CoupledBEEquilibriumSub

Derivative of equilibrium species concentration wrt time

Derivative of concentration of $var element = document.getElementById("moose-equation-fe347e72-f0aa-4c90-a7d4-4671341827e7");katex.render("j^{\\mathrm{th}}", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ primary species present in the secondary equilibrium species wrt time. Implements the weak form of $var element = document.getElementById("moose-equation-9209428e-ecfb-4ec7-b391-31d18d54b47e");katex.render("\\frac{\\partial}{\\partial t} \\left(\\phi \\sum_i \\nu_{ji} C_i\\right),", element, {displayMode:true,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ where $var element = document.getElementById("moose-equation-79a0ce2a-f89e-4658-9090-e0d6b7f5c7f9");katex.render("\\phi", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ is porosity, $var element = document.getElementById("moose-equation-5288c553-ddf2-4cba-9d3d-e310773c7342");katex.render("\\nu_{ji}", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ are the stoichiometric coefficients, and $var element = document.getElementById("moose-equation-6b80a078-6a75-4723-969d-d07168473e47");katex.render("C_i", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ is the concentration of the $var element = document.getElementById("moose-equation-2a23ad1c-94d6-4b8f-a5da-17d5f7fb3ae2");katex.render("i^{\\mathrm{th}}", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ secondary equilibrium species.

Input Parameters

variableThe name of the variable that this Kernel operates on
C++ Type:NonlinearVariableName
Options:
Description:The name of the variable that this Kernel operates on

Required Parameters

blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector
Options:
Description:The list of block ids (SubdomainID) that this object will be applied
displacementsThe displacements
C++ Type:std::vector
Options:
Description:The displacements
gamma_eq1.0Activity coefficient of this equilibrium species
Default:1.0
C++ Type:std::vector
Options:
Description:Activity coefficient of this equilibrium species
gamma_u1.0Activity coefficient of primary species that this kernel operates on
Default:1.0
C++ Type:std::vector
Options:
Description:Activity coefficient of primary species that this kernel operates on
gamma_v1.0Activity coefficients of coupled primary species
Default:1.0
C++ Type:std::vector
Options:
Description:Activity coefficients of coupled primary species
log_kThe equilibrium constant of this equilibrium species
C++ Type:std::vector
Options:
Description:The equilibrium constant of this equilibrium species
lumpingFalseTrue for mass matrix lumping, false otherwise
Default:False
C++ Type:bool
Options:
Description:True for mass matrix lumping, false otherwise
sto_u1The stoichiometric coefficient of the primary species this kernel operates on
Default:1
C++ Type:double
Options:
Description:The stoichiometric coefficient of the primary species this kernel operates on
sto_vThe stoichiometric coefficients of coupled primary species
C++ Type:std::vector
Options:
Description:The stoichiometric coefficients of coupled primary species
vCoupled primary species constituting the equilibrium species
C++ Type:std::vector
Options:
Description:Coupled primary species constituting the equilibrium species
weight1The weight of the equilibrium species in total concentration
Default:1
C++ Type:double
Options:
Description:The weight of the equilibrium species in total concentration

Optional Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector
Options:
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
Options:
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
Options:
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
Options:
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
Options:
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
Options:
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
Options:
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

extra_matrix_tagsThe extra tags for the matrices this Kernel should fill
C++ Type:std::vector
Options:
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
Options:
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
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
Description:The tag for the vectors this Kernel should fill

Tagging Parameters

Input Files

modules/chemical_reactions/test/tests/exceptions/missing_sto2.i
modules/chemical_reactions/test/tests/exceptions/missing_gamma2.i
modules/chemical_reactions/test/tests/parser/equilibrium_without_action.i
modules/chemical_reactions/test/tests/jacobian/coupled_equilsub2.i
modules/chemical_reactions/test/tests/aqueous_equilibrium/2species_eqaux.i
modules/chemical_reactions/test/tests/aqueous_equilibrium/1species_without_action.i
modules/chemical_reactions/test/tests/jacobian/coupled_equilsub.i
modules/chemical_reactions/test/tests/aqueous_equilibrium/2species_without_action.i

modules/chemical_reactions/test/tests/exceptions/missing_sto2.i

# Missing stoichiometric coefficient in CoupledBEEquilibriumSub Kernel

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

[Variables]
  [./a]
  [../]
  [./b]
  [../]
  [./c]
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./c_ie]
    type = PrimaryTimeDerivative
    variable = c
  [../]
  [./aeq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = 1
    weight = 2
    sto_u = 2
    v = 'b c'
    sto_v = 1
    gamma_v = '2 2'
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = porosity
    prop_values = 0.2
  [../]
[]

[Executioner]
  type = Transient
  end_time = 1
[]

modules/chemical_reactions/test/tests/exceptions/missing_gamma2.i

# Missing activity coefficient in CoupledBEEquilibriumSub Kernel

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

[Variables]
  [./a]
  [../]
  [./b]
  [../]
  [./c]
  [../]
[]

[AuxVariables]
  [./gamma_a]
  [../]
  [./gamma_b]
  [../]
  [./gamma_c]
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./c_ie]
    type = PrimaryTimeDerivative
    variable = c
  [../]
  [./aeq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = 1
    weight = 2
    sto_u = 2
    v = 'b c'
    sto_v = '1 1'
    gamma_v = gamma_b
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = porosity
    prop_values = 0.2
  [../]
[]

[Executioner]
  type = Transient
  end_time = 1
[]

modules/chemical_reactions/test/tests/parser/equilibrium_without_action.i

# Test AqueousEquilibriumReactions parser

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

[Variables]
  [./a]
  [../]
  [./b]
  [../]
[]

[AuxVariables]
  [./pressure]
  [../]
  [./pa2]
  [../]
  [./pab]
  [../]
[]

[AuxKernels]
  [./pa2]
    type = AqueousEquilibriumRxnAux
    variable = pa2
    v = a
    log_k = 2
    sto_v = 2
  [../]
  [./pab]
    type = AqueousEquilibriumRxnAux
    variable = pab
    v = 'a b'
    log_k = -2
    sto_v = '1 1'
  [../]
[]

[ICs]
  [./a]
    type = BoundingBoxIC
    variable = a
    x1 = 0.0
    y1 = 0.0
    x2 = 1.0e-10
    y2 = 1
    inside = 1.0e-2
    outside = 1.0e-10
  [../]
  [./b]
    type = BoundingBoxIC
    variable = b
    x1 = 0.0
    y1 = 0.0
    x2 = 1.0e-10
    y2 = 1
    inside = 1.0e-2
    outside = 1.0e-10
  [../]
  [./pressure]
    type = FunctionIC
    variable = pressure
    function = 2-x
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./a_diff]
    type = PrimaryDiffusion
    variable = a
  [../]
  [./a_conv]
    type = PrimaryConvection
    variable = a
    p = pressure
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./b_diff]
    type = PrimaryDiffusion
    variable = b
  [../]
  [./b_conv]
    type = PrimaryConvection
    variable = b
    p = pressure
  [../]
  [./a1_eq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
  [../]
  [./a1_diff]
    type = CoupledDiffusionReactionSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
  [../]
  [./a1_conv]
    type = CoupledConvectionReactionSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
    p = pressure
  [../]
  [./a2_eq]
    type = CoupledBEEquilibriumSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2_diff]
    type = CoupledDiffusionReactionSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2_conv]
    type = CoupledConvectionReactionSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
  [./b2_eq]
    type = CoupledBEEquilibriumSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2_diff]
    type = CoupledDiffusionReactionSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2_conv]
    type = CoupledConvectionReactionSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
[]

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

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = PJFNK
  nl_abs_tol = 1e-12
  end_time = 10
  dt = 10
[]

[Outputs]
  file_base = equilibrium_out
  exodus = true
  perf_graph = true
  print_linear_residuals = true
[]

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

modules/chemical_reactions/test/tests/jacobian/coupled_equilsub2.i

# Test the Jacobian terms for the CoupledBEEquilibriumSub Kernel using
# activity coefficients not equal to unity

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 2
  ny = 2
[]

[Variables]
  [./a]
    order = FIRST
    family = LAGRANGE
  [../]
  [./b]
    order = FIRST
    family = LAGRANGE
  [../]
  [./pressure]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[ICs]
  [./pressure]
    type = RandomIC
    variable = pressure
    min = 1
    max = 5
  [../]
  [./a]
    type = RandomIC
    variable = a
    max = 1
    min = 0
  [../]
  [./b]
    type = RandomIC
    variable = b
    max = 1
    min = 0
  [../]
[]

[Kernels]
  [./diff]
    type = DarcyFluxPressure
    variable = pressure
  [../]
  [./diff_b]
    type = Diffusion
    variable = b
  [../]
  [./a]
    type = CoupledBEEquilibriumSub
    variable = a
    v = b
    log_k = 2
    weight = 2
    sto_v = 1.5
    sto_u = 2
    gamma_eq = 2
    gamma_u = 2.5
    gamma_v = 1.5
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  end_time = 1
[]

[Outputs]
  perf_graph = true
[]

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

modules/chemical_reactions/test/tests/aqueous_equilibrium/2species_eqaux.i

# In this example, two primary species a and b are transported by diffusion and convection
# from the left of the porous medium, reacting to form two equilibrium species pa2 and pab
# according to the equilibrium reaction specified in the AqueousEquilibriumReactions block as:
#
#      reactions = '2a = pa2     2
#                   a + b = pab -2'
#
# where the 2 is the weight of the equilibrium species, the 2 on the RHS of the first reaction
# refers to the equilibrium constant (log10(Keq) = 2), and the -2 on the RHS of the second
# reaction equates to log10(Keq) = -2.
#
# This example is identical to 2species.i, except that it explicitly includes all AuxKernels
# and Kernels that are set up by the action in 2species.i, and that the equilbrium constants
# are provided by AuxVariables

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
[]

[Variables]
  [./a]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = BoundingBoxIC
      x1 = 0.0
      y1 = 0.0
      x2 = 1.0e-10
      y2 = 1
      inside = 1.0e-2
      outside = 1.0e-10
    [../]
  [../]
  [./b]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = BoundingBoxIC
      x1 = 0.0
      y1 = 0.0
      x2 = 1.0e-10
      y2 = 1
      inside = 1.0e-2
      outside = 1.0e-10
    [../]
  [../]
[]

[AuxVariables]
  [./pressure]
    order = FIRST
    family = LAGRANGE
  [../]
  [./pa2]
  [../]
  [./pab]
  [../]
  [./pa2_logk]
    initial_condition = 2
  [../]
  [./pab_logk]
    initial_condition = -2
  [../]
[]

[AuxKernels]
  [./pa2eq]
    type = AqueousEquilibriumRxnAux
    variable = pa2
    v = a
    sto_v = 2
    log_k = pa2_logk
  [../]
  [./pabeq]
    type = AqueousEquilibriumRxnAux
    variable = pab
    v = 'a b'
    sto_v = '1 1'
    log_k = pab_logk
  [../]
[]

[ICs]
  [./pressure]
    type = FunctionIC
    variable = pressure
    function = 2-x
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./a_diff]
    type = PrimaryDiffusion
    variable = a
  [../]
  [./a_conv]
    type = PrimaryConvection
    variable = a
    p = pressure
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./b_diff]
    type = PrimaryDiffusion
    variable = b
  [../]
  [./b_conv]
    type = PrimaryConvection
    variable = b
    p = pressure
  [../]
  [./a1eq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = pa2_logk
    weight = 2
    sto_u = 2
  [../]
  [./a1diff]
    type = CoupledDiffusionReactionSub
    variable = a
    log_k = pa2_logk
    weight = 2
    sto_u = 2
  [../]
  [./a1conv]
    type = CoupledConvectionReactionSub
    variable = a
    log_k = pa2_logk
    weight = 2
    sto_u = 2
    p = pressure
  [../]
  [./a2eq]
    type = CoupledBEEquilibriumSub
    variable = a
    v = b
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2diff]
    type = CoupledDiffusionReactionSub
    variable = a
    v = b
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2conv]
    type = CoupledConvectionReactionSub
    variable = a
    v = b
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
  [./b2eq]
    type = CoupledBEEquilibriumSub
    variable = b
    v = a
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2diff]
    type = CoupledDiffusionReactionSub
    variable = b
    v = a
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2conv]
    type = CoupledConvectionReactionSub
    variable = b
    v = a
    log_k = pab_logk
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
[]

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

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  nl_abs_tol = 1e-12
  start_time = 0.0
  end_time = 100
  dt = 10.0
[]

[Outputs]
  file_base = 2species_out
  exodus = true
  perf_graph = true
  print_linear_residuals = true
  hide = 'pa2_logk pab_logk'
[]

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

modules/chemical_reactions/test/tests/aqueous_equilibrium/1species_without_action.i

# Simple equilibrium reaction example.
# This simulation is identical to 1species.i, but explicitly includes the AuxVariables,
# AuxKernels, and Kernels that the action in 1species.i adds

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
[]

[Variables]
  [./a]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = BoundingBoxIC
      x1 = 0.0
      y1 = 0.0
      x2 = 1e-2
      y2 = 1
      inside = 1.0e-2
      outside = 1.0e-10
      variable = a
    [../]
  [../]
[]

[AuxVariables]
  [./pressure]
    order = FIRST
    family = LAGRANGE
  [../]
  [./pa2]
  [../]
[]

[AuxKernels]
  [./pa2eq]
    type = AqueousEquilibriumRxnAux
    variable = pa2
    v = a
    sto_v = 2
    log_k = 1
  [../]
[]

[ICs]
  [./pressure]
    type = FunctionIC
    variable = pressure
    function = 2-x
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./a_diff]
    type = PrimaryDiffusion
    variable = a
  [../]
  [./a_conv]
    type = PrimaryConvection
    variable = a
    p = pressure
  [../]
  [./aeq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = 1
    weight = 2
    sto_u = 2
  [../]
  [./adiff]
    type = CoupledDiffusionReactionSub
    variable = a
    log_k = 1
    weight = 2
    sto_u = 2
  [../]
  [./aconv]
    type = CoupledConvectionReactionSub
    variable = a
    log_k = 1
    weight = 2
    sto_u = 2
    p = pressure
  [../]
[]

[BCs]
  [./a_right]
    type = ChemicalOutFlowBC
    variable = a
    boundary = right
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  nl_abs_tol = 1e-12
  start_time = 0.0
  end_time = 100
  dt = 10.0
[]

[Outputs]
  file_base = 1species_out
  exodus = true
  perf_graph = true
  print_linear_residuals = true
[]

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

modules/chemical_reactions/test/tests/jacobian/coupled_equilsub.i

# Test the Jacobian terms for the CoupledBEEquilibriumSub Kernel

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 2
  ny = 2
[]

[Variables]
  [./a]
    order = FIRST
    family = LAGRANGE
  [../]
  [./b]
    order = FIRST
    family = LAGRANGE
  [../]
  [./pressure]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[ICs]
  [./pressure]
    type = RandomIC
    variable = pressure
    min = 1
    max = 5
  [../]
  [./a]
    type = RandomIC
    variable = a
    max = 1
    min = 0
  [../]
  [./b]
    type = RandomIC
    variable = b
    max = 1
    min = 0
  [../]
[]

[Kernels]
  [./diff]
    type = DarcyFluxPressure
    variable = pressure
  [../]
  [./diff_b]
    type = Diffusion
    variable = b
  [../]
  [./a]
    type = CoupledBEEquilibriumSub
    variable = a
    v = b
    log_k = 2
    weight = 2
    sto_v = 1.5
    sto_u = 2
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  end_time = 1
[]

[Outputs]
  perf_graph = true
[]

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

modules/chemical_reactions/test/tests/aqueous_equilibrium/2species_without_action.i

# Simple equilibrium reaction example to illustrate the use of the AqueousEquilibriumReactions
# action.
# In this example, two primary species a and b are transported by diffusion and convection
# from the left of the porous medium, reacting to form two equilibrium species pa2 and pab
# according to the equilibrium reaction specified in the AqueousEquilibriumReactions block as:
#
#      reactions = '2a = pa2     2
#                   a + b = pab -2'
#
# where the 2 is the weight of the equilibrium species, the 2 on the RHS of the first reaction
# refers to the equilibrium constant (log10(Keq) = 2), and the -2 on the RHS of the second
# reaction equates to log10(Keq) = -2.
#
# This example is identical to 2species.i, except that it explicitly includes all AuxKernels
# and Kernels that are set up by the action in 2species.i

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
[]

[Variables]
  [./a]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = BoundingBoxIC
      x1 = 0.0
      y1 = 0.0
      x2 = 1.0e-10
      y2 = 1
      inside = 1.0e-2
      outside = 1.0e-10
    [../]
  [../]
  [./b]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = BoundingBoxIC
      x1 = 0.0
      y1 = 0.0
      x2 = 1.0e-10
      y2 = 1
      inside = 1.0e-2
      outside = 1.0e-10
    [../]
  [../]
[]

[AuxVariables]
  [./pressure]
    order = FIRST
    family = LAGRANGE
  [../]
  [./pa2]
  [../]
  [./pab]
  [../]
[]

[AuxKernels]
  [./pa2eq]
    type = AqueousEquilibriumRxnAux
    variable = pa2
    v = a
    sto_v = 2
    log_k = 2
  [../]
  [./pabeq]
    type = AqueousEquilibriumRxnAux
    variable = pab
    v = 'a b'
    sto_v = '1 1'
    log_k = -2
  [../]
[]

[ICs]
  [./pressure]
    type = FunctionIC
    variable = pressure
    function = 2-x
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./a_diff]
    type = PrimaryDiffusion
    variable = a
  [../]
  [./a_conv]
    type = PrimaryConvection
    variable = a
    p = pressure
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./b_diff]
    type = PrimaryDiffusion
    variable = b
  [../]
  [./b_conv]
    type = PrimaryConvection
    variable = b
    p = pressure
  [../]
  [./a1eq]
    type = CoupledBEEquilibriumSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
  [../]
  [./a1diff]
    type = CoupledDiffusionReactionSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
  [../]
  [./a1conv]
    type = CoupledConvectionReactionSub
    variable = a
    log_k = 2
    weight = 2
    sto_u = 2
    p = pressure
  [../]
  [./a2eq]
    type = CoupledBEEquilibriumSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2diff]
    type = CoupledDiffusionReactionSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./a2conv]
    type = CoupledConvectionReactionSub
    variable = a
    v = b
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
  [./b2eq]
    type = CoupledBEEquilibriumSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2diff]
    type = CoupledDiffusionReactionSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
  [../]
  [./b2conv]
    type = CoupledConvectionReactionSub
    variable = b
    v = a
    log_k = -2
    weight = 1
    sto_v = 1
    sto_u = 1
    p = pressure
  [../]
[]

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

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '1e-4 1e-4 0.2'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  nl_abs_tol = 1e-12
  start_time = 0.0
  end_time = 100
  dt = 10.0
[]

[Outputs]
  file_base = 2species_out
  exodus = true
  perf_graph = true
  print_linear_residuals = true
[]

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

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