- PorousFlowDictatorThe UserObject that holds the list of PorousFlow variable names
C++ Type:UserObjectName
Description:The UserObject that holds the list of PorousFlow variable names
PorousFlow Aqueous PreDis Mineral
This Material forms a std::vector of mineral concentrations (volume-of-mineral/volume-of-material) appropriate to the aqueous precipitation-dissolution system provided.
This computes mineral concentrations that result from a precipitation-dissolution (PreDis) kinetic reaction system. The Material Property may be saved in an AuxVariable using the PorousFlowPropertyAux AuxKernel. The mineral concentration computed has units m(precipitate)/m(porous material).
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 doesn't cause porosity to become negative or exceed unity.
The computation uses a lagged approach for porosity to calculate the mineral concentration, : where is the reaction rate (dependent on primary concentrations, etc) and is the saturation of the aqueous phase. Notice the use of the old value for porosity. This is an approximation. It breaks the cyclic dependency between mineral concentration and porosity: see Porosity for more details.
Input Parameters
- at_nodesFalseEvaluate Material properties at nodes instead of quadpoints
Default:False
C++ Type:bool
Options:
Description:Evaluate Material properties at nodes instead of quadpoints
- 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
- boundaryThe list of boundary IDs from the mesh where this boundary condition applies
C++ Type:std::vector
Options:
Description:The list of boundary IDs from the mesh where this boundary condition applies
- computeTrueWhen false, MOOSE will not call compute methods on this material. The user must call computeProperties() after retrieving the MaterialBase via MaterialBasePropertyInterface::getMaterialBase(). Non-computed MaterialBases are not sorted for dependencies.
Default:True
C++ Type:bool
Options:
Description:When false, MOOSE will not call compute methods on this material. The user must call computeProperties() after retrieving the MaterialBase via MaterialBasePropertyInterface::getMaterialBase(). Non-computed MaterialBases are not sorted for dependencies.
- constant_onNONEWhen ELEMENT, MOOSE will only call computeQpProperties() for the 0th quadrature point, and then copy that value to the other qps.When SUBDOMAIN, MOOSE will only call computeSubdomainProperties() for the 0th quadrature point, and then copy that value to the other qps. Evaluations on element qps will be skipped
Default:NONE
C++ Type:MooseEnum
Options:NONE ELEMENT SUBDOMAIN
Description:When ELEMENT, MOOSE will only call computeQpProperties() for the 0th quadrature point, and then copy that value to the other qps.When SUBDOMAIN, MOOSE will only call computeSubdomainProperties() for the 0th quadrature point, and then copy that value to the other qps. Evaluations on element qps will be skipped
- initial_concentrationsInitial concentrations for the mineral species (m^{3}(precipitate)/m^{3}(porous material)). Default = 0
C++ Type:std::vector
Options:
Description:Initial concentrations for the mineral species (m^{3}(precipitate)/m^{3}(porous material)). Default = 0
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.
- 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
- 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
- output_propertiesList of material properties, from this material, to output (outputs must also be defined to an output type)
C++ Type:std::vector
Options:
Description:List of material properties, from this material, to output (outputs must also be defined to an output type)
- outputsnone Vector of output names were you would like to restrict the output of variables(s) associated with this object
Default:none
C++ Type:std::vector
Options:
Description:Vector of output names were you would like to restrict the output of variables(s) associated with this object
Outputs Parameters
Input Files
- modules/porous_flow/test/tests/chemistry/except20.i
- modules/porous_flow/test/tests/jacobian/chem11.i
- modules/porous_flow/test/tests/chemistry/except14.i
- modules/porous_flow/test/tests/chemistry/except15.i
- modules/porous_flow/test/tests/chemistry/dissolution.i
- modules/porous_flow/test/tests/chemistry/except12.i
- modules/porous_flow/test/tests/jacobian/chem04.i
- modules/porous_flow/test/tests/jacobian/chem10.i
- modules/porous_flow/test/tests/chemistry/except19.i
- modules/porous_flow/test/tests/jacobian/chem13.i
- modules/porous_flow/test/tests/jacobian/chem03.i
- modules/porous_flow/test/tests/jacobian/chem09.i
- modules/porous_flow/test/tests/chemistry/2species_predis.i
- modules/porous_flow/test/tests/chemistry/except10.i
- modules/porous_flow/test/tests/chemistry/except9.i
- modules/porous_flow/test/tests/chemistry/precipitation_2phase.i
- modules/porous_flow/test/tests/chemistry/precipitation.i
- modules/porous_flow/test/tests/jacobian/chem14.i
- modules/porous_flow/test/tests/chemistry/dissolution_limited.i
- modules/porous_flow/test/tests/jacobian/chem01.i
- modules/porous_flow/examples/tutorial/07.i
- modules/porous_flow/test/tests/chemistry/except13.i
- modules/porous_flow/test/tests/jacobian/chem02.i
- modules/porous_flow/test/tests/jacobian/chem06.i
- modules/porous_flow/test/tests/jacobian/chem05.i
- modules/porous_flow/test/tests/chemistry/except16.i
- modules/porous_flow/test/tests/chemistry/except22.i
- modules/porous_flow/test/tests/jacobian/chem12.i
- modules/porous_flow/test/tests/chemistry/except8.i
- modules/porous_flow/test/tests/chemistry/precipitation_porosity_change.i
- modules/porous_flow/test/tests/jacobian/chem07.i
- modules/porous_flow/test/tests/chemistry/except11.i
- modules/porous_flow/test/tests/jacobian/chem08.i
- modules/porous_flow/examples/tutorial/13.i
- modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i
- modules/porous_flow/test/tests/chemistry/except18.i
modules/porous_flow/test/tests/chemistry/except20.i
# Exception test
# No reference chemistry
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./dummy]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./a]
initial_condition = 0.5
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./porosity]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./dummy]
type = Diffusion
variable = dummy
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = dummy
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[Materials]
[./temperature_qp]
type = PorousFlowTemperature
temperature = 1
[../]
[./predis_qp]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc_qp]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./porosity]
type = PorousFlowPorosity
chemical = true
porosity_zero = 0.6
initial_mineral_concentrations = ini_mineral_conc
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.1
end_time = 0.4
[]
[Postprocessors]
[./porosity]
type = PointValue
point = '0 0 0'
variable = porosity
[../]
[./c]
type = PointValue
point = '0 0 0'
variable = mineral
[../]
[]
[Outputs]
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem11.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with three primary variables and four reactions
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[./b]
initial_condition = 0.1
[../]
[./c]
initial_condition = 0.15
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k0]
initial_condition = 0.1
[../]
[./eqm_k1]
initial_condition = 0.2
[../]
[./eqm_k2]
initial_condition = -0.2
[../]
[./eqm_k3]
initial_condition = 0.0
[../]
[./ini_sec_conc0]
initial_condition = 0.02
[../]
[./ini_sec_conc1]
initial_condition = 0.04
[../]
[./ini_sec_conc2]
initial_condition = 0.06
[../]
[./ini_sec_conc3]
initial_condition = 0.08
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = '1E10 2E10 3E10 4E10'
stoichiometry = '1 1 2 0.1'
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = '1.1E10 2.2E10 3.3E10 4.4E10'
stoichiometry = '2 2 0.1 0.5'
[../]
[./c]
type = PorousFlowPreDis
variable = c
mineral_density = '0.1E10 0.2E10 0.3E10 0.4E10'
stoichiometry = '3 3 0.1 1'
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b c temp'
number_fluid_phases = 1
number_fluid_components = 4
number_aqueous_kinetic = 4
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b c'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b c'
num_reactions = 4
equilibrium_constants_as_log10 = true
equilibrium_constants = 'eqm_k0 eqm_k1 eqm_k2 eqm_k3'
primary_activity_coefficients = '0.5 0.8 0.9'
reactions = '1 2 3
1 -2 -3
2 0.1 0.1
0.1 0.5 1'
specific_reactive_surface_area = '-44.4E-2 22.1E-2 32.1E-1 -50E-2'
kinetic_rate_constant = '0.678 0.999 1.23 0.3'
activation_energy = '4.4 3.3 4.5 4.0'
molar_volume = '3.3 4.4 5.5 6.6'
reference_temperature = 1
gas_constant = 7.4
theta_exponent = '1.0 1.1 1.2 0.9'
eta_exponent = '1.2 1.01 1.1 1.2'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 'ini_sec_conc0 ini_sec_conc1 ini_sec_conc2 ini_sec_conc3'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/except14.i
# Exception test.
# Incorrect number of initial concentrations
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./ini_conc_0]
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 'ini_conc_0 ini_conc_0'
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/except15.i
# Exception test
# Incorrect number of secondary densities
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = '1 1'
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 1
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '1 1'
reactions = '2 3'
specific_reactive_surface_area = 1.0
kinetic_rate_constant = 1.0e-8
activation_energy = 1.5e4
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/dissolution.i
# The dissolution reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.3
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./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 = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/chemistry/except12.i
# Exception test.
# Incorrect number of theta exponents
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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
theta_exponent = '1 1'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/jacobian/chem04.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Precipitation with temperature
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.6
[../]
[./b]
initial_condition = 0.4
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E-5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E-5
stoichiometry = 3
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b temp'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '2.5 3.8'
reactions = '1.1 1.2'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/jacobian/chem10.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with two primary variables = 0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.0
[../]
[./b]
initial_condition = 0.0
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b temp'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '1 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.0
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/except19.i
# Exception test
# No initial_mineral_concentrations
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./dummy]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./a]
initial_condition = 0.5
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./porosity]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./dummy]
type = Diffusion
variable = dummy
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = dummy
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[Materials]
[./temperature_qp]
type = PorousFlowTemperature
temperature = 1
[../]
[./predis_qp]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc_qp]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./porosity]
type = PorousFlowPorosity
chemical = true
porosity_zero = 0.6
reference_chemistry = ini_mineral_conc
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.1
end_time = 0.4
[]
[Postprocessors]
[./porosity]
type = PointValue
point = '0 0 0'
variable = porosity
[../]
[./c]
type = PointValue
point = '0 0 0'
variable = mineral
[../]
[]
[Outputs]
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem13.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with three primary variables and four reactions, and some zero concnetrations
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0
[../]
[./b]
initial_condition = 0
[../]
[./c]
initial_condition = 0
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k0]
initial_condition = 1.234
[../]
[./eqm_k1]
initial_condition = 1.999
[../]
[./eqm_k2]
initial_condition = 0.789
[../]
[./eqm_k3]
initial_condition = 1.111
[../]
[./ini_sec_conc0]
initial_condition = 0.02
[../]
[./ini_sec_conc1]
initial_condition = 0.04
[../]
[./ini_sec_conc2]
initial_condition = 0.06
[../]
[./ini_sec_conc3]
initial_condition = 0.08
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = '1E10 2E10 3E10 4E10'
stoichiometry = '1 1 2 0'
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = '1.1E10 2.2E10 3.3E10 4.4E10'
stoichiometry = '2 -2 0 0.5'
[../]
[./c]
type = PorousFlowPreDis
variable = c
mineral_density = '0.1E10 0.2E10 0.3E10 0.4E10'
stoichiometry = '3 -3 0 1'
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b c temp'
number_fluid_phases = 1
number_fluid_components = 4
number_aqueous_kinetic = 4
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b c'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b c'
num_reactions = 4
equilibrium_constants = 'eqm_k0 eqm_k1 eqm_k2 eqm_k3'
primary_activity_coefficients = '0.5 0.8 0.9'
reactions = '0.5 2 3
1.5 -2 3
2 0 0
0 0.5 1'
specific_reactive_surface_area = '-44.4E-2 22.1E-2 32.1E-1 -50E-2'
kinetic_rate_constant = '0.678 0.999 1.23 0.3'
activation_energy = '4.4 3.3 4.5 4.0'
molar_volume = '3.3 4.4 5.5 6.6'
reference_temperature = 1
gas_constant = 7.4
theta_exponent = '1.0 1.1 1.2 0.9'
eta_exponent = '1.2 1.01 1.1 1.2'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 'ini_sec_conc0 ini_sec_conc1 ini_sec_conc2 ini_sec_conc3'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/jacobian/chem03.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.1
[../]
[./b]
initial_condition = 0.2
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E-5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E-5
stoichiometry = 3
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b temp'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '2 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/jacobian/chem09.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with one primary variable = 0 and stoichiometry = 1
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.0
[../]
[./b]
initial_condition = 0.2
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E10
stoichiometry = 1
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E10
stoichiometry = 3
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b temp'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '1 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
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
[../]
[]
[Modules]
[./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
[]
modules/porous_flow/test/tests/chemistry/except10.i
# Exception test.
# Incorrect number of activation energies
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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 1'
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/except9.i
# Exception test.
# Incorrect number of kinetic rate constants
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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 1'
activation_energy = '1.5e4'
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/precipitation_2phase.i
# Using a two-phase system (see precipitation.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to precipitation.i
#
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * (porosity * saturation)
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.9
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure0]
[../]
[./saturation1]
initial_condition = 0.25
[../]
[./b]
initial_condition = 0.123
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 2
number_fluid_components = 2
number_aqueous_kinetic = 1
aqueous_phase_number = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
[../]
[]
[Modules]
[./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 = 1
[../]
[./ppss]
type = PorousFlow2PhasePS
capillary_pressure = pc
phase0_porepressure = pressure0
phase1_saturation = saturation1
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = 'b a'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid0]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./simple_fluid1]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 1
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.4
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/chemistry/precipitation.i
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.9
[../]
[]
[AuxVariables]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./k]
initial_condition = 0.5
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./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 = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem14.i
# Check derivatives of PorousFlowPorosity with chemical=true
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.1
[../]
[]
[AuxVariables]
[./eqm_k0]
initial_condition = 1.234
[../]
[./eqm_k1]
initial_condition = 0.987
[../]
[./temp]
initial_condition = 0.5
[../]
[./ini_sec_conc0]
initial_condition = 0.111
[../]
[./ini_sec_conc1]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowMassTimeDerivative # this is rather irrelevant: we just want something with Porosity in it
variable = a
fluid_component = 0
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 2
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = temp
at_nodes = true
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
at_nodes = true
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = a
at_nodes = true
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 2
equilibrium_constants = 'eqm_k0 eqm_k1'
primary_activity_coefficients = 1
reactions = '1E-10
2E-10' # so that mass_frac = a
specific_reactive_surface_area = '-44.4E-2 -12E-2'
kinetic_rate_constant = '0.678 0.7'
activation_energy = '4.4 3.3'
molar_volume = '3.3 2.2'
reference_temperature = 1
gas_constant = 7.4
at_nodes = true
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 'ini_sec_conc0 ini_sec_conc1'
at_nodes = true
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
at_nodes = true
phase = 0
[../]
[./porosity]
type = PorousFlowPorosity
chemical = true
porosity_zero = 0.1
reference_chemistry = 'ini_sec_conc0 ini_sec_conc1'
initial_mineral_concentrations = 'ini_sec_conc0 ini_sec_conc1'
chemical_weights = '1.111 0.888' # so derivatives of porosity are big
at_nodes = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/dissolution_limited.i
# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.015
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./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 = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem01.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.25
[../]
[./b]
initial_condition = 0.2
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./temp]
initial_condition = 0.5
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '2 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/examples/tutorial/07.i
# Darcy flow with a tracer that precipitates causing mineralisation and porosity changes and permeability changes
[Mesh]
[annular]
type = AnnularMeshGenerator
nr = 10
rmin = 1.0
rmax = 10
growth_r = 1.4
nt = 4
dmin = 0
dmax = 90
[]
[./make3D]
input = annular
type = MeshExtruderGenerator
extrusion_vector = '0 0 12'
num_layers = 3
bottom_sideset = 'bottom'
top_sideset = 'top'
[../]
[./shift_down]
type = TransformGenerator
transform = TRANSLATE
vector_value = '0 0 -6'
input = make3D
[../]
[./aquifer]
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 0 -2'
top_right = '10 10 2'
input = shift_down
[../]
[./injection_area]
type = ParsedGenerateSideset
combinatorial_geometry = 'x*x+y*y<1.01'
included_subdomain_ids = 1
new_sideset_name = 'injection_area'
input = 'aquifer'
[../]
[./rename]
type = RenameBlockGenerator
old_block_id = '0 1'
new_block_name = 'caps aquifer'
input = 'injection_area'
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Variables]
[./porepressure]
[../]
[./tracer_concentration]
[../]
[]
[PorousFlowFullySaturated]
porepressure = porepressure
coupling_type = Hydro
gravity = '0 0 0'
fp = the_simple_fluid
mass_fraction_vars = tracer_concentration
number_aqueous_kinetic = 1
temperature = 283.0
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.1
[../]
[./mineral_conc]
family = MONOMIAL
order = CONSTANT
[../]
[./initial_and_reference_conc]
initial_condition = 0
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[./permeability]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral_conc]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral_conc
[../]
[./porosity]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[../]
[./permeability]
type = PorousFlowPropertyAux
property = permeability
column = 0
row = 0
variable = permeability
[../]
[]
[Kernels]
[./precipitation_dissolution]
type = PorousFlowPreDis
mineral_density = 1000.0
stoichiometry = 1
variable = tracer_concentration
[../]
[]
[BCs]
[./constant_injection_of_tracer]
type = PorousFlowSink
variable = tracer_concentration
flux_function = -5E-3
boundary = injection_area
[../]
[./constant_outer_porepressure]
type = DirichletBC
variable = porepressure
value = 0
boundary = rmax
[../]
[]
[Modules]
[./FluidProperties]
[./the_simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2E9
viscosity = 1.0E-3
density0 = 1000.0
[../]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
chemical = true
initial_mineral_concentrations = initial_and_reference_conc
reference_chemistry = initial_and_reference_conc
[../]
[./permeability_aquifer]
type = PorousFlowPermeabilityKozenyCarman
block = aquifer
k0 = 1E-14
m = 2
n = 3
phi0 = 0.1
poroperm_function = kozeny_carman_phi0
[../]
[./permeability_caps]
type = PorousFlowPermeabilityKozenyCarman
block = caps
k0 = 1E-15
k_anisotropy = '1 0 0 0 1 0 0 0 0.1'
m = 2
n = 3
phi0 = 0.1
poroperm_function = kozeny_carman_phi0
[../]
[./precipitation_dissolution]
type = PorousFlowAqueousPreDisChemistry
reference_temperature = 283.0
activation_energy = 1 # irrelevant because T=Tref
equilibrium_constants = eqm_k # equilibrium tracer concentration
kinetic_rate_constant = 1E-8
molar_volume = 1
num_reactions = 1
primary_activity_coefficients = 1
primary_concentrations = tracer_concentration
reactions = 1
specific_reactive_surface_area = 1
[../]
[./mineral_concentration]
type = PorousFlowAqueousPreDisMineral
[../]
[]
[Preconditioning]
active = basic
[./basic]
type = SMP
full = true
petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = ' asm lu NONZERO 2'
[../]
[./preferred_but_might_not_be_installed]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1E6
dt = 1E5
nl_abs_tol = 1E-10
[]
[Outputs]
exodus = true
[]
modules/porous_flow/test/tests/chemistry/except13.i
# Exception test.
# Incorrect number of eta exponents
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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
eta_exponent = '1 1'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/jacobian/chem02.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Precipitation with temperature
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.6
[../]
[./b]
initial_condition = 0.4
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./temp]
initial_condition = 0.5
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '2.5 3.8'
reactions = '1.1 1.2'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/jacobian/chem06.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with no temperature dependence, with one primary variable = 0 and stoichiometry = 1
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.2
[../]
[./b]
initial_condition = 0.0
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./temp]
initial_condition = 0.5
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '3 1'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/jacobian/chem05.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with no temperature dependence, with one primary variable = 0 and stoichiometry > 1
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.0
[../]
[./b]
initial_condition = 0.2
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '2 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/except16.i
# Exception test
# Incorrect number of stoichiometry
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1
stoichiometry = '2 3'
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 1
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '1 1'
reactions = '2 3'
specific_reactive_surface_area = 1.0
kinetic_rate_constant = 1.0e-8
activation_energy = 1.5e4
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/except22.i
# Exception test
# Zero fluid phases
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./dummy]
[../]
[]
[AuxVariables]
[./a]
initial_condition = 0.5
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./porosity]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./dummy]
type = Diffusion
variable = dummy
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = dummy
number_fluid_phases = 0
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[Materials]
[./temperature_qp]
type = PorousFlowTemperature
temperature = 1
[../]
[./predis_qp]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = 0.5
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc_qp]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./porosity]
type = PorousFlowPorosity
chemical = true
porosity_zero = 0.6
reference_chemistry = ini_mineral_conc
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.1
end_time = 0.4
[]
[Postprocessors]
[./porosity]
type = PointValue
point = '0 0 0'
variable = porosity
[../]
[./c]
type = PointValue
point = '0 0 0'
variable = mineral
[../]
[]
[Outputs]
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem12.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with three primary variables and four reactions
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[./b]
initial_condition = 0.1
[../]
[./c]
initial_condition = 0.15
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k0]
initial_condition = 1.234
[../]
[./eqm_k1]
initial_condition = 1.999
[../]
[./eqm_k2]
initial_condition = 0.789
[../]
[./eqm_k3]
initial_condition = 1.111
[../]
[./ini_sec_conc0]
initial_condition = 0.02
[../]
[./ini_sec_conc1]
initial_condition = 0.04
[../]
[./ini_sec_conc2]
initial_condition = 0.06
[../]
[./ini_sec_conc3]
initial_condition = 0.08
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = '1E10 2E10 3E10 4E10'
stoichiometry = '1 1 2 0'
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = '1.1E10 2.2E10 3.3E10 4.4E10'
stoichiometry = '2 -2 0 0.5'
[../]
[./c]
type = PorousFlowPreDis
variable = c
mineral_density = '0.1E10 0.2E10 0.3E10 0.4E10'
stoichiometry = '3 -3 0 1'
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b c temp'
number_fluid_phases = 1
number_fluid_components = 4
number_aqueous_kinetic = 4
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b c'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b c'
num_reactions = 4
equilibrium_constants = 'eqm_k0 eqm_k1 eqm_k2 eqm_k3'
primary_activity_coefficients = '0.5 0.8 0.9'
reactions = '1 2 3
1 -2 -3
2 0 0
0 0.5 1'
specific_reactive_surface_area = '-44.4E-2 22.1E-2 32.1E-1 -50E-2'
kinetic_rate_constant = '0.678 0.999 1.23 0.3'
activation_energy = '4.4 3.3 4.5 4.0'
molar_volume = '3.3 4.4 5.5 6.6'
reference_temperature = 1
gas_constant = 7.4
theta_exponent = '1.0 1.1 1.2 0.9'
eta_exponent = '1.2 1.01 1.1 1.2'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 'ini_sec_conc0 ini_sec_conc1 ini_sec_conc2 ini_sec_conc3'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/except8.i
# Exception test.
# Incorrect number of reactive surface areas
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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 1.0'
kinetic_rate_constant = '1.0e-8'
activation_energy = '1.5e4'
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/chemistry/precipitation_porosity_change.i
# Test to illustrate porosity evolution due to precipitation
#
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral". Using theta = 1 = eta, the DE that describes the prcipitation is
# reaction_rate = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative (ie precipitation) for a > 0.25
#
# a is held fixed at 0.5, so
# reaction_rate = - (1 - 2) = 1
#
# The mineral volume fraction evolves according to
# Mineral = mineral_old + dt * porosity_old * reaction_rate = mineral_old + dt * porosity_old
#
# Porosity evolves according to
# porosity = porosity(t=0) - (mineral - mineral(t=0))
# = porosity(t=0) - (mineral_old + dt * porosity_old * reaction_rate - mineral(t=0))
#
# Specifically:
# time mineral porosity
# 0 0.2 0.6
# 0.1 0.26 0.54
# 0.2 0.314 0.486
# 0.3 0.3626 0.4374
# 0.4 0.40634 0.39366
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./dummy]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./a]
initial_condition = 0.5
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./porosity]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./dummy]
type = Diffusion
variable = dummy
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = dummy
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = dummy
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./porosity]
type = PorousFlowPorosity
chemical = true
porosity_zero = 0.6
reference_chemistry = ini_mineral_conc
initial_mineral_concentrations = ini_mineral_conc
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.1
end_time = 0.4
[]
[Postprocessors]
[./porosity]
type = PointValue
point = '0 0 0'
variable = porosity
[../]
[./c]
type = PointValue
point = '0 0 0'
variable = mineral
[../]
[]
[Outputs]
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/jacobian/chem07.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with no temperature dependence, with two primary variables = 0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.0
[../]
[./b]
initial_condition = 0.0
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./temp]
initial_condition = 0.5
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E5
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E5
stoichiometry = 3
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '1 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.0
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/test/tests/chemistry/except11.i
# Exception test.
# Incorrect number of molar volumes
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
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 1'
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]
modules/porous_flow/test/tests/jacobian/chem08.i
# PorousFlowPreDis, which is essentially checking the derivatives of the secondary concentrations in PorousFlowMassFractionAqueousPreDisChemistry
# Dissolution with temperature, with one primary variable = 0 and stoichiometry > 1
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.2
[../]
[./b]
initial_condition = 0.0
[../]
[./temp]
initial_condition = 0.5
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1.234
[../]
[./ini_sec_conc]
initial_condition = 0.222
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = PorousFlowPreDis
variable = a
mineral_density = 1E10
stoichiometry = 2
[../]
[./b]
type = PorousFlowPreDis
variable = b
mineral_density = 2.2E10
stoichiometry = 3
[../]
[./temp]
type = Diffusion
variable = temp
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b temp'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[../]
[]
[AuxVariables]
[./pressure]
[../]
[]
[Materials]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.9
[../]
[./temperature]
type = PorousFlowTemperature
temperature = temp
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '0.5 0.8'
reactions = '2 3'
specific_reactive_surface_area = -44.4E-2
kinetic_rate_constant = 0.678
activation_energy = 4.4
molar_volume = 3.3
reference_temperature = 1
gas_constant = 7.4
theta_exponent = 1.1
eta_exponent = 1.2
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_sec_conc
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 0.1
end_time = 0.1
[]
[Preconditioning]
[./check]
type = SMP
full = true
petsc_options = '-snes_test_display'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -snes_type'
petsc_options_value = 'bcgs bjacobi 1E-15 1E-10 10000 test'
[../]
[]
modules/porous_flow/examples/tutorial/13.i
# Example of reactive transport model with dissolution of dolomite
#
# The equilibrium system has 5 primary species (Variables) and
# 5 secondary species (PorousFlowMassFractionAqueousEquilibrium).
# Some of the equilibrium constants have been chosen rather arbitrarily.
#
# Equilibrium reactions
# H+ + HCO3- = CO2(aq)
# -H+ + HCO3- = CO32-
# HCO3- + Ca2+ = CaHCO3+
# HCO3- + Mg2+ = MgHCO3+
# HCO3- + Fe2+ = FeHCO3+
#
# The kinetic reaction that dissolves dolomite involves all 5 primary species.
#
# -2H+ + 2HCO3- + Ca2+ + 0.8Mg2+ + 0.2Fe2+ = CaMg0.8Fe0.2(CO3)2
#
# The initial concentration of precipitated dolomite is high, so it starts
# to dissolve immediately, increasing the concentrations of the primary species.
#
# Only single-phase, fully saturated physics is used.
# The pressure gradient is fixed, so that the Darcy velocity is 0.1m/s.
#
# Primary species are injected from the left side, and they flow to the right.
# Less dolomite dissolution therefore occurs on the left side (where
# the primary species have higher concentration).
#
# This test is more fully documented in tutorial_13
[Mesh]
type = GeneratedMesh
dim = 1
nx = 100
xmax = 1
[]
[Variables]
[./h+]
[../]
[./hco3-]
[../]
[./ca2+]
[../]
[./mg2+]
[../]
[./fe2+]
[../]
[]
[AuxVariables]
[./eqm_k0]
initial_condition = 2.19E6
[../]
[./eqm_k1]
initial_condition = 4.73E-11
[../]
[./eqm_k2]
initial_condition = 0.222
[../]
[./eqm_k3]
initial_condition = 1E-2
[../]
[./eqm_k4]
initial_condition = 1E-3
[../]
[./kinetic_k]
initial_condition = 326.2
[../]
[./pressure]
[../]
[./dolomite]
family = MONOMIAL
order = CONSTANT
[../]
[./dolomite_initial]
initial_condition = 1E-7
[../]
[]
[AuxKernels]
[./dolomite]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = dolomite
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
gravity = '0 0 0'
[]
[ICs]
[./pressure_ic]
type = FunctionIC
variable = pressure
function = '(1 - x) * 1E6'
[../]
[./h+_ic]
type = BoundingBoxIC
variable = h+
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.25
inside = 5.0e-2
outside = 1.0e-6
[../]
[./hco3_ic]
type = BoundingBoxIC
variable = hco3-
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.25
inside = 5.0e-2
outside = 1.0e-6
[../]
[./ca2_ic]
type = BoundingBoxIC
variable = ca2+
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.25
inside = 5.0e-2
outside = 1.0e-6
[../]
[./mg2_ic]
type = BoundingBoxIC
variable = mg2+
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.25
inside = 5.0e-2
outside = 1.0e-6
[../]
[./fe2_ic]
type = BoundingBoxIC
variable = fe2+
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.25
inside = 5.0e-2
outside = 1.0e-6
[../]
[]
[Kernels]
[./h+_ie]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = h+
[../]
[./h+_conv]
type = PorousFlowAdvectiveFlux
fluid_component = 0
variable = h+
[../]
[./predis_h+]
type = PorousFlowPreDis
variable = h+
mineral_density = 2875.0
stoichiometry = -2
[../]
[./hco3-_ie]
type = PorousFlowMassTimeDerivative
fluid_component = 1
variable = hco3-
[../]
[./hco3-_conv]
type = PorousFlowAdvectiveFlux
fluid_component = 1
variable = hco3-
[../]
[./predis_hco3-]
type = PorousFlowPreDis
variable = hco3-
mineral_density = 2875.0
stoichiometry = 2
[../]
[./ca2+_ie]
type = PorousFlowMassTimeDerivative
fluid_component = 2
variable = ca2+
[../]
[./ca2+_conv]
type = PorousFlowAdvectiveFlux
fluid_component = 2
variable = ca2+
[../]
[./predis_ca2+]
type = PorousFlowPreDis
variable = ca2+
mineral_density = 2875.0
stoichiometry = 1
[../]
[./mg2+_ie]
type = PorousFlowMassTimeDerivative
fluid_component = 3
variable = mg2+
[../]
[./mg2+_conv]
type = PorousFlowAdvectiveFlux
fluid_component = 3
variable = mg2+
[../]
[./predis_mg2+]
type = PorousFlowPreDis
variable = mg2+
mineral_density = 2875.0
stoichiometry = 0.8
[../]
[./fe2+_ie]
type = PorousFlowMassTimeDerivative
fluid_component = 4
variable = fe2+
[../]
[./fe2+_conv]
type = PorousFlowAdvectiveFlux
fluid_component = 4
variable = fe2+
[../]
[./predis_fe2+]
type = PorousFlowPreDis
variable = fe2+
mineral_density = 2875.0
stoichiometry = 0.2
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'h+ hco3- ca2+ mg2+ fe2+'
number_fluid_phases = 1
number_fluid_components = 6
number_aqueous_equilibrium = 5
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
viscosity = 1E-3
[../]
[../]
[]
[BCs]
[./hco3-_left]
type = DirichletBC
variable = hco3-
boundary = left
value = 5E-2
[../]
[./h+_left]
type = DirichletBC
variable = h+
boundary = left
value = 5E-2
[../]
[./ca2+_left]
type = DirichletBC
variable = ca2+
boundary = left
value = 5E-2
[../]
[./mg2+_left]
type = DirichletBC
variable = mg2+
boundary = left
value = 5E-2
[../]
[./fe2+_left]
type = DirichletBC
variable = fe2+
boundary = left
value = 5E-2
[../]
[./hco3-_right]
type = DirichletBC
variable = hco3-
boundary = right
value = 1E-6
[../]
[./h+_right]
type = DirichletBC
variable = h+
boundary = right
value = 1e-6
[../]
[./ca2+_right]
type = DirichletBC
variable = ca2+
boundary = right
value = 1E-6
[../]
[./mg2+_right]
type = DirichletBC
variable = mg2+
boundary = right
value = 1E-6
[../]
[./fe2+_right]
type = DirichletBC
variable = fe2+
boundary = right
value = 1E-6
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 298.15
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./equilibrium_massfrac]
type = PorousFlowMassFractionAqueousEquilibriumChemistry
mass_fraction_vars = 'h+ hco3- ca2+ mg2+ fe2+'
num_reactions = 5
equilibrium_constants = 'eqm_k0 eqm_k1 eqm_k2 eqm_k3 eqm_k4'
primary_activity_coefficients = '1 1 1 1 1'
secondary_activity_coefficients = '1 1 1 1 1'
reactions = '1 1 0 0 0
-1 1 0 0 0
0 1 1 0 0
0 1 0 1 0
0 1 0 0 1'
[../]
[./kinetic]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'h+ hco3- ca2+ mg2+ fe2+'
num_reactions = 1
equilibrium_constants = kinetic_k
primary_activity_coefficients = '1 1 1 1 1'
reactions = '-2 2 1 0.8 0.2'
specific_reactive_surface_area = '1.2E-8'
kinetic_rate_constant = '3E-4'
activation_energy = '1.5e4'
molar_volume = 64365.0
gas_constant = 8.314
reference_temperature = 298.15
[../]
[./dolomite_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = dolomite_initial
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.2
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1E-10 0 0 0 1E-10 0 0 0 1E-10'
[../]
[./relp]
type = PorousFlowRelativePermeabilityConst
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.1
[../]
[]
[Preconditioning]
active = basic
[./basic]
type = SMP
full = true
petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = ' asm lu NONZERO 2'
[../]
[./preferred_but_might_not_be_installed]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[]
[Outputs]
print_linear_residuals = false
perf_graph = true
exodus = true
[]
modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i
# Using a two-phase system (see dissolution_limited.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to dissolution_limited.i
#
# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity * saturation
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure0]
[../]
[./saturation1]
initial_condition = 0.25
[../]
[./b]
initial_condition = 0.123
[../]
[./ini_mineral_conc]
initial_condition = 0.015
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 2
number_fluid_components = 2
number_aqueous_kinetic = 1
aqueous_phase_number = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
[../]
[]
[Modules]
[./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 = 1
[../]
[./ppss]
type = PorousFlow2PhasePS
capillary_pressure = pc
phase0_porepressure = pressure0
phase1_saturation = saturation1
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = 'b a'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid0]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./simple_fluid1]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 1
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.4
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/chemistry/except18.i
# Exception test
# Incorrect number of kinetic in dictator
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./a]
type = Diffusion
variable = a
[../]
[./b]
type = Diffusion
variable = b
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_equilibrium = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
[../]
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 1E-6
[../]
[./pressure]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '1 1'
reactions = '2 3'
specific_reactive_surface_area = 1.0
kinetic_rate_constant = 1.0e-8
activation_energy = 1.5e4
molar_volume = 1
[../]
[./mineral]
type = PorousFlowAqueousPreDisMineral
[../]
[./porosity]
type = PorousFlowPorosity
porosity_zero = 0.1
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1
[]