PorousFlow PreDis

Precipitation-dissolution of chemical species

This Kernel implements the residual $var element = document.getElementById("moose-equation-c97ead2f-2bf4-49dc-8595-7d71d4b334f8");katex.render(" \\phi_{\\mathrm{old}} S_{\\mathrm{aq}} \\sum_{m}\\nu_{m}\\rho_{m}I_{m} \\ .", element, {displayMode:true,throwOnError:false});$ In this equation, $var element = document.getElementById("moose-equation-1f6a0899-90a1-4a07-915e-93f1acba7f15");katex.render("\\phi", element, {displayMode:false,throwOnError:false});$ is the porosity (only the old value is used), $var element = document.getElementById("moose-equation-a1f77075-01ed-4cc9-aba2-ef3f9479de89");katex.render("S_{\\mathrm{aq}}", element, {displayMode:false,throwOnError:false});$ is the aqueous saturation, the sum over $var element = document.getElementById("moose-equation-dfaabfcc-a424-4930-940a-7542b30bc4f4");katex.render("m", element, {displayMode:false,throwOnError:false});$ is a sum over all the precipitated-or-dissolved (PreDis) mineral species, $var element = document.getElementById("moose-equation-ce463853-780c-4954-bf8a-e8d21f8d2ad8");katex.render("\\nu_{m}", element, {displayMode:false,throwOnError:false});$ are stoichiometric coefficients, $var element = document.getElementById("moose-equation-2e4ea787-4369-41fd-a005-b12a548eaddb");katex.render("\\rho_{m}", element, {displayMode:false,throwOnError:false});$ is the density of a solid lump of the mineral, and $var element = document.getElementById("moose-equation-f0e8c00f-9db8-4d37-b52b-f57b68ec9020");katex.render("I_{m}", element, {displayMode:false,throwOnError:false});$ is the mineral reaction rate (m $var element = document.getElementById("moose-equation-98c9c5d8-5317-4f01-95ff-221e35b0aaf3");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ (precipitate)/m $var element = document.getElementById("moose-equation-c5d95cbc-8a56-48b2-af81-c6e8e2ec576f");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ (solution).s $var element = document.getElementById("moose-equation-f89382e4-bf1e-4f5b-8bea-d876ebbdf875");katex.render("^{-1}", element, {displayMode:false,throwOnError:false});$ ) which is computed by PorousFlowAqueousPreDisChemistry.

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

warning

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 $var element = document.getElementById("moose-equation-22abced8-e9ea-4f7b-ada1-0acbb7b37e74");katex.render("a + b \\rightleftharpoons \\mathrm{mineral}", element, {displayMode:true,throwOnError:false});$ 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
  []
[]

Appropriate stoichiometric coefficients must be supplied to this Kernel. Consider the reaction system $var element = document.getElementById("moose-equation-b1f2aba5-b38a-4d91-9f6b-bca0c39538b6");katex.render("\\begin{array}{rcl} 1a + 2b - 3c & \\rightleftharpoons & \\mathrm{mineral0} \\\\ 4a -5b + 6c & \\rightleftharpoons & \\mathrm{mineral1} \\ . \\end{array}", element, {displayMode:true,throwOnError:false});$

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

note

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>
Unit:(no unit assumed)
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>
Unit:(no unit assumed)
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
Unit:(no unit assumed)
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>
Unit:(no unit assumed)
Controllable:No
Description:The displacements
matrix_onlyFalseWhether this object is only doing assembly to matrices (no vectors)
Default:False
C++ Type:bool
Controllable:No
Description:Whether this object is only doing assembly to matrices (no vectors)

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

Contribution To Tagged Field Data 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>
Unit:(no unit assumed)
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>
Unit:(no unit assumed)
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

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
Unit:(no unit assumed)
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.

Material Property Retrieval Parameters

(moose/modules/porous_flow/test/tests/chemistry/2species_predis.i)

# PorousFlow analogy of chemical_reactions/test/tests/solid_kinetics/2species_without_action.i
#
# Simple equilibrium reaction example to illustrate the use of PorousFlowAqueousPreDisChemistry
#
# In this example, two primary species a and b diffuse towards each other from
# opposite ends of a porous medium, reacting when they meet to form a mineral
# precipitate. The kinetic reaction is
#
# a + b = mineral
#
# where a and b are the primary species (reactants), and mineral is the precipitate.
# At the time of writing, the results of this test differ from chemical_reactions because
# in PorousFlow the mineral_concentration is measured in m^3 (precipitate) / m^3 (porous_material)
# in chemical_reactions the mineral_concentration is measured in m^3 (precipitate) / m^3 (fluid)
# ie, PorousFlow_mineral_concentration = porosity * chemical_reactions_mineral_concentration

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmax = 1
  ymax = 1
  nx = 40
[]

[Variables]
  [a]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0
  []
  [b]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0
  []
[]

[AuxVariables]
  [eqm_k]
    initial_condition = 1E-6
  []
  [pressure]
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
  gravity = '0 0 0'
[]

[Kernels]
  [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
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'a b'
    number_fluid_phases = 1
    number_fluid_components = 3
    number_aqueous_kinetic = 1
  []
[]

[FluidProperties]
  [simple_fluid]
    type = SimpleFluidProperties
    bulk_modulus = 2e9 # huge, so mimic chemical_reactions
    density0 = 1000
    thermal_expansion = 0
    viscosity = 1e-3
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 298.15
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = pressure
  []
  [massfrac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'a b'
  []
  [chem]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = 'a b'
    num_reactions = 1
    equilibrium_constants = eqm_k
    primary_activity_coefficients = '1 1'
    reactions = '1 1'
    specific_reactive_surface_area = '1.0'
    kinetic_rate_constant = '1.0e-8'
    activation_energy = '1.5e4'
    molar_volume = 1
    gas_constant = 8.314
    reference_temperature = 298.15
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.4
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    # porous_flow permeability / porous_flow viscosity = chemical_reactions conductivity = 4E-3
    permeability = '4E-6 0 0 0 4E-6 0 0 0 4E-6'
  []
  [relp]
    type = PorousFlowRelativePermeabilityConst
    phase = 0
  []
  [diff]
    type = PorousFlowDiffusivityConst
    # porous_flow diffusion_coeff * tortuousity * porosity = chemical_reactions diffusivity = 5E-4
    diffusion_coeff = '12.5E-4 12.5E-4 12.5E-4'
    tortuosity = 1.0
  []
[]

[BCs]
  [a_left]
    type = DirichletBC
    variable = a
    boundary = left
    value = 1.0e-2
  []
  [a_right]
    type = DirichletBC
    variable = a
    boundary = right
    value = 0
  []
  [b_left]
    type = DirichletBC
    variable = b
    boundary = left
    value = 0
  []
  [b_right]
    type = DirichletBC
    variable = b
    boundary = right
    value = 1.0e-2
  []
[]

[Preconditioning]
  [smp]
    type = SMP
    full = true
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 5
  end_time = 50
[]

[Outputs]
  print_linear_residuals = true
  exodus = true
  perf_graph = true
  hide = eqm_k
[]

Input Parameters

Theory

Usage

Development