- PorousFlowDictatorThe UserObject that holds the list of PorousFlow variable names
C++ Type:UserObjectName
Controllable:No
Description:The UserObject that holds the list of PorousFlow variable names
- activation_energyActivation energy, J/mol (one for each reaction)
C++ Type:std::vector<double>
Controllable:No
Description:Activation energy, J/mol (one for each reaction)
- equilibrium_constantsEquilibrium constant for each equation (dimensionless). If these are temperature dependent AuxVariables, the Jacobian will not be exact
C++ Type:std::vector<VariableName>
Controllable:No
Description:Equilibrium constant for each equation (dimensionless). If these are temperature dependent AuxVariables, the Jacobian will not be exact
- kinetic_rate_constantKinetic rate constant in mol/(m^2 s), at the reference temperature (one for each reaction)
C++ Type:std::vector<double>
Controllable:No
Description:Kinetic rate constant in mol/(m^2 s), at the reference temperature (one for each reaction)
- molar_volumeVolume occupied by one mole of the secondary species (L(solution)/mol) (one for each reaction)
C++ Type:std::vector<double>
Controllable:No
Description:Volume occupied by one mole of the secondary species (L(solution)/mol) (one for each reaction)
- num_reactionsNumber of equations in the system of chemical reactions
C++ Type:unsigned int
Controllable:No
Description:Number of equations in the system of chemical reactions
- primary_activity_coefficientsActivity coefficients for the primary species (dimensionless) (one for each)
C++ Type:std::vector<double>
Controllable:No
Description:Activity coefficients for the primary species (dimensionless) (one for each)
- primary_concentrationsList of MOOSE Variables that represent the concentrations of the primary species
C++ Type:std::vector<VariableName>
Controllable:No
Description:List of MOOSE Variables that represent the concentrations of the primary species
- reactionsA matrix defining the aqueous reactions. The matrix is entered as a long vector: the first row is entered first, followed by the second row, etc. There should be num_reactions rows. All primary species should appear only on the LHS of each reaction (and there should be just one secondary species on the RHS, by definition) so they may have negative coefficients. Each row should have number of primary_concentrations entries, which are the stoichiometric coefficients. The first coefficient must always correspond to the first primary species, etc
C++ Type:std::vector<double>
Controllable:No
Description:A matrix defining the aqueous reactions. The matrix is entered as a long vector: the first row is entered first, followed by the second row, etc. There should be num_reactions rows. All primary species should appear only on the LHS of each reaction (and there should be just one secondary species on the RHS, by definition) so they may have negative coefficients. Each row should have number of primary_concentrations entries, which are the stoichiometric coefficients. The first coefficient must always correspond to the first primary species, etc
- specific_reactive_surface_areaSpecific reactive surface area in m^2/(L solution).
C++ Type:std::vector<double>
Controllable:No
Description:Specific reactive surface area in m^2/(L solution).
PorousFlow Aqueous PreDis Chemistry
This Material forms a std::vector of mineralisation reaction rates (L(precipitate)/L(solution)/s) appropriate to the aqueous precipitation-dissolution system provided. Note: the PorousFlowTemperature must be measured in Kelvin.
This computes reaction rates resulting from a precipitation-dissolution (PreDis) kinetic reaction system.
warningwarning
The numerical implementation of the chemical-reactions part of PorousFlow is quite simplistic, with very few guards against strange numerical behavior that might arise during the non-linear iterative process that MOOSE uses to find the solution. Therefore, care must be taken to define your chemical reactions so that the primary species concentrations remain small, but nonzero, and that mineralisation doesn't cause porosity to become negative or exceed unity.
Details concerning precipitation-dissolution kinetic chemistry may be found in the chemical reactions module. There are two main differences between the chemical reactions module and PorousFlow. These are:
The molar volumes must be specified in
PorousFlow. This is so that the concentrations may be measured in rather than mol.m.Unlike the
chemical reactionsmodule, users ofPorousFlowmust specify the stoichiometric coefficients themselves. In each reaction, the primary concentrations (variables) must be brought to the left-hand-side. The right-hand-sides are the minerals, by definition. For instance, consider a 2-reaction system consisting of 3 primary variables, , and . The reactions areThen the
reactionsinput is1 2 -3 4 -5 6.
commentnote
If the equilibrium constants are AuxVariables that depend on temperature (or other Variables) the computed Jacobian will not be exact and you may experience poor nonlinear convergence. If this becomes frustrating, please contact the MOOSE Discussion forum.
Input Parameters
- at_nodesFalseEvaluate Material properties at nodes instead of quadpoints
Default:False
C++ Type:bool
Controllable:No
Description:Evaluate Material properties at nodes instead of quadpoints
- blockThe list of blocks (ids or names) that this object will be applied
C++ Type:std::vector<SubdomainName>
Controllable:No
Description:The list of blocks (ids or names) that this object will be applied
- boundaryThe list of boundaries (ids or names) from the mesh where this object applies
C++ Type:std::vector<BoundaryName>
Controllable:No
Description:The list of boundaries (ids or names) from the mesh where this object 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
Controllable:No
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 computeQpProperties() 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
Controllable:No
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 computeQpProperties() for the 0th quadrature point, and then copy that value to the other qps. Evaluations on element qps will be skipped
- declare_suffixAn optional suffix parameter that can be appended to any declared properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Controllable:No
Description:An optional suffix parameter that can be appended to any declared properties. The suffix will be prepended with a '_' character.
- equilibrium_constants_as_log10FalseIf true, the equilibrium constants are written in their log10 form, eg, -2. If false, the equilibrium constants are written in absolute terms, eg, 0.01
Default:False
C++ Type:bool
Controllable:No
Description:If true, the equilibrium constants are written in their log10 form, eg, -2. If false, the equilibrium constants are written in absolute terms, eg, 0.01
- eta_exponentEta exponent. Defaults to 1. (one for each reaction)
C++ Type:std::vector<double>
Controllable:No
Description:Eta exponent. Defaults to 1. (one for each reaction)
- gas_constant8.31434Gas constant, in J/(mol K)
Default:8.31434
C++ Type:double
Controllable:No
Description:Gas constant, in J/(mol K)
- prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Controllable:No
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
- reference_temperature298.15Reference temperature, K
Default:298.15
C++ Type:double
Controllable:No
Description:Reference temperature, K
- theta_exponentTheta exponent. Defaults to 1. (one for each reaction)
C++ Type:std::vector<double>
Controllable:No
Description:Theta exponent. Defaults to 1. (one for each reaction)
- use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Default:False
C++ Type:bool
Controllable:No
Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Controllable:Yes
Description:Set the enabled status of the MooseObject.
- implicitTrueDetermines whether this object is calculated using an implicit or explicit form
Default:True
C++ Type:bool
Controllable:No
Description:Determines whether this object is calculated using an implicit or explicit form
- seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Controllable:No
Description:The seed for the master random number generator
- use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Controllable:No
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Advanced Parameters
- output_propertiesList of material properties, from this material, to output (outputs must also be defined to an output type)
C++ Type:std::vector<std::string>
Controllable:No
Description:List of material properties, from this material, to output (outputs must also be defined to an output type)
- outputsnone Vector of output names where you would like to restrict the output of variables(s) associated with this object
Default:none
C++ Type:std::vector<OutputName>
Controllable:No
Description:Vector of output names where you would like to restrict the output of variables(s) associated with this object
Outputs Parameters
Input Files
- (modules/porous_flow/test/tests/chemistry/except16.i)
- (modules/porous_flow/test/tests/chemistry/dissolution.i)
- (modules/porous_flow/test/tests/chemistry/except14.i)
- (modules/porous_flow/test/tests/jacobian/chem10.i)
- (modules/porous_flow/test/tests/chemistry/except10.i)
- (modules/porous_flow/test/tests/jacobian/chem05.i)
- (modules/porous_flow/test/tests/jacobian/chem07.i)
- (modules/porous_flow/test/tests/chemistry/precipitation.i)
- (modules/porous_flow/test/tests/jacobian/chem02.i)
- (modules/porous_flow/examples/tutorial/07.i)
- (modules/porous_flow/test/tests/jacobian/chem13.i)
- (modules/porous_flow/test/tests/chemistry/except18.i)
- (modules/porous_flow/test/tests/jacobian/chem11.i)
- (modules/porous_flow/test/tests/jacobian/chem08.i)
- (modules/porous_flow/test/tests/jacobian/chem12.i)
- (modules/porous_flow/test/tests/chemistry/except13.i)
- (modules/porous_flow/test/tests/chemistry/precipitation_porosity_change.i)
- (modules/porous_flow/examples/tutorial/13.i)
- (modules/porous_flow/test/tests/chemistry/2species_predis.i)
- (modules/porous_flow/examples/thm_example/2D_c.i)
- (modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i)
- (modules/porous_flow/test/tests/chemistry/precipitation_2phase.i)
- (modules/porous_flow/test/tests/jacobian/chem14.i)
- (modules/porous_flow/test/tests/jacobian/chem04.i)
- (modules/porous_flow/test/tests/jacobian/chem06.i)
- (modules/porous_flow/test/tests/jacobian/chem09.i)
- (modules/porous_flow/test/tests/chemistry/except12.i)
- (modules/porous_flow/test/tests/chemistry/except22.i)
- (modules/porous_flow/test/tests/chemistry/except8.i)
- (modules/porous_flow/test/tests/chemistry/except20.i)
- (modules/porous_flow/test/tests/chemistry/dissolution_limited.i)
- (modules/porous_flow/test/tests/chemistry/except19.i)
- (modules/porous_flow/test/tests/chemistry/except9.i)
- (modules/porous_flow/test/tests/jacobian/chem03.i)
- (modules/porous_flow/test/tests/jacobian/chem01.i)
- (modules/porous_flow/test/tests/chemistry/except15.i)
- (modules/porous_flow/test/tests/chemistry/except11.i)
(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
[]
[]
[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
coupled_variables = 'mineral a'
expression = '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
[]
[]
[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]
time_step_interval = 10
csv = true
perf_graph = true
[]
(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
[]
[]
[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/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/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
[]
[]
[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/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/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/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
coupled_variables = 'mineral a'
expression = '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
[]
[]
[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]
time_step_interval = 10
csv = true
perf_graph = true
[]
(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/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_subdomains = 1
new_sideset_name = 'injection_area'
input = 'aquifer'
[]
[rename]
type = RenameBlockGenerator
old_block = '0 1'
new_block = '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
stabilization = none # Note to reader: try this with other stabilization and compare the results
[]
[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
[]
[]
[FluidProperties]
[the_simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2E9
viscosity = 1.0E-3
density0 = 1000.0
[]
[]
[Materials]
[porosity_mat]
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_mat]
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/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/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
[]
[]
[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/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/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/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/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
[]
[]
[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/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
[]
[]
[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/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
[]
[]
[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/2species_predis.i)
# PorousFlow analogy of chemical_reactions/test/tests/solid_kinetics/2species_without_action.i
#
# Simple equilibrium reaction example to illustrate the use of PorousFlowAqueousPreDisChemistry
#
# In this example, two primary species a and b diffuse towards each other from
# opposite ends of a porous medium, reacting when they meet to form a mineral
# precipitate. The kinetic reaction is
#
# a + b = mineral
#
# where a and b are the primary species (reactants), and mineral is the precipitate.
# At the time of writing, the results of this test differ from chemical_reactions because
# in PorousFlow the mineral_concentration is measured in m^3 (precipitate) / m^3 (porous_material)
# in chemical_reactions the mineral_concentration is measured in m^3 (precipitate) / m^3 (fluid)
# ie, PorousFlow_mineral_concentration = porosity * chemical_reactions_mineral_concentration
[Mesh]
type = GeneratedMesh
dim = 2
xmax = 1
ymax = 1
nx = 40
[]
[Variables]
[a]
order = FIRST
family = LAGRANGE
initial_condition = 0
[]
[b]
order = FIRST
family = LAGRANGE
initial_condition = 0
[]
[]
[AuxVariables]
[eqm_k]
initial_condition = 1E-6
[]
[pressure]
[]
[mineral]
family = MONOMIAL
order = CONSTANT
[]
[]
[AuxKernels]
[mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[]
[]
[GlobalParams]
PorousFlowDictator = dictator
gravity = '0 0 0'
[]
[Kernels]
[mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[]
[diff_a]
type = PorousFlowDispersiveFlux
variable = a
fluid_component = 0
disp_trans = 0
disp_long = 0
[]
[predis_a]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[]
[mass_b]
type = PorousFlowMassTimeDerivative
fluid_component = 1
variable = b
[]
[diff_b]
type = PorousFlowDispersiveFlux
variable = b
fluid_component = 1
disp_trans = 0
disp_long = 0
[]
[predis_b]
type = PorousFlowPreDis
variable = b
mineral_density = 1000
stoichiometry = 1
[]
[]
[UserObjects]
[dictator]
type = PorousFlowDictator
porous_flow_vars = 'a b'
number_fluid_phases = 1
number_fluid_components = 3
number_aqueous_kinetic = 1
[]
[]
[FluidProperties]
[simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[]
[]
[Materials]
[temperature]
type = PorousFlowTemperature
temperature = 298.15
[]
[ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[]
[massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'a b'
[]
[chem]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = 'a b'
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = '1 1'
reactions = '1 1'
specific_reactive_surface_area = '1.0'
kinetic_rate_constant = '1.0e-8'
activation_energy = '1.5e4'
molar_volume = 1
gas_constant = 8.314
reference_temperature = 298.15
[]
[mineral_conc]
type = PorousFlowAqueousPreDisMineral
[]
[simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[]
[porosity]
type = PorousFlowPorosityConst
porosity = 0.4
[]
[permeability]
type = PorousFlowPermeabilityConst
# porous_flow permeability / porous_flow viscosity = chemical_reactions conductivity = 4E-3
permeability = '4E-6 0 0 0 4E-6 0 0 0 4E-6'
[]
[relp]
type = PorousFlowRelativePermeabilityConst
phase = 0
[]
[diff]
type = PorousFlowDiffusivityConst
# porous_flow diffusion_coeff * tortuousity * porosity = chemical_reactions diffusivity = 5E-4
diffusion_coeff = '12.5E-4 12.5E-4 12.5E-4'
tortuosity = 1.0
[]
[]
[BCs]
[a_left]
type = DirichletBC
variable = a
boundary = left
value = 1.0e-2
[]
[a_right]
type = DirichletBC
variable = a
boundary = right
value = 0
[]
[b_left]
type = DirichletBC
variable = b
boundary = left
value = 0
[]
[b_right]
type = DirichletBC
variable = b
boundary = right
value = 1.0e-2
[]
[]
[Preconditioning]
[smp]
type = SMP
full = true
[]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 5
end_time = 50
[]
[Outputs]
print_linear_residuals = true
exodus = true
perf_graph = true
hide = eqm_k
[]
(modules/porous_flow/examples/thm_example/2D_c.i)
# Two phase, temperature-dependent, with mechanics and chemistry, radial with fine mesh, constant injection of cold co2 into a overburden-reservoir-underburden containing mostly water
# species=0 is water
# species=1 is co2
# phase=0 is liquid, and since massfrac_ph0_sp0 = 1, this is all water
# phase=1 is gas, and since massfrac_ph1_sp0 = 0, this is all co2
#
# The mesh used below has very high resolution, so the simulation takes a long time to complete.
# Some suggested meshes of different resolution:
# nx=50, bias_x=1.2
# nx=100, bias_x=1.1
# nx=200, bias_x=1.05
# nx=400, bias_x=1.02
# nx=1000, bias_x=1.01
# nx=2000, bias_x=1.003
[Mesh]
type = GeneratedMesh
dim = 2
nx = 2000
bias_x = 1.003
xmin = 0.1
xmax = 5000
ny = 1
ymin = 0
ymax = 11
[]
[Problem]
coord_type = RZ
[]
[GlobalParams]
displacements = 'disp_r disp_z'
PorousFlowDictator = dictator
gravity = '0 0 0'
biot_coefficient = 1.0
[]
[Variables]
[pwater]
initial_condition = 18.3e6
[]
[sgas]
initial_condition = 0.0
[]
[temp]
initial_condition = 358
[]
[disp_r]
[]
[]
[AuxVariables]
[rate]
[]
[disp_z]
[]
[massfrac_ph0_sp0]
initial_condition = 1 # all H20 in phase=0
[]
[massfrac_ph1_sp0]
initial_condition = 0 # no H2O in phase=1
[]
[pgas]
family = MONOMIAL
order = FIRST
[]
[swater]
family = MONOMIAL
order = FIRST
[]
[stress_rr]
order = CONSTANT
family = MONOMIAL
[]
[stress_tt]
order = CONSTANT
family = MONOMIAL
[]
[stress_zz]
order = CONSTANT
family = MONOMIAL
[]
[mineral_conc_m3_per_m3]
family = MONOMIAL
order = CONSTANT
initial_condition = 0.1
[]
[eqm_const]
initial_condition = 0.0
[]
[porosity]
family = MONOMIAL
order = CONSTANT
[]
[]
[Kernels]
[mass_water_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = pwater
[]
[flux_water]
type = PorousFlowAdvectiveFlux
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[]
[mass_co2_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 1
variable = sgas
[]
[flux_co2]
type = PorousFlowAdvectiveFlux
fluid_component = 1
use_displaced_mesh = false
variable = sgas
[]
[energy_dot]
type = PorousFlowEnergyTimeDerivative
variable = temp
[]
[advection]
type = PorousFlowHeatAdvection
use_displaced_mesh = false
variable = temp
[]
[conduction]
type = PorousFlowExponentialDecay
use_displaced_mesh = false
variable = temp
reference = 358
rate = rate
[]
[grad_stress_r]
type = StressDivergenceRZTensors
temperature = temp
eigenstrain_names = thermal_contribution
variable = disp_r
use_displaced_mesh = false
component = 0
[]
[poro_r]
type = PorousFlowEffectiveStressCoupling
variable = disp_r
use_displaced_mesh = false
component = 0
[]
[]
[AuxKernels]
[rate]
type = FunctionAux
variable = rate
execute_on = timestep_begin
function = decay_rate
[]
[pgas]
type = PorousFlowPropertyAux
property = pressure
phase = 1
variable = pgas
[]
[swater]
type = PorousFlowPropertyAux
property = saturation
phase = 0
variable = swater
[]
[stress_rr]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_rr
index_i = 0
index_j = 0
[]
[stress_tt]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_tt
index_i = 2
index_j = 2
[]
[stress_zz]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_zz
index_i = 1
index_j = 1
[]
[mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral_conc_m3_per_m3
[]
[eqm_const_auxk]
type = ParsedAux
variable = eqm_const
coupled_variables = temp
expression = '(358 - temp) / (358 - 294)'
[]
[porosity_auxk]
type = PorousFlowPropertyAux
property = porosity
variable = porosity
[]
[]
[Functions]
[decay_rate]
# Eqn(26) of the first paper of LaForce et al.
# Ka * (rho C)_a = 10056886.914
# h = 11
type = ParsedFunction
expression = 'sqrt(10056886.914/t)/11.0'
[]
[]
[UserObjects]
[dictator]
type = PorousFlowDictator
porous_flow_vars = 'temp pwater sgas disp_r'
number_fluid_phases = 2
number_fluid_components = 2
number_aqueous_kinetic = 1
aqueous_phase_number = 1
[]
[pc]
type = PorousFlowCapillaryPressureConst
pc = 0
[]
[]
[FluidProperties]
[water]
type = SimpleFluidProperties
bulk_modulus = 2.27e14
density0 = 970.0
viscosity = 0.3394e-3
cv = 4149.0
cp = 4149.0
porepressure_coefficient = 0.0
thermal_expansion = 0
[]
[co2]
type = SimpleFluidProperties
bulk_modulus = 2.27e14
density0 = 516.48
viscosity = 0.0393e-3
cv = 2920.5
cp = 2920.5
porepressure_coefficient = 0.0
thermal_expansion = 0
[]
[]
[Materials]
[temperature]
type = PorousFlowTemperature
temperature = temp
[]
[ppss]
type = PorousFlow2PhasePS
phase0_porepressure = pwater
phase1_saturation = sgas
capillary_pressure = pc
[]
[massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'massfrac_ph0_sp0 massfrac_ph1_sp0'
[]
[water]
type = PorousFlowSingleComponentFluid
fp = water
phase = 0
[]
[gas]
type = PorousFlowSingleComponentFluid
fp = co2
phase = 1
[]
[porosity_reservoir]
type = PorousFlowPorosity
porosity_zero = 0.2
chemical = true
reference_chemistry = 0.1
initial_mineral_concentrations = 0.1
[]
[permeability_reservoir]
type = PorousFlowPermeabilityConst
permeability = '2e-12 0 0 0 0 0 0 0 0'
[]
[relperm_liquid]
type = PorousFlowRelativePermeabilityCorey
n = 4
phase = 0
s_res = 0.200
sum_s_res = 0.405
[]
[relperm_gas]
type = PorousFlowRelativePermeabilityBC
phase = 1
s_res = 0.205
sum_s_res = 0.405
nw_phase = true
lambda = 2
[]
[thermal_conductivity_reservoir]
type = PorousFlowThermalConductivityIdeal
dry_thermal_conductivity = '0 0 0 0 1.320 0 0 0 0'
wet_thermal_conductivity = '0 0 0 0 3.083 0 0 0 0'
[]
[internal_energy_reservoir]
type = PorousFlowMatrixInternalEnergy
specific_heat_capacity = 1100
density = 2350.0
[]
[elasticity_tensor]
type = ComputeIsotropicElasticityTensor
shear_modulus = 6.0E9
poissons_ratio = 0.2
[]
[strain]
type = ComputeAxisymmetricRZSmallStrain
eigenstrain_names = 'thermal_contribution ini_stress'
[]
[ini_strain]
type = ComputeEigenstrainFromInitialStress
initial_stress = '-12.8E6 0 0 0 -51.3E6 0 0 0 -12.8E6'
eigenstrain_name = ini_stress
[]
[thermal_contribution]
type = ComputeThermalExpansionEigenstrain
temperature = temp
stress_free_temperature = 358
thermal_expansion_coeff = 5E-6
eigenstrain_name = thermal_contribution
[]
[stress]
type = ComputeLinearElasticStress
[]
[eff_fluid_pressure]
type = PorousFlowEffectiveFluidPressure
[]
[vol_strain]
type = PorousFlowVolumetricStrain
[]
[predis]
type = PorousFlowAqueousPreDisChemistry
num_reactions = 1
primary_concentrations = 1.0 # fixed activity
equilibrium_constants_as_log10 = true
equilibrium_constants = eqm_const
primary_activity_coefficients = 1.0 # fixed activity
reactions = 1
kinetic_rate_constant = 1E-6
molar_volume = 1.0
specific_reactive_surface_area = 1.0
activation_energy = 0.0 # no Arrhenius
[]
[mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = 0.1
[]
[predis_nodes]
type = PorousFlowAqueousPreDisChemistry
at_nodes = true
num_reactions = 1
primary_concentrations = 1.0 # fixed activity
equilibrium_constants_as_log10 = true
equilibrium_constants = eqm_const
primary_activity_coefficients = 1.0 # fixed activity
reactions = 1
kinetic_rate_constant = 1E-6
molar_volume = 1.0
specific_reactive_surface_area = 1.0
activation_energy = 0.0 # no Arrhenius
[]
[mineral_conc_nodes]
type = PorousFlowAqueousPreDisMineral
at_nodes = true
initial_concentrations = 0.1
[]
[]
[BCs]
[outer_pressure_fixed]
type = DirichletBC
boundary = right
value = 18.3e6
variable = pwater
[]
[outer_saturation_fixed]
type = DirichletBC
boundary = right
value = 0.0
variable = sgas
[]
[outer_temp_fixed]
type = DirichletBC
boundary = right
value = 358
variable = temp
[]
[fixed_outer_r]
type = DirichletBC
variable = disp_r
value = 0
boundary = right
[]
[co2_injection]
type = PorousFlowSink
boundary = left
variable = sgas
use_mobility = false
use_relperm = false
fluid_phase = 1
flux_function = 'min(t/100.0,1)*(-2.294001475)' # 5.0E5 T/year = 15.855 kg/s, over area of 2Pi*0.1*11
[]
[cold_co2]
type = DirichletBC
boundary = left
variable = temp
value = 294
[]
[cavity_pressure_x]
type = Pressure
boundary = left
variable = disp_r
component = 0
postprocessor = p_bh # note, this lags
use_displaced_mesh = false
[]
[]
[Postprocessors]
[p_bh]
type = PointValue
variable = pwater
point = '0.1 0 0'
execute_on = timestep_begin
use_displaced_mesh = false
[]
[mineral_bh] # mineral concentration (m^3(mineral)/m^3(rock)) at the borehole
type = PointValue
variable = mineral_conc_m3_per_m3
point = '0.1 0 0'
use_displaced_mesh = false
[]
[]
[VectorPostprocessors]
[ptsuss]
type = LineValueSampler
use_displaced_mesh = false
start_point = '0.1 0 0'
end_point = '5000 0 0'
sort_by = x
num_points = 50000
outputs = csv
variable = 'pwater temp sgas disp_r stress_rr stress_tt mineral_conc_m3_per_m3 porosity'
[]
[]
[Preconditioning]
active = 'smp'
[smp]
type = SMP
full = true
#petsc_options = '-snes_converged_reason -ksp_diagonal_scale -ksp_diagonal_scale_fix -ksp_gmres_modifiedgramschmidt -snes_linesearch_monitor'
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu NONZERO 2 1E2 1E-5 50'
[]
[mumps]
type = SMP
full = true
petsc_options = '-snes_converged_reason -ksp_diagonal_scale -ksp_diagonal_scale_fix -ksp_gmres_modifiedgramschmidt -snes_linesearch_monitor'
petsc_options_iname = '-ksp_type -pc_type -pc_factor_mat_solver_package -pc_factor_shift_type -snes_rtol -snes_atol -snes_max_it'
petsc_options_value = 'gmres lu mumps NONZERO 1E-5 1E2 50'
[]
[]
[Executioner]
type = Transient
solve_type = NEWTON
end_time = 1.5768e8
#dtmax = 1e6
[TimeStepper]
type = IterationAdaptiveDT
dt = 1
growth_factor = 1.1
[]
[]
[Outputs]
print_linear_residuals = false
sync_times = '3600 86400 2.592E6 1.5768E8'
perf_graph = true
exodus = true
[csv]
type = CSV
sync_only = 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
coupled_variables = 'mineral a'
expression = '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
[]
[]
[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]
time_step_interval = 10
csv = true
perf_graph = true
[]
(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
coupled_variables = 'mineral a'
expression = '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
[]
[]
[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]
time_step_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
[]
[]
[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/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/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/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/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
[]
[]
[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/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
[]
[]
[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/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
[]
[]
[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/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
[]
[]
[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/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
coupled_variables = 'mineral a'
expression = '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
[]
[]
[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]
time_step_interval = 10
csv = true
perf_graph = true
[]
(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
[]
[]
[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/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
[]
[]
[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/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/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/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
[]
[]
[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/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
[]
[]
[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
[]