PorousFlow PreDis

Precipitation-dissolution of chemical species

This Kernel implements the residual In this equation, is the porosity (only the old value is used), is the aqueous saturation, the sum over is a sum over all the precipitated-or-dissolved (PreDis) mineral species, are stoichiometric coefficients, is the density of a solid lump of the mineral, and is the mineral reaction rate (m(precipitate)/m(solution).s) which is computed by PorousFlowAqueousPreDisChemistry.

Details concerning precipitation-dissolution kinetic chemistry may be found in the chemical reactions module.

warningwarning

The numerical implementation of the chemical-reactions part of PorousFlow is quite simplistic, with very few guards against strange numerical behavior that might arise during the non-linear iterative process that MOOSE uses to find the solution. Therefore, care must be taken to define your chemical reactions so that the primary species concentrations remain small, but nonzero, and that mineralisation does not cause porosity to become negative or exceed unity.

This Kernel is usually added to a PorousFlowMassTimeDerivative Kernel to simulate precipitation-dissolution of a mineral from some primary chemical species. For instance in the case of just one precipitation-dissolution kinetic reaction and including diffusion and dispersion, the Kernels block looks like

  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [diff_a]
    type = PorousFlowDispersiveFlux
    variable = a
    fluid_component = 0
    disp_trans = 0
    disp_long = 0
  []
  [predis_a]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
  [mass_b]
    type = PorousFlowMassTimeDerivative
    fluid_component = 1
    variable = b
  []
  [diff_b]
    type = PorousFlowDispersiveFlux
    variable = b
    fluid_component = 1
    disp_trans = 0
    disp_long = 0
  []
  [predis_b]
    type = PorousFlowPreDis
    variable = b
    mineral_density = 1000
    stoichiometry = 1
  []
[]
(modules/porous_flow/test/tests/chemistry/2species_predis.i)

Appropriate stoichiometric coefficients must be supplied to this Kernel. Consider the reaction system

Then the stoichiometric coefficients for the PorousFlowPreDis Kernels would be:

- stoichiometry = '1 4' for Variable a - stoichiometry = '2 -5' for Variable b - stoichiometry = '-3 6' for Variable c

commentnote

This Kernel lumps the mineral masses to the nodes. It also only uses the old values of porosity, which is an approximation: see porosity for a discussion.

See mass lumping for details.

Input Parameters

  • PorousFlowDictatorThe UserObject that holds the list of PorousFlow variable names.

    C++ Type:UserObjectName

    Controllable:No

    Description:The UserObject that holds the list of PorousFlow variable names.

  • mineral_densityDensity (kg(precipitate)/m^3(precipitate)) of each secondary species in the aqueous precipitation-dissolution reaction system

    C++ Type:std::vector<double>

    Controllable:No

    Description:Density (kg(precipitate)/m^3(precipitate)) of each secondary species in the aqueous precipitation-dissolution reaction system

  • stoichiometryA vector of stoichiometric coefficients for the primary species that is the Variable of this Kernel: one for each precipitation-dissolution reaction (these are one columns of the 'reactions' matrix)

    C++ Type:std::vector<double>

    Controllable:No

    Description:A vector of stoichiometric coefficients for the primary species that is the Variable of this Kernel: one for each precipitation-dissolution reaction (these are one columns of the 'reactions' matrix)

  • variableThe name of the variable that this residual object operates on

    C++ Type:NonlinearVariableName

    Controllable:No

    Description:The name of the variable that this residual object operates on

Required Parameters

  • blockThe list of blocks (ids or names) that this object will be applied

    C++ Type:std::vector<SubdomainName>

    Controllable:No

    Description:The list of blocks (ids or names) that this object will be applied

  • displacementsThe displacements

    C++ Type:std::vector<VariableName>

    Controllable:No

    Description:The displacements

  • prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.

    C++ Type:MaterialPropertyName

    Controllable:No

    Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.

  • use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

Optional Parameters

  • absolute_value_vector_tagsThe tags for the vectors this residual object should fill with the absolute value of the residual contribution

    C++ Type:std::vector<TagName>

    Controllable:No

    Description:The tags for the vectors this residual object should fill with the absolute value of the residual contribution

  • extra_matrix_tagsThe extra tags for the matrices this Kernel should fill

    C++ Type:std::vector<TagName>

    Controllable:No

    Description:The extra tags for the matrices this Kernel should fill

  • extra_vector_tagsThe extra tags for the vectors this Kernel should fill

    C++ Type:std::vector<TagName>

    Controllable:No

    Description:The extra tags for the vectors this Kernel should fill

  • matrix_tagssystem timeThe tag for the matrices this Kernel should fill

    Default:system time

    C++ Type:MultiMooseEnum

    Options:nontime, system, time

    Controllable:No

    Description:The tag for the matrices this Kernel should fill

  • vector_tagstimeThe tag for the vectors this Kernel should fill

    Default:time

    C++ Type:MultiMooseEnum

    Options:nontime, time

    Controllable:No

    Description:The tag for the vectors this Kernel should fill

Tagging Parameters

  • control_tagsAdds user-defined labels for accessing object parameters via control logic.

    C++ Type:std::vector<std::string>

    Controllable:No

    Description:Adds user-defined labels for accessing object parameters via control logic.

  • diag_save_inThe name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)

    C++ Type:std::vector<AuxVariableName>

    Controllable:No

    Description:The name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)

  • enableTrueSet the enabled status of the MooseObject.

    Default:True

    C++ Type:bool

    Controllable:Yes

    Description:Set the enabled status of the MooseObject.

  • implicitTrueDetermines whether this object is calculated using an implicit or explicit form

    Default:True

    C++ Type:bool

    Controllable:No

    Description:Determines whether this object is calculated using an implicit or explicit form

  • save_inThe name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)

    C++ Type:std::vector<AuxVariableName>

    Controllable:No

    Description:The name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)

  • seed0The seed for the master random number generator

    Default:0

    C++ Type:unsigned int

    Controllable:No

    Description:The seed for the master random number generator

  • use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

Input Files