                          | are defined.                                                           |          |           |
+--------------------------+------------------------------------------------------------------------+----------+-----------+



Example inputs
--------------

Fluid species as passive scalars
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In the following example, two species are defined and assigned to the fluid. We are required
to define the species diffusivity and initial and boundary conditions.  The
``IncompressibleFluid`` constraint is used, and the fluid density and species mass fractions
are defined in the initial and boundary conditions.
The fluid energy equation is not solved, and because we are not updating fluid density, the
local species concentrations do not affect the fluid.


.. code-block:: bash
   :caption: Snippet of inputs defining species as passive tracers. This is not a complete input file.

   mfix.constraint = IncompressibleFluid

   mfix.advect_density  = 0
   mfix.advect_enthalpy = 0
   mfix.solve_species   = 1


   # Species model settings
   # -----------------------------------------------------------------------
   species.solve  =  N2  O2

   species.diffusivity = constant
   species.diffusivity.constant  = 1.9e-5


   # Fluid model settings
   # -----------------------------------------------------------------------
   fluid.solve = fluid

   fluid.viscosity.molecular = constant
   fluid.viscosity.molecular.constant = 2.0e-5

   fluid.species =  N2  O2

   # Initial Conditions
   # -----------------------------------------------------------------------
   ic.regions = full-domain

   ic.full-domain.fluid.volfrac   =  1.0
   ic.full-domain.fluid.density   =  1.0

   ic.full-domain.fluid.velocity  =  0.0  0.0  0.0

   ic.full-domain.fluid.species.N2   =  0.77
   ic.full-domain.fluid.species.O2   =  0.23

   # Boundary Conditions
   # -----------------------------------------------------------------------
   bc.regions = inlet  outlet

   bc.inlet = mi
   bc.inlet.fluid.volfrac  =  1.0
   bc.inlet.fluid.density  =  1.0

   bc.inlet.fluid.velocity =  1.0e-8  0.0  0.0

   bc.inlet.fluid.species.N2   =  0.77
   bc.inlet.fluid.species.O2   =  0.23

   bc.outlet = po
   bc.outlet.fluid.pressure =  0.


Fluid as mixture
^^^^^^^^^^^^^^^^

In this example, the fluid is treated as a mixture of two species and the
``IdealGasOpenSystem`` constraint is used. Because we are solving the
energy equation, the fluid thermal conductivity is provided and the
specific heats for both species are needed. The species specific heat
model is set to ``NASA7-poly``; therefore 12 coefficients (6 low-temperature range
coefficients and 6 high-temperature range coefficients) are defined for each species.
Additionally, species molecular weights are provided to compute the mixture
molecular weights needed to evaluate the ideal-gas equation of state.

Fluid temperature is specified by the initial and boundary conditions, and unlike
the previous example, density is no longer provided. Instead, the ideal gas
equation of state is used to compute density from temperature, fluid composition,
and the thermodynamic pressure.  The thermodynamic pressure is taken as the
outflow boundary condition pressure which is set here to 1 atmosphere.

.. code-block:: bash
   :caption: Snippet of inputs defining fluid as a mixture with ``NASA7-poly`` specific heat model. This is not a complete input file.

   mfix.constraint = IdealGasOpenSystem

   mfix.advect_density  = 1
   mfix.solve_species   = 1
   mfix.advect_enthalpy = 1

   # Species model settings
   # -----------------------------------------------------------------------
   species.solve  =  N2  O2

   species.diffusivity = constant
   species.diffusivity.constant  = 1.9e-5

   species.O2.molecular_weight = 31.99880e-3
   species.N2.molecular_weight = 28.01340e-3

   species.specific_heat = NASA7-poly

   # Oxygen
   species.O2.molecular_weight = 31.99880e-3
   species.O2.specific_heat.NASA7.a0    =  3.78245636E+00    3.66096065E+00
   species.O2.specific_heat.NASA7.a1    = -2.99673416E-03    6.56365811E-04
   species.O2.specific_heat.NASA7.a2    =  9.84730201E-06   -1.41149627E-07
   species.O2.specific_heat.NASA7.a3    = -9.68129509E-09    2.05797935E-11
   species.O2.specific_heat.NASA7.a4    =  3.24372837E-12   -1.29913436E-15
   species.O2.specific_heat.NASA7.a5    = -1.06394356E+03   -1.21597718E+03

   # Nitrogen
   species.N2.molecular_weight = 28.01340e-3
   species.N2.specific_heat.NASA7.a0    =  3.53100528E+00    2.95257637E+00
   species.N2.specific_heat.NASA7.a1    = -1.23660988E-04    1.39690040E-03
   species.N2.specific_heat.NASA7.a2    = -5.02999433E-07   -4.92631603E-07
   species.N2.specific_heat.NASA7.a3    =  2.43530612E-09    7.86010195E-11
   species.N2.specific_heat.NASA7.a4    = -1.40881235E-12   -4.60755204E-15
   species.N2.specific_heat.NASA7.a5    = -1.04697628E+03   -9.23948688E+02


   # Fluid model settings
   # -----------------------------------------------------------------------
   fluid.solve = fluid

   fluid.viscosity.molecular = constant
   fluid.viscosity.molecular.constant = 2.0e-5

   fluid.thermal_conductivity = constant
   fluid.thermal_conductivity.constant = 0.026

   fluid.specific_heat = mixture

   fluid.species =  N2  O2

   # Initial Conditions
   # -----------------------------------------------------------------------
   ic.regions = full-domain

   ic.full-domain.fluid.volfrac   =  1.0

   ic.full-domain.fluid.velocity  =  0.0  0.0  0.0

   ic.full-domain.fluid.species.N2  =  0.77
   ic.full-domain.fluid.species.O2  =  0.23

   ic.full-domain.fluid.temperature = 300.0

   # Boundary Conditions
   # -----------------------------------------------------------------------
   bc.regions = inlet  outlet

   bc.inlet = mi
   bc.inlet.fluid.volfrac  =  1.0

   bc.inlet.fluid.velocity =  1.0e-8  0.0  0.0

   bc.inlet.fluid.species.N2   = 0.77
   bc.inlet.fluid.species.O2   = 0.23

   bc.inlet.fluid.temperature = 300.0

   bc.outlet = po
   bc.outlet.fluid.pressure =  101325.
