KineticDisPreConcAux

Concentration of secondary kinetic species

Calculates the concentration of mineral using the kinetic reaction rate $var element = document.getElementById("moose-equation-46394ca6-fcd0-4602-9b98-1d9bf5d00af3");katex.render("I_m", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ (calculated using KineticDisPreRateAux),

$var element = document.getElementById("moose-equation-0857c63c-ecb2-4701-941f-fa2a40e0d8e8");katex.render("\\frac{d C_m}{d t} = I_m.", element, {displayMode:true,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$

Input Parameters

sto_vThe stoichiometric coefficients of reactant species
C++ Type:std::vector<double>
Options:
Description:The stoichiometric coefficients of reactant species
variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Options:
Description:The name of the variable that this object applies to

Required Parameters

blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector<SubdomainName>
Options:
Description:The list of block ids (SubdomainID) that this object will be applied
boundaryThe list of boundary IDs from the mesh where this boundary condition applies
C++ Type:std::vector<BoundaryName>
Options:
Description:The list of boundary IDs from the mesh where this boundary condition applies
check_boundary_restrictedTrueWhether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
Default:True
C++ Type:bool
Options:
Description:Whether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
e_act29100Activation energy, J/mol
Default:29100
C++ Type:double
Options:
Description:Activation energy, J/mol
execute_onLINEAR TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
Default:LINEAR TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE
Description:The list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
gas_const8.31434Gas constant, in J/mol K
Default:8.31434
C++ Type:double
Options:
Description:Gas constant, in J/mol K
log_kThe equilibrium constant of the dissolution reaction
C++ Type:std::vector<VariableName>
Options:
Description:The equilibrium constant of the dissolution reaction
r_area0.1Specific reactive surface area in m^2/L solution
Default:0.1
C++ Type:double
Options:
Description:Specific reactive surface area in m^2/L solution
ref_kconst6.45654e-08Kinetic rate constant in mol/m^2 s
Default:6.45654e-08
C++ Type:double
Options:
Description:Kinetic rate constant in mol/m^2 s
ref_temp298.15Reference temperature, K
Default:298.15
C++ Type:double
Options:
Description:Reference temperature, K
sys_temp298.15System temperature, K
Default:298.15
C++ Type:std::vector<VariableName>
Options:
Description:System temperature, K
vThe list of reactant species
C++ Type:std::vector<VariableName>
Options:
Description:The list of reactant species

Optional Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
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

Input Files

(modules/chemical_reactions/test/tests/parser/kinetic_without_action.i)
(modules/chemical_reactions/test/tests/exceptions/missing_sto3.i)
(modules/chemical_reactions/test/tests/kinetic_rate/arrhenius.i)
(modules/chemical_reactions/test/tests/solid_kinetics/2species_without_action.i)

(modules/chemical_reactions/test/tests/parser/kinetic_without_action.i)

# Explicitly adds all Kernels and AuxKernels. Used to check that the
# SolidKineticReactions parser is working correctly

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

[Variables]
  [./a]
    initial_condition = 0.1
  [../]
  [./b]
    initial_condition = 0.1
  [../]
  [./c]
    initial_condition = 0.1
  [../]
  [./d]
    initial_condition = 0.1
  [../]
[]

[AuxVariables]
  [./m1]
  [../]
  [./m2]
  [../]
  [./m3]
  [../]
[]

[AuxKernels]
  [./m1]
    type = KineticDisPreConcAux
    variable = m1
    v = 'a b'
    sto_v = '1 1'
    log_k = -8
    r_area = 1
    ref_kconst = 1e-8
    e_act = 1e4
    gas_const = 8.314
    ref_temp = 298.15
    sys_temp = 298.15
  [../]
  [./m2]
    type = KineticDisPreConcAux
    variable = m2
    v = 'c d'
    sto_v = '2 3'
    log_k = -8
    r_area = 2
    ref_kconst = 2e-8
    e_act = 2e4
    gas_const = 8.314
    ref_temp = 298.15
    sys_temp = 298.15
  [../]
  [./m3]
    type = KineticDisPreConcAux
    variable = m3
    v = 'a c'
    sto_v = '1 -2'
    log_k = -8
    r_area = 3
    ref_kconst = 3e-8
    e_act = 3e4
    gas_const = 8.314
    ref_temp = 298.15
    sys_temp = 298.15
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./c_ie]
    type = PrimaryTimeDerivative
    variable = c
  [../]
  [./d_ie]
    type = PrimaryTimeDerivative
    variable = d
  [../]
  [./a_kin]
    type = CoupledBEKinetic
    variable = a
    v = 'm1 m3'
    weight = '1 1'
  [../]
  [./b_kin]
    type = CoupledBEKinetic
    variable = b
    v = m1
    weight = 1
  [../]
  [./c_kin]
    type = CoupledBEKinetic
    variable = c
    v = 'm2 m3'
    weight = '2 -2'
  [../]
  [./d_kin]
    type = CoupledBEKinetic
    variable = d
    v = m2
    weight = 3
  [../]
[]

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = porosity
    prop_values = 0.1
  [../]
[]

[Executioner]
  type = Transient
  solve_type = PJFNK
  end_time = 1
  l_tol = 1e-10
  nl_rel_tol = 1e-10
[]

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

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

(modules/chemical_reactions/test/tests/exceptions/missing_sto3.i)

# Missing stoichiometric coefficient in AqueousEquilibriumRxnAux AuxKernel
# Simple reaction-diffusion example without using the action.
# 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
# This simulation is identical to 2species.i, but explicitly includes the AuxVariables,
# AuxKernels, and Kernels that the action in 2species.i adds

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

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

[AuxVariables]
  [./mineral]
  [../]
[]

[AuxKernels]
  [./mineral_conc]
    type = KineticDisPreConcAux
    variable = mineral
    sto_v = 1
    v = 'a b'
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
[]

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

[Executioner]
  type = Transient
  end_time = 1
[]

(modules/chemical_reactions/test/tests/kinetic_rate/arrhenius.i)

# Check the correct temperature dependence of the kinetic rate constant using
# the Arrhenius equation. Two kinetic reactions take place at different system
# temperatures. The Arrhenius equation states that the kinetic rate increases
# with temperature, so more mineral should be precipitated for the higher system
# temperature. In this case, the AuxVariables kinetic_rate1 and mineral1 should
# be larger than kinetic_rate0 and mineral0.

[Mesh]
  type = GeneratedMesh
  dim = 2
[]

[Variables]
  [./a0]
    initial_condition = 0.1
  [../]
  [./b0]
    initial_condition = 0.1
  [../]
  [./a1]
    initial_condition = 0.1
  [../]
  [./b1]
    initial_condition = 0.1
  [../]
[]

[AuxVariables]
  [./mineral0]
  [../]
  [./mineral1]
  [../]
  [./kinetic_rate0]
  [../]
  [./kinetic_rate1]
  [../]
[]

[AuxKernels]
  [./kinetic_rate0]
    type = KineticDisPreRateAux
    variable = kinetic_rate0
    e_act = 1.5e4
    r_area = 1
    log_k = -6
    ref_kconst = 1e-8
    gas_const = 8.31434
    ref_temp = 298.15
    sys_temp = 298.15
    sto_v = '1 1'
    v = 'a0 b0'
  [../]
  [./kinetic_rate1]
    type = KineticDisPreRateAux
    variable = kinetic_rate1
    e_act = 1.5e4
    r_area = 1
    log_k = -6
    ref_kconst = 1e-8
    gas_const = 8.31434
    ref_temp = 298.15
    sys_temp = 323.15
    sto_v = '1 1'
    v = 'a1 b1'
  [../]
  [./mineral0_conc]
    type = KineticDisPreConcAux
    variable = mineral0
    e_act = 1.5e4
    r_area = 1
    log_k = -6
    ref_kconst = 1e-8
    gas_const = 8.31434
    ref_temp = 298.15
    sys_temp = 298.15
    sto_v = '1 1'
    v = 'a0 b0'
  [../]
  [./mineral1_conc]
    type = KineticDisPreConcAux
    variable = mineral1
    e_act = 1.5e4
    r_area = 1
    log_k = -6
    ref_kconst = 1e-8
    gas_const = 8.31434
    ref_temp = 298.15
    sys_temp = 323.15
    sto_v = '1 1'
    v = 'a1 b1'
  [../]
[]

[Kernels]
  [./a0_ie]
    type = PrimaryTimeDerivative
    variable = a0
  [../]
  [./b0_ie]
    type = PrimaryTimeDerivative
    variable = b0
  [../]
  [./a0_r]
    type = CoupledBEKinetic
    variable = a0
    v = mineral0
    weight = 1
  [../]
  [./b0_r]
    type = CoupledBEKinetic
    variable = b0
    v = mineral0
    weight = 1
  [../]
  [./a1_ie]
    type = PrimaryTimeDerivative
    variable = a1
  [../]
  [./b1_ie]
    type = PrimaryTimeDerivative
    variable = b1
  [../]
  [./a1_r]
    type = CoupledBEKinetic
    variable = a1
    v = mineral1
    weight = 1
  [../]
  [./b1_r]
    type = CoupledBEKinetic
    variable = b1
    v = mineral1
    weight = 1
  [../]
[]

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

[Executioner]
  type = Transient
  solve_type = PJFNK
  end_time = 1
  dt = 1
[]

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

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

(modules/chemical_reactions/test/tests/solid_kinetics/2species_without_action.i)

# Simple reaction-diffusion example without using the action.
# 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
# This simulation is identical to 2species.i, but explicitly includes the AuxVariables,
# AuxKernels, and Kernels that the action in 2species.i adds

[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]
  [./mineral]
  [../]
[]

[AuxKernels]
  [./mineral_conc]
    type = KineticDisPreConcAux
    variable = mineral
    e_act = 1.5e4
    r_area = 1
    log_k = -6
    ref_kconst = 1e-8
    gas_const = 8.314
    ref_temp = 298.15
    sys_temp = 298.15
    sto_v = '1 1'
    v = 'a b'
  [../]
[]

[Kernels]
  [./a_ie]
    type = PrimaryTimeDerivative
    variable = a
  [../]
  [./a_pd]
    type = PrimaryDiffusion
    variable = a
  [../]
  [./b_ie]
    type = PrimaryTimeDerivative
    variable = b
  [../]
  [./b_pd]
    type = PrimaryDiffusion
    variable = b
  [../]
  [./a_r]
    type = CoupledBEKinetic
    variable = a
    v = mineral
    weight = 1
  [../]
  [./b_r]
    type = CoupledBEKinetic
    variable = b
    v = mineral
    weight = 1
  [../]
[]

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

[Materials]
  [./porous]
    type = GenericConstantMaterial
    prop_names = 'diffusivity conductivity porosity'
    prop_values = '5e-4 4e-3 0.4'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = 'PJFNK'
  end_time = 50
  dt = 5
[]

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

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

Input Parameters
Input Files

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