- intrinsic_rate_constantThe intrinsic rate constant for the reaction
C++ Type:double
Description:The intrinsic rate constant for the reaction
- kinetic_species_nameThe name of the kinetic species that will be controlled by this rate
C++ Type:std::string
Description:The name of the kinetic species that will be controlled by this rate
GeochemistryKineticRate
Defines a kinetic rate for a kinetic species. The general form of this rate is This is a rather complicated equation, and simple examples are given below. In this equation:
(units: mol.s) is the rate of the kinetic reaction. If it is positive then the kinetic species' mass will be decreasing (eg, dissolution). If it is negative then the kinetic species' mass will be increasing (eg, precipitation).
is the intrinsic rate constant. The product has units mol.s (assuming the simulation's time units are seconds). Note that mole units are used, even if the initial amount of the kinetic species is given in mass or volume units. Examples of are given below.
is either the surface area (units: m) for the kinetic species, or the specific surface area (units: m.g)
(units: g) is the mass of the kinetic species. It is optional. Examples are given below.
is a label denoting a promoting species
is either: mass of solvent water (in kg) if the promoting species is HO; fugacity of a gas if the promoting species is a gas; activity if the promoting species is either H or OH; mobility, otherwise.
is a dimensionless power
is the activity product defined by the kinetic species' reaction in the database file
is the reaction's equilibrium constant defined in the database file
and are dimensionless exponents
(units: J.mol) is the activation energy
J.K.mol is the gas constant
(units: K) is a reference temperature
(units: K) is the temperature
is -1 if (kinetic species mass will increase with time), 1 if (kinetic species mass will decrease with time).
commentnote
Note that more than one GeochemistryKineticRate can be prescribed to a single kinetic species. The sum of all the individual rates defines the overall rate for each species (see Example 6). Simply supply your GeochemicalModelDefinition with a list of all the rates.
Example 1
Suppose that the kinetic rate is just a constant: for both the forward and backward reactions (ie, for precipitation and dissolution). Then set:
to the constant value, with units mol.s (assuming the simulation time is measured in seconds)
and
multiply_by_mass = falsedo not use any
promoting_species_namesorpromoting_species_indicesset and
set .
Example 2
Suppose that the kinetic rate for a certain mineral is proportional the mineral's surface area and that the surface area is known and fixed. Then set:
to the coefficient of proportionality, with units mol.m.s (assuming the simulation time is measured in seconds)
to the known mineral surface area, with units m
multiply_by_mass = falsedo not use any
promoting_species_namesorpromoting_species_indicesset and
set .
Example 3
Suppose that the kinetic rate for a certain mineral is proportional the mineral's free mass Then set
to the coefficient of proportionality, with units mol.g.s (assuming the simulation time is measured in seconds)
multiply_by_mass = true. MOOSE will automatically calculate the mineral's free mass depending on its molar mass and the number of free moles.do not use any
promoting_species_namesorpromoting_species_indicesset and
set .
Example 4
Suppose that the kinetic rate for a certain mineral is proportional the mineral surface area but that the surface area itself isn't known. Only the mineral's specific surface area (surface area per gram of free mineral m.g) is known. Then set
to the coefficient of proportionality, with units mol.m.s (assuming the simulation time is measured in seconds)
to be the mineral specific surface area, with units m.g.
multiply_by_mass = true. MOOSE will automatically calculate the mineral's free mass depending on its molar mass and the number of free moles.do not use any
promoting_species_namesorpromoting_species_indicesset and
set .
Example 5
Suppose that the kinetic rate for a certain redox couple is proportional the quantity of solvent water present: Then set
to the coefficient of proportionality, with units mol.kg.s (assuming the simulation time is measured in seconds)
and
multiply_by_mass = false.promoting_species_names = H2Oandpromoting_species_indices = 1set and
set .
Example 6
Suppose that the kinetic rate for a certain redox couple depends on the pH: For this, two GeochemistryKineticRate UserObjects must be created. Each has , multiply_by_mass = false, , and .
The first has ,
promoting_species_names = H+andpromoting_species_indices = 1.The second has ,
promoting_species_names = OH-andpromoting_species_indices = 1.5.
These are then supplied to the GeochemicalModelDefinition using its kinetic_rate_descriptions input.
Example 7
Suppose that the kinetic rate for a certain redox couple depends on the pH, the molality of Ca and the temperature: Then set
and
multiply_by_mass = falsepromoting_species_names = "H+ Ca++" and and promoting_species_indices = "1.5 0.3"
one_over_T0 = 0
Input Parameters
- activation_energy0Activation energy, in J.mol^-1, which appears in exp(activation_energy / R * (1/T0 - 1/T))
Default:0
C++ Type:double
Options:
Description:Activation energy, in J.mol^-1, which appears in exp(activation_energy / R * (1/T0 - 1/T))
- area_quantity1The surface area of the kinetic species in m^2 (if multiply_by_mass = false) or the specific surface area of the kinetic species in m^2/g (if multiply_by_mass = true)
Default:1
C++ Type:double
Options:
Description:The surface area of the kinetic species in m^2 (if multiply_by_mass = false) or the specific surface area of the kinetic species in m^2/g (if multiply_by_mass = true)
- eta1Eta parameter, which appears in |1 - (Q/K)^theta|^eta
Default:1
C++ Type:double
Options:
Description:Eta parameter, which appears in |1 - (Q/K)^theta|^eta
- execute_onTIMESTEP_ENDThe list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM.
Default:TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM
Description:The list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM.
- multiply_by_massFalseWhether the rate should be multiplied by the kinetic species mass
Default:False
C++ Type:bool
Options:
Description:Whether the rate should be multiplied by the kinetic species mass
- one_over_T001/T0, in 1/Kelvin, which appears in exp(activation_energy / R * (1/T0 - 1/T))
Default:0
C++ Type:double
Options:
Description:1/T0, in 1/Kelvin, which appears in exp(activation_energy / R * (1/T0 - 1/T))
- promoting_species_indicesIndices of the promoting species
C++ Type:std::vector<double>
Options:
Description:Indices of the promoting species
- promoting_species_namesNames of any promoting species
C++ Type:std::vector<std::string>
Options:
Description:Names of any promoting species
- theta1Theta parameter, which appears in |1 - (Q/K)^theta|^eta
Default:1
C++ Type:double
Options:
Description:Theta parameter, which appears in |1 - (Q/K)^theta|^eta
Optional Parameters
- allow_duplicate_execution_on_initialFalseIn the case where this UserObject is depended upon by an initial condition, allow it to be executed twice during the initial setup (once before the IC and again after mesh adaptivity (if applicable).
Default:False
C++ Type:bool
Options:
Description:In the case where this UserObject is depended upon by an initial condition, allow it to be executed twice during the initial setup (once before the IC and again after mesh adaptivity (if applicable).
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
- force_preauxFalseForces the GeneralUserObject to be executed in PREAUX
Default:False
C++ Type:bool
Options:
Description:Forces the GeneralUserObject to be executed in PREAUX
- force_preicFalseForces the GeneralUserObject to be executed in PREIC during initial setup
Default:False
C++ Type:bool
Options:
Description:Forces the GeneralUserObject to be executed in PREIC during initial setup
- use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Options:
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Advanced Parameters
Input Files
- (modules/combined/examples/geochem-porous_flow/forge/aquifer_geochemistry.i)
- (modules/combined/examples/geochem-porous_flow/forge/kinetic.i)
- (modules/geochemistry/test/tests/kinetics/quartz_deposition.i)
- (modules/geochemistry/test/tests/geochemistry_quantity_aux/kinetic_rate.i)
- (modules/geochemistry/test/tests/time_dependent_reactions/flushing_case2.i)
- (modules/geochemistry/test/tests/time_dependent_reactions/flushing_case1.i)
- (modules/geochemistry/test/tests/time_dependent_reactions/flushing_case3.i)
- (modules/geochemistry/test/tests/time_dependent_reactions/flushing.i)
- (modules/combined/examples/geochem-porous_flow/forge/reservoir_and_water_3.i)
- (modules/geochemistry/test/tests/kinetics/quartz_dissolution.i)
- (modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_geochemistry.i)
- (modules/combined/examples/geochem-porous_flow/forge/natural_reservoir.i)
- (modules/geochemistry/test/tests/kinetics/kinetic_albite.i)
- (modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_un_quartz_geochemistry.i)
(modules/combined/examples/geochem-porous_flow/forge/aquifer_geochemistry.i)
# Simulates geochemistry in the aquifer. This input file may be run in standalone fashion, which will study the natural kinetically-controlled mineral changes in the same way as natural_reservoir.i. To simulate the FORGE injection scenario, run the porous_flow.i simulation which couples to this input file using MultiApps.
# This file receives pf_rate_H pf_rate_Na pf_rate_K pf_rate_Ca pf_rate_Mg pf_rate_SiO2 pf_rate_Al pf_rate_Cl pf_rate_SO4 pf_rate_HCO3 pf_rate_H2O and temperature as AuxVariables from porous_flow.i
# The pf_rate quantities are kg/s changes of fluid-component mass at each node, but the geochemistry module expects rates-of-changes of moles at every node. Secondly, since this input file considers just 1 litre of aqueous solution at every node, the nodal_void_volume is used to convert pf_rate_* into rate_*_per_1l, which is measured in mol/s/1_litre_of_aqueous_solution.
# This file sends massfrac_H massfrac_Na massfrac_K massfrac_Ca massfrac_Mg massfrac_SiO2 massfrac_Al massfrac_Cl massfrac_SO4 massfrac_HCO3 to porous_flow.i. These are computed from the corresponding transported_* quantities.
# The results depend on the kinetic rates used and these are recognised to be poorly constrained by experiment
[UserObjects]
[rate_Albite]
type = GeochemistryKineticRate
kinetic_species_name = Albite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 69.8E3
one_over_T0 = 0.003354
[]
[rate_Anhydrite]
type = GeochemistryKineticRate
kinetic_species_name = Anhydrite
intrinsic_rate_constant = 1.0E-7
multiply_by_mass = true
area_quantity = 10
activation_energy = 14.3E3
one_over_T0 = 0.003354
[]
[rate_Anorthite]
type = GeochemistryKineticRate
kinetic_species_name = Anorthite
intrinsic_rate_constant = 1.0E-13
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Calcite]
type = GeochemistryKineticRate
kinetic_species_name = Calcite
intrinsic_rate_constant = 1.0E-10
multiply_by_mass = true
area_quantity = 10
activation_energy = 23.5E3
one_over_T0 = 0.003354
[]
[rate_Chalcedony]
type = GeochemistryKineticRate
kinetic_species_name = Chalcedony
intrinsic_rate_constant = 1.0E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Clinochl-7A]
type = GeochemistryKineticRate
kinetic_species_name = Clinochl-7A
intrinsic_rate_constant = 1.0E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 88.0E3
one_over_T0 = 0.003354
[]
[rate_Illite]
type = GeochemistryKineticRate
kinetic_species_name = Illite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 29E3
one_over_T0 = 0.003354
[]
[rate_K-feldspar]
type = GeochemistryKineticRate
kinetic_species_name = K-feldspar
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 38E3
one_over_T0 = 0.003354
[]
[rate_Kaolinite]
type = GeochemistryKineticRate
kinetic_species_name = Kaolinite
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 22.2E3
one_over_T0 = 0.003354
[]
[rate_Quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Paragonite]
type = GeochemistryKineticRate
kinetic_species_name = Paragonite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Phlogopite]
type = GeochemistryKineticRate
kinetic_species_name = Phlogopite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Laumontite]
type = GeochemistryKineticRate
kinetic_species_name = Laumontite
intrinsic_rate_constant = 1.0E-15
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Zoisite]
type = GeochemistryKineticRate
kinetic_species_name = Zoisite
intrinsic_rate_constant = 1E-16
multiply_by_mass = true
area_quantity = 10
activation_energy = 66.1E3
one_over_T0 = 0.003354
[]
[definition]
type = GeochemicalModelDefinition
database_file = '../../../../geochemistry/database/moose_geochemdb.json'
basis_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
remove_all_extrapolated_secondary_species = true
kinetic_minerals = 'Albite Anhydrite Anorthite Calcite Chalcedony Clinochl-7A Illite K-feldspar Kaolinite Quartz Paragonite Phlogopite Zoisite Laumontite'
kinetic_rate_descriptions = 'rate_Albite rate_Anhydrite rate_Anorthite rate_Calcite rate_Chalcedony rate_Clinochl-7A rate_Illite rate_K-feldspar rate_Kaolinite rate_Quartz rate_Paragonite rate_Phlogopite rate_Zoisite rate_Laumontite'
[]
[nodal_void_volume_uo]
type = NodalVoidVolume
porosity = porosity
execute_on = 'initial timestep_end' # "initial" means this is evaluated properly for the first timestep
[]
[]
[SpatialReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = 'Cl-'
constraint_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
# Following numbers are from water_60_to_220degC_out.csv
constraint_value = ' 1.0006383866109 9.5165072498215e-07 0.100020379171 0.0059389061065 0.011570884507621 4.6626763057447e-06 0.0045110404925255 5.8096968688789e-17 0.13500708594394 6.6523540147676e-05 7.7361407898089e-05'
constraint_meaning = 'kg_solvent_water free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration bulk_composition free_concentration free_concentration'
constraint_unit = ' kg molal molal molal molal molal molal molal moles molal molal'
initial_temperature = 220
temperature = temperature
kinetic_species_name = ' Albite Anorthite K-feldspar Quartz Phlogopite Paragonite Calcite Anhydrite Chalcedony Illite Kaolinite Clinochl-7A Zoisite Laumontite'
kinetic_species_initial_value = '4.324073236492E+02 4.631370307325E+01 2.685015418378E+02 7.720095013956E+02 1.235192062541E+01 7.545461404965E-01 4.234651808835E-04 4.000485907930E-04 4.407616361072E+00 1.342524904876E+01 1.004823151125E+00 4.728132387707E-01 7.326007326007E-01 4.818116116598E-01'
kinetic_species_unit = ' moles moles moles moles moles moles moles moles moles moles moles moles moles moles'
evaluate_kinetic_rates_always = true # otherwise will easily "run out" of dissolving species
source_species_names = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
source_species_rates = 'rate_H2O_per_1l rate_H_per_1l rate_Na_per_1l rate_K_per_1l rate_Ca_per_1l rate_Mg_per_1l rate_SiO2_per_1l rate_Al_per_1l rate_Cl_per_1l rate_SO4_per_1l rate_HCO3_per_1l'
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
execute_console_output_on = ''
add_aux_molal = false # save some memory and reduce variables in output exodus
add_aux_mg_per_kg = false # save some memory and reduce variables in output exodus
add_aux_free_mg = false # save some memory and reduce variables in output exodus
add_aux_activity = false # save some memory and reduce variables in output exodus
add_aux_bulk_moles = false # save some memory and reduce variables in output exodus
adaptive_timestepping = true
[]
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 15
ny = 10
xmin = -100
xmax = 200
ymin = -100
ymax = 100
[]
[injection_node]
input = gen
type = ExtraNodesetGenerator
new_boundary = injection_node
coord = '0 0 0'
[]
[]
[Executioner]
type = Transient
[TimeStepper]
type = FunctionDT
function = 'max(1E6, 0.3 * t)'
[]
end_time = 4E12
[]
[AuxVariables]
[temperature]
initial_condition = 220.0
[]
[porosity]
initial_condition = 0.01
[]
[nodal_void_volume]
[]
[free_cm3_Kfeldspar] # necessary because of the minus sign in K-feldspar which does not parse correctly in the porosity AuxKernel
[]
[free_cm3_Clinochl7A] # necessary because of the minus sign in Clinochl-7A which does not parse correctly in the porosity AuxKernel
[]
[pf_rate_H] # change in H mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_Na]
[]
[pf_rate_K]
[]
[pf_rate_Ca]
[]
[pf_rate_Mg]
[]
[pf_rate_SiO2]
[]
[pf_rate_Al]
[]
[pf_rate_Cl]
[]
[pf_rate_SO4]
[]
[pf_rate_HCO3]
[]
[pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[rate_H_per_1l]
[]
[rate_Na_per_1l]
[]
[rate_K_per_1l]
[]
[rate_Ca_per_1l]
[]
[rate_Mg_per_1l]
[]
[rate_SiO2_per_1l]
[]
[rate_Al_per_1l]
[]
[rate_Cl_per_1l]
[]
[rate_SO4_per_1l]
[]
[rate_HCO3_per_1l]
[]
[rate_H2O_per_1l]
[]
[transported_H]
[]
[transported_Na]
[]
[transported_K]
[]
[transported_Ca]
[]
[transported_Mg]
[]
[transported_SiO2]
[]
[transported_Al]
[]
[transported_Cl]
[]
[transported_SO4]
[]
[transported_HCO3]
[]
[transported_H2O]
[]
[transported_mass]
[]
[massfrac_H]
[]
[massfrac_Na]
[]
[massfrac_K]
[]
[massfrac_Ca]
[]
[massfrac_Mg]
[]
[massfrac_SiO2]
[]
[massfrac_Al]
[]
[massfrac_Cl]
[]
[massfrac_SO4]
[]
[massfrac_HCO3]
[]
[massfrac_H2O]
[]
[]
[AuxKernels]
[free_cm3_Kfeldspar]
type = GeochemistryQuantityAux
variable = free_cm3_Kfeldspar
species = 'K-feldspar'
quantity = free_cm3
execute_on = 'timestep_begin timestep_end'
[]
[free_cm3_Clinochl7A]
type = GeochemistryQuantityAux
variable = free_cm3_Clinochl7A
species = 'Clinochl-7A'
quantity = free_cm3
execute_on = 'timestep_begin timestep_end'
[]
[porosity_auxk]
type = ParsedAux
args = 'free_cm3_Albite free_cm3_Anhydrite free_cm3_Anorthite free_cm3_Calcite free_cm3_Chalcedony free_cm3_Clinochl7A free_cm3_Illite free_cm3_Kfeldspar free_cm3_Kaolinite free_cm3_Quartz free_cm3_Paragonite free_cm3_Phlogopite free_cm3_Zoisite free_cm3_Laumontite'
function = '1000.0 / (1000.0 + free_cm3_Albite + free_cm3_Anhydrite + free_cm3_Anorthite + free_cm3_Calcite + free_cm3_Chalcedony + free_cm3_Clinochl7A + free_cm3_Illite + free_cm3_Kfeldspar + free_cm3_Kaolinite + free_cm3_Quartz + free_cm3_Paragonite + free_cm3_Phlogopite + free_cm3_Zoisite + free_cm3_Laumontite)'
variable = porosity
execute_on = 'timestep_end'
[]
[nodal_void_volume_auxk]
type = NodalVoidVolumeAux
variable = nodal_void_volume
nodal_void_volume_uo = nodal_void_volume_uo
execute_on = 'initial timestep_end' # "initial" to ensure it is properly evaluated for the first timestep
[]
[rate_H_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_H nodal_void_volume'
variable = rate_H_per_1l
function = 'pf_rate_H / 1.0079 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Na_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_Na nodal_void_volume'
variable = rate_Na_per_1l
function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_K_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_K nodal_void_volume'
variable = rate_K_per_1l
function = 'pf_rate_K / 39.0983 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Ca_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_Ca nodal_void_volume'
variable = rate_Ca_per_1l
function = 'pf_rate_Ca / 40.08 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Mg_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_Mg nodal_void_volume'
variable = rate_Mg_per_1l
function = 'pf_rate_Mg / 24.305 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_SiO2_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_SiO2 nodal_void_volume'
variable = rate_SiO2_per_1l
function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Al_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_Al nodal_void_volume'
variable = rate_Al_per_1l
function = 'pf_rate_Al / 26.9815 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Cl_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_Cl nodal_void_volume'
variable = rate_Cl_per_1l
function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_SO4_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_SO4 nodal_void_volume'
variable = rate_SO4_per_1l
function = 'pf_rate_SO4 / 96.0576 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_HCO3_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_HCO3 nodal_void_volume'
variable = rate_HCO3_per_1l
function = 'pf_rate_HCO3 / 61.0171 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_H2O_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_H2O nodal_void_volume'
variable = rate_H2O_per_1l
function = 'pf_rate_H2O / 18.01801802 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[transported_H_auxk]
type = GeochemistryQuantityAux
variable = transported_H
species = 'H+'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_Na_auxk]
type = GeochemistryQuantityAux
variable = transported_Na
species = 'Na+'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_K_auxk]
type = GeochemistryQuantityAux
variable = transported_K
species = 'K+'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_Ca_auxk]
type = GeochemistryQuantityAux
variable = transported_Ca
species = 'Ca++'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_Mg_auxk]
type = GeochemistryQuantityAux
variable = transported_Mg
species = 'Mg++'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_SiO2_auxk]
type = GeochemistryQuantityAux
variable = transported_SiO2
species = 'SiO2(aq)'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_Al_auxk]
type = GeochemistryQuantityAux
variable = transported_Al
species = 'Al+++'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_Cl_auxk]
type = GeochemistryQuantityAux
variable = transported_Cl
species = 'Cl-'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_SO4_auxk]
type = GeochemistryQuantityAux
variable = transported_SO4
species = 'SO4--'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_HCO3_auxk]
type = GeochemistryQuantityAux
variable = transported_HCO3
species = 'HCO3-'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_H2O_auxk]
type = GeochemistryQuantityAux
variable = transported_H2O
species = 'H2O'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_begin'
[]
[transported_mass_auxk]
type = ParsedAux
args = ' transported_H transported_Na transported_K transported_Ca transported_Mg transported_SiO2 transported_Al transported_Cl transported_SO4 transported_HCO3 transported_H2O'
variable = transported_mass
function = 'transported_H * 1.0079 + transported_Cl * 35.453 + transported_SO4 * 96.0576 + transported_HCO3 * 61.0171 + transported_SiO2 * 60.0843 + transported_Al * 26.9815 + transported_Ca * 40.08 + transported_Mg * 24.305 + transported_K * 39.0983 + transported_Na * 22.9898 + transported_H2O * 18.01801802'
execute_on = 'timestep_end'
[]
[massfrac_H_auxk]
type = ParsedAux
args = 'transported_H transported_mass'
variable = massfrac_H
function = 'transported_H * 1.0079 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Na_auxk]
type = ParsedAux
args = 'transported_Na transported_mass'
variable = massfrac_Na
function = 'transported_Na * 22.9898 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_K_auxk]
type = ParsedAux
args = 'transported_K transported_mass'
variable = massfrac_K
function = 'transported_K * 39.0983 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Ca_auxk]
type = ParsedAux
args = 'transported_Ca transported_mass'
variable = massfrac_Ca
function = 'transported_Ca * 40.08 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Mg_auxk]
type = ParsedAux
args = 'transported_Mg transported_mass'
variable = massfrac_Mg
function = 'transported_Mg * 24.305 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_SiO2_auxk]
type = ParsedAux
args = 'transported_SiO2 transported_mass'
variable = massfrac_SiO2
function = 'transported_SiO2 * 60.0843 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Al_auxk]
type = ParsedAux
args = 'transported_Al transported_mass'
variable = massfrac_Al
function = 'transported_Al * 26.9815 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Cl_auxk]
type = ParsedAux
args = 'transported_Cl transported_mass'
variable = massfrac_Cl
function = 'transported_Cl * 35.453 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_SO4_auxk]
type = ParsedAux
args = 'transported_SO4 transported_mass'
variable = massfrac_SO4
function = 'transported_SO4 * 96.0576 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_HCO3_auxk]
type = ParsedAux
args = 'transported_HCO3 transported_mass'
variable = massfrac_HCO3
function = 'transported_HCO3 * 61.0171 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_H2O_auxk]
type = ParsedAux
args = 'transported_H2O transported_mass'
variable = massfrac_H2O
function = 'transported_H2O * 18.01801802 / transported_mass'
execute_on = 'timestep_end'
[]
[]
[GlobalParams]
point = '0 0 0'
reactor = reactor
[]
[Postprocessors]
[temperature]
type = PointValue
variable = 'solution_temperature'
[]
[porosity]
type = PointValue
variable = porosity
[]
[solution_temperature]
type = PointValue
variable = solution_temperature
[]
[massfrac_H]
type = PointValue
variable = massfrac_H
[]
[massfrac_Na]
type = PointValue
variable = massfrac_Na
[]
[massfrac_K]
type = PointValue
variable = massfrac_K
[]
[massfrac_Ca]
type = PointValue
variable = massfrac_Ca
[]
[massfrac_Mg]
type = PointValue
variable = massfrac_Mg
[]
[massfrac_SiO2]
type = PointValue
variable = massfrac_SiO2
[]
[massfrac_Al]
type = PointValue
variable = massfrac_Al
[]
[massfrac_Cl]
type = PointValue
variable = massfrac_Cl
[]
[massfrac_SO4]
type = PointValue
variable = massfrac_SO4
[]
[massfrac_HCO3]
type = PointValue
variable = massfrac_HCO3
[]
[massfrac_H2O]
type = PointValue
variable = massfrac_H2O
[]
[cm3_Albite]
type = PointValue
variable = 'free_cm3_Albite'
[]
[cm3_Anhydrite]
type = PointValue
variable = 'free_cm3_Anhydrite'
[]
[cm3_Anorthite]
type = PointValue
variable = 'free_cm3_Anorthite'
[]
[cm3_Calcite]
type = PointValue
variable = 'free_cm3_Calcite'
[]
[cm3_Chalcedony]
type = PointValue
variable = 'free_cm3_Chalcedony'
[]
[cm3_Clinochl-7A]
type = PointValue
variable = 'free_cm3_Clinochl-7A'
[]
[cm3_Illite]
type = PointValue
variable = 'free_cm3_Illite'
[]
[cm3_K-feldspar]
type = PointValue
variable = 'free_cm3_K-feldspar'
[]
[cm3_Kaolinite]
type = PointValue
variable = 'free_cm3_Kaolinite'
[]
[cm3_Quartz]
type = PointValue
variable = 'free_cm3_Quartz'
[]
[cm3_Paragonite]
type = PointValue
variable = 'free_cm3_Paragonite'
[]
[cm3_Phlogopite]
type = PointValue
variable = 'free_cm3_Phlogopite'
[]
[cm3_Zoisite]
type = PointValue
variable = 'free_cm3_Zoisite'
[]
[cm3_Laumontite]
type = PointValue
variable = 'free_cm3_Laumontite'
[]
[cm3_mineral]
type = LinearCombinationPostprocessor
pp_names = 'cm3_Albite cm3_Anhydrite cm3_Anorthite cm3_Calcite cm3_Chalcedony cm3_Clinochl-7A cm3_Illite cm3_K-feldspar cm3_Kaolinite cm3_Quartz cm3_Paragonite cm3_Phlogopite cm3_Zoisite cm3_Laumontite'
pp_coefs = '1 1 1 1 1 1 1 1 1 1 1 1 1 1'
[]
[pH]
type = PointValue
variable = 'pH'
[]
[]
[Outputs]
[exo]
type = Exodus
execute_on = final
[]
csv = true
[]
(modules/combined/examples/geochem-porous_flow/forge/kinetic.i)
# Simulation to check that the output of water_60_to_220degC is indeed at equilibrium with the mineral assemblage.
# The initial mole numbers of the kinetic species are unimportant for this simulation, but are chosen to be consistent with other input files. The numerical values are such that:
# - the mass fractions are: Albite 0.44; Anorthite 0.05; K-feldspar 0.29; Quartz 0.18, Phlgoptite 0.04 with trace amounts of Calcite and Anhydrite. These are similar to that measured in bulk X-ray diffraction results of 10 samples from well 58-32, assuming that "plagioclase feldspar" consists of Albite and Anorthite in the ratio 9:1, and that Biotite is Phlogoptite, and the 2% Illite is added to Phlogoptite. Precisely:
# - it is assumed that water_60_to_220degC consists of 1 litre of water (there is 1kg of solvent water) and that the porosity is 0.01, so the amount of rock should be 99000cm^3
# - the cm^3 of the trace minerals Calcite and Anhydrite is exactly given by water_60_to_220degC (0.016 and 0.018 respectively)
# - the total mineral volume is 99000cm^3, so that the porosity is 0.01
# - see initial_kinetic_moles.xlsx for the remaining mole numbers
[UserObjects]
[rate_Albite]
type = GeochemistryKineticRate
kinetic_species_name = Albite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 69.8E3
one_over_T0 = 0.003354
[]
[rate_Anhydrite]
type = GeochemistryKineticRate
kinetic_species_name = Anhydrite
intrinsic_rate_constant = 1.0E-7
multiply_by_mass = true
area_quantity = 10
activation_energy = 14.3E3
one_over_T0 = 0.003354
[]
[rate_Anorthite]
type = GeochemistryKineticRate
kinetic_species_name = Anorthite
intrinsic_rate_constant = 1.0E-13
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Calcite]
type = GeochemistryKineticRate
kinetic_species_name = Calcite
intrinsic_rate_constant = 1.0E-10
multiply_by_mass = true
area_quantity = 10
activation_energy = 23.5E3
one_over_T0 = 0.003354
[]
[rate_Chalcedony]
type = GeochemistryKineticRate
kinetic_species_name = Chalcedony
intrinsic_rate_constant = 1.0E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Clinochl-7A]
type = GeochemistryKineticRate
kinetic_species_name = Clinochl-7A
intrinsic_rate_constant = 1.0E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 88.0E3
one_over_T0 = 0.003354
[]
[rate_Illite]
type = GeochemistryKineticRate
kinetic_species_name = Illite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 29E3
one_over_T0 = 0.003354
[]
[rate_K-feldspar]
type = GeochemistryKineticRate
kinetic_species_name = K-feldspar
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 38E3
one_over_T0 = 0.003354
[]
[rate_Kaolinite]
type = GeochemistryKineticRate
kinetic_species_name = Kaolinite
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 22.2E3
one_over_T0 = 0.003354
[]
[rate_Quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Paragonite]
type = GeochemistryKineticRate
kinetic_species_name = Paragonite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Phlogopite]
type = GeochemistryKineticRate
kinetic_species_name = Phlogopite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Zoisite]
type = GeochemistryKineticRate
kinetic_species_name = Zoisite
intrinsic_rate_constant = 1E-16
multiply_by_mass = true
area_quantity = 10
activation_energy = 66.1E3
one_over_T0 = 0.003354
[]
[definition]
type = GeochemicalModelDefinition
database_file = '../../../../geochemistry/database/moose_geochemdb.json'
basis_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
remove_all_extrapolated_secondary_species = true
kinetic_minerals = 'Albite Anhydrite Anorthite Calcite Chalcedony Clinochl-7A Illite K-feldspar Kaolinite Quartz Paragonite Phlogopite'
kinetic_rate_descriptions = 'rate_Albite rate_Anhydrite rate_Anorthite rate_Calcite rate_Chalcedony rate_Clinochl-7A rate_Illite rate_K-feldspar rate_Kaolinite rate_Quartz rate_Paragonite rate_Phlogopite'
[]
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = 'Cl-'
constraint_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
# Following numbers are from water_60_to_220degC_out.csv
constraint_value = ' 1.0006383866109 9.5165072498215e-07 0.100020379171 0.0059389061065 0.011570884507621 4.6626763057447e-06 0.0045110404925255 5.8096968688789e-17 0.13500708594394 6.6523540147676e-05 7.7361407898089e-05'
constraint_meaning = 'kg_solvent_water free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration bulk_composition free_concentration free_concentration'
constraint_unit = ' kg molal molal molal molal molal molal molal moles molal molal'
initial_temperature = 220
temperature = 220
kinetic_species_name = ' Albite Anorthite K-feldspar Quartz Phlogopite Paragonite Calcite Anhydrite Chalcedony Illite Kaolinite Clinochl-7A'
kinetic_species_initial_value = '4.3511787009E+02 4.660402064E+01 2.701846444E+02 7.7684884497E+02 2.4858697344E+01 1E-10 0.000423465 0.000400049 1E-10 1E-10 1E-10 1E-10'
kinetic_species_unit = ' moles moles moles moles moles moles moles moles moles moles moles moles'
evaluate_kinetic_rates_always = true # otherwise will easily "run out" of dissolving species
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
mol_cutoff = 0.1
execute_console_output_on = ''
[]
[Executioner]
type = Transient
[TimeStepper]
type = FunctionDT
function = '1E8'
[]
end_time = 4E8
[]
[GlobalParams]
point = '0 0 0'
[]
[Postprocessors]
[cm3_Albite]
type = PointValue
variable = 'free_cm3_Albite'
[]
[cm3_Anhydrite]
type = PointValue
variable = 'free_cm3_Anhydrite'
[]
[cm3_Anorthite]
type = PointValue
variable = 'free_cm3_Anorthite'
[]
[cm3_Calcite]
type = PointValue
variable = 'free_cm3_Calcite'
[]
[cm3_Chalcedony]
type = PointValue
variable = 'free_cm3_Chalcedony'
[]
[cm3_Clinochl-7A]
type = PointValue
variable = 'free_cm3_Clinochl-7A'
[]
[cm3_Illite]
type = PointValue
variable = 'free_cm3_Illite'
[]
[cm3_K-feldspar]
type = PointValue
variable = 'free_cm3_K-feldspar'
[]
[cm3_Kaolinite]
type = PointValue
variable = 'free_cm3_Kaolinite'
[]
[cm3_Quartz]
type = PointValue
variable = 'free_cm3_Quartz'
[]
[cm3_Paragonite]
type = PointValue
variable = 'free_cm3_Paragonite'
[]
[cm3_Phlogopite]
type = PointValue
variable = 'free_cm3_Phlogopite'
[]
[cm3_mineral]
type = LinearCombinationPostprocessor
pp_names = 'cm3_Albite cm3_Anhydrite cm3_Anorthite cm3_Calcite cm3_Chalcedony cm3_Clinochl-7A cm3_Illite cm3_K-feldspar cm3_Kaolinite cm3_Quartz cm3_Paragonite cm3_Phlogopite'
pp_coefs = '1 1 1 1 1 1 1 1 1 1 1 1'
[]
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/kinetics/quartz_deposition.i)
# Example of quartz deposition in a fracture, as the temperature is reduced from 300degC to 25degC
# The initial free molality of SiO2(aq) is determined using quartz_equilibrium_at300degC
[GlobalParams]
point = '0 0 0'
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
constraint_species = "H2O Na+ Cl- SiO2(aq)"
constraint_value = " 1.0 1E-10 1E-10 0.009722905"
constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
constraint_unit = " kg moles moles molal"
initial_temperature = 300.0
temperature = temp_controller
kinetic_species_name = Quartz
kinetic_species_initial_value = 400
kinetic_species_unit = g
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
add_aux_pH = false # there is no H+ in this system
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
execute_console_output_on = '' # only CSV output used in this example
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 7.4112E2 # 2.35E-5mol/s/cm^2 = 7.411E2mol/yr/cm^2
multiply_by_mass = true
area_quantity = 1
activation_energy = 72800.0
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O SiO2(aq) Na+ Cl-"
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[Executioner]
type = Transient
dt = 0.02
end_time = 1 # measured in years
[]
[AuxVariables]
[temp_controller]
[]
[diss_rate]
[]
[]
[AuxKernels]
[temp_controller_auxk]
type = FunctionAux
function = '300 - 275 * t'
variable = temp_controller
execute_on = 'timestep_begin'
[]
[diss_rate]
type = ParsedAux
args = mol_change_Quartz
function = '-mol_change_Quartz / 0.02' # 0.02 = timestep size
variable = diss_rate
[]
[]
[Postprocessors]
[mg_per_kg_sio2]
type = PointValue
variable = "mg_per_kg_SiO2(aq)"
[]
[rate_mole_per_year]
type = PointValue
variable = diss_rate
[]
[temperature]
type = PointValue
variable = "solution_temperature"
[]
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/geochemistry_quantity_aux/kinetic_rate.i)
#Extract -(kinetic rate times dt)
[TimeDependentReactionSolver]
model_definition = definition
charge_balance_species = "Cl-"
constraint_species = "H2O H+ Cl- Fe+++ >(s)FeOH >(w)FeOH"
constraint_value = " 1.0 4.0 1.0 0.1 1.0E-6 1.0E-6"
constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration free_concentration free_concentration"
constraint_unit = "kg moles moles molal molal molal"
kinetic_species_name = "Fe(OH)3(ppd)"
kinetic_species_initial_value = "1.0"
kinetic_species_unit = "moles"
max_ionic_strength = 0.0
ramp_max_ionic_strength_initial = 0
[]
[UserObjects]
[constant_rate]
type = GeochemistryKineticRate
kinetic_species_name = "Fe(OH)3(ppd)"
intrinsic_rate_constant = 1E-3
eta = 0.0
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../database/ferric_hydroxide_sorption.json"
basis_species = "H2O H+ Cl- Fe+++ >(s)FeOH >(w)FeOH"
kinetic_minerals = "Fe(OH)3(ppd)"
kinetic_rate_descriptions = "constant_rate"
[]
[]
[Executioner]
type = Transient
dt = 2
end_time = 2
[]
[AuxVariables]
[the_aux]
[]
[]
[AuxKernels]
[the_aux]
type = GeochemistryQuantityAux
species = "Fe(OH)3(ppd)"
reactor = geochemistry_reactor
variable = the_aux
quantity = kinetic_additions
[]
[]
[Postprocessors]
[value]
type = PointValue
point = '0 0 0'
variable = the_aux
[]
[value_from_action]
type = PointValue
point = '0 0 0'
variable = "mol_change_Fe(OH)3(ppd)"
[]
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case2.i)
# Alkali flushing of a reservoir (an example of flushing): adding Na2CO3
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates. Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
point = '0 0 0'
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
constraint_species = "H2O H+ Cl- Na+ Ca++ Calcite Dolomite-ord Muscovite Kaolinite SiO2(aq)"
constraint_value = " 1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177 1.320907 1.1432682 6.318e-05"
constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
constraint_unit = " kg dimensionless moles moles moles moles moles moles moles molal"
initial_temperature = 70.0
temperature = 70.0
kinetic_species_name = Quartz
kinetic_species_initial_value = 226.992243
kinetic_species_unit = moles
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
close_system_at_time = 0.0
remove_fixed_activity_name = "H+"
remove_fixed_activity_time = 0.0
mode = 3 # flush through the NaOH solution specified below:
source_species_names = "H2O Na+ CO3--"
source_species_rates = "27.755 0.25 0.125" # 1kg water/2days = 27.755moles/day. 0.5mol Na+/2days = 0.25mol/day
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
promoting_species_names = "H+"
promoting_species_indices = "-0.5"
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[AuxVariables]
[diss_rate]
[]
[]
[AuxKernels]
[diss_rate]
type = ParsedAux
args = mol_change_Quartz
function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
variable = diss_rate
[]
[]
[Postprocessors]
[pH]
type = PointValue
variable = "pH"
[]
[rate_mole_per_day]
type = PointValue
variable = diss_rate
[]
[cm3_Calcite]
type = PointValue
variable = free_cm3_Calcite
[]
[cm3_Dolomite]
type = PointValue
variable = free_cm3_Dolomite-ord
[]
[cm3_Muscovite]
type = PointValue
variable = free_cm3_Muscovite
[]
[cm3_Kaolinite]
type = PointValue
variable = free_cm3_Kaolinite
[]
[cm3_Quartz]
type = PointValue
variable = free_cm3_Quartz
[]
[cm3_Paragonite]
type = PointValue
variable = free_cm3_Paragonite
[]
[cm3_Analcime]
type = PointValue
variable = free_cm3_Analcime
[]
[cm3_Phlogopite]
type = PointValue
variable = free_cm3_Phlogopite
[]
[cm3_Tridymite]
type = PointValue
variable = free_cm3_Tridymite
[]
[]
[Executioner]
type = Transient
dt = 1
end_time = 20 # measured in days
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case1.i)
# Alkali flushing of a reservoir (an example of flushing): adding NaOH
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates. Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
point = '0 0 0'
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
constraint_species = "H2O H+ Cl- Na+ Ca++ Calcite Dolomite-ord Muscovite Kaolinite SiO2(aq)"
constraint_value = " 1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177 1.320907 1.1432682 6.318e-05"
constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
constraint_unit = " kg dimensionless moles moles moles moles moles moles moles molal"
initial_temperature = 70.0
temperature = 70.0
kinetic_species_name = Quartz
kinetic_species_initial_value = 226.992243
kinetic_species_unit = moles
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
close_system_at_time = 0.0
remove_fixed_activity_name = "H+"
remove_fixed_activity_time = 0.0
mode = 3 # flush through the NaOH solution specified below:
source_species_names = "H2O Na+ OH-"
source_species_rates = "27.755 0.25 0.25" # 1kg water/2days = 27.755moles/day. 0.5mol Na+/2days = 0.25mol/day
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
promoting_species_names = "H+"
promoting_species_indices = "-0.5"
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[AuxVariables]
[diss_rate]
[]
[]
[AuxKernels]
[diss_rate]
type = ParsedAux
args = mol_change_Quartz
function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
variable = diss_rate
[]
[]
[Postprocessors]
[pH]
type = PointValue
variable = "pH"
[]
[rate_mole_per_day]
type = PointValue
variable = diss_rate
[]
[cm3_Calcite]
type = PointValue
variable = free_cm3_Calcite
[]
[cm3_Dolomite]
type = PointValue
variable = free_cm3_Dolomite-ord
[]
[cm3_Muscovite]
type = PointValue
variable = free_cm3_Muscovite
[]
[cm3_Kaolinite]
type = PointValue
variable = free_cm3_Kaolinite
[]
[cm3_Quartz]
type = PointValue
variable = free_cm3_Quartz
[]
[cm3_Paragonite]
type = PointValue
variable = free_cm3_Paragonite
[]
[cm3_Analcime]
type = PointValue
variable = free_cm3_Analcime
[]
[cm3_Phlogopite]
type = PointValue
variable = free_cm3_Phlogopite
[]
[cm3_Tridymite]
type = PointValue
variable = free_cm3_Tridymite
[]
[]
[Executioner]
type = Transient
dt = 1
end_time = 20 # measured in days
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case3.i)
# Alkali flushing of a reservoir (an example of flushing): adding Na2SiO3
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates. Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
point = '0 0 0'
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
constraint_species = "H2O H+ Cl- Na+ Ca++ Calcite Dolomite-ord Muscovite Kaolinite SiO2(aq)"
constraint_value = " 1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177 1.320907 1.1432682 6.318e-05"
constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
constraint_unit = " kg dimensionless moles moles moles moles moles moles moles molal"
initial_temperature = 70.0
temperature = 70.0
kinetic_species_name = Quartz
kinetic_species_initial_value = 226.992243
kinetic_species_unit = moles
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
close_system_at_time = 0.0
remove_fixed_activity_name = "H+"
remove_fixed_activity_time = 0.0
mode = 3 # flush through the NaOH solution specified below:
source_species_names = "H2O H+ Na+ SiO2(aq)"
source_species_rates = "27.88 -0.25 0.25 0.125" # 1kg water/2days = 27.755moles/day. 0.25mol Na2O/2days = 0.25*(--2mol H+ + 2mol Na+ + 1mol H2O)/2days
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
promoting_species_names = "H+"
promoting_species_indices = "-0.5"
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[AuxVariables]
[diss_rate]
[]
[]
[AuxKernels]
[diss_rate]
type = ParsedAux
args = mol_change_Quartz
function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
variable = diss_rate
[]
[]
[Postprocessors]
[pH]
type = PointValue
variable = "pH"
[]
[rate_mole_per_day]
type = PointValue
variable = diss_rate
[]
[cm3_Calcite]
type = PointValue
variable = free_cm3_Calcite
[]
[cm3_Dolomite]
type = PointValue
variable = free_cm3_Dolomite-ord
[]
[cm3_Muscovite]
type = PointValue
variable = free_cm3_Muscovite
[]
[cm3_Kaolinite]
type = PointValue
variable = free_cm3_Kaolinite
[]
[cm3_Quartz]
type = PointValue
variable = free_cm3_Quartz
[]
[cm3_Paragonite]
type = PointValue
variable = free_cm3_Paragonite
[]
[cm3_Analcime]
type = PointValue
variable = free_cm3_Analcime
[]
[cm3_Phlogopite]
type = PointValue
variable = free_cm3_Phlogopite
[]
[cm3_Tridymite]
type = PointValue
variable = free_cm3_Tridymite
[]
[]
[Executioner]
type = Transient
dt = 0.1
end_time = 20E-1 # measured in days
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/time_dependent_reactions/flushing.i)
# Alkali flushing of a reservoir (an example of flushing): adding NaOH solution
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1.5552E-13 # 1.8E-18mol/s/cm^2 = 1.5552E-13mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
promoting_species_names = "H+"
promoting_species_indices = "-0.5"
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
equilibrium_minerals = "Analcime Calcite Dawsonite Dolomite-ord Gibbsite Kaolinite Muscovite Paragonite Phlogopite"
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
constraint_species = "H2O H+ Cl- Na+ Ca++ Calcite Dolomite-ord Muscovite Kaolinite SiO2(aq)"
constraint_value = " 1.0 -5 1.0 1.0 0.2 9.88249 3.652471265 1.2792268 1.2057878 0.000301950628974"
constraint_meaning = "kg_solvent_water log10activity bulk_composition bulk_composition bulk_composition free_mineral free_mineral free_mineral free_mineral free_concentration"
constraint_unit = " kg dimensionless moles moles moles moles moles moles moles molal"
initial_temperature = 70.0
temperature = 70.0
kinetic_species_name = Quartz
kinetic_species_initial_value = 226.992243
kinetic_species_unit = moles
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
close_system_at_time = 0.0
remove_fixed_activity_name = "H+"
remove_fixed_activity_time = 0.0
mode = 3 # flush through the NaOH solution specified below:
source_species_names = "H2O Na+ OH-"
source_species_rates = "27.75 0.25 0.25" # 1kg water/2days = 27.75moles/day. 0.5mol Na+/2days = 0.25mol/day
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
stoichiometric_ionic_str_using_Cl_only = true
execute_console_output_on = '' # only CSV output for this test
abs_tol = 1E-13
[]
[Executioner]
type = Transient
dt = 1
end_time = 20 # measured in days
[]
[GlobalParams]
point = '0 0 0'
[]
[Postprocessors]
[pH]
type = PointValue
variable = "pH"
[]
[cm3_Analcime]
type = PointValue
variable = free_cm3_Analcime
[]
[cm3_Calcite]
type = PointValue
variable = free_cm3_Calcite
[]
[cm3_Dawsonite]
type = PointValue
variable = free_cm3_Dawsonite
[]
[cm3_Dolomite]
type = PointValue
variable = free_cm3_Dolomite-ord
[]
[cm3_Gibbsite]
type = PointValue
variable = free_cm3_Gibbsite
[]
[cm3_Kaolinite]
type = PointValue
variable = free_cm3_Kaolinite
[]
[cm3_Muscovite]
type = PointValue
variable = free_cm3_Muscovite
[]
[cm3_Paragonite]
type = PointValue
variable = free_cm3_Paragonite
[]
[cm3_Phlogopite]
type = PointValue
variable = free_cm3_Phlogopite
[]
[cm3_Quartz]
type = PointValue
variable = free_cm3_Quartz
[]
[]
[Outputs]
csv = true
[]
(modules/combined/examples/geochem-porous_flow/forge/reservoir_and_water_3.i)
# Simulation to assess possible changes in the reservoir. The rock composition from natural_reservoir.i is mixed with the water from water_3.i Note that the free_concentration values are used from water_3.i and that composition is held fixed throughout this entire simulation. This models water_3 continually flushing through the rock mineral assemblage: as soon as a mineral dissolves the aqueous components are swept away and replaced by a new batch of water_3; as soon as mineral precipitates more water_3 sweeps into the system providing a limitless source of aqueous components (in set ratios) at 70degC
# The results depend on the kinetic rates used and these are recognised to be poorly constrained by experiment
[UserObjects]
[rate_Albite]
type = GeochemistryKineticRate
kinetic_species_name = Albite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 69.8E3
one_over_T0 = 0.003354
[]
[rate_Anhydrite]
type = GeochemistryKineticRate
kinetic_species_name = Anhydrite
intrinsic_rate_constant = 1.0E-7
multiply_by_mass = true
area_quantity = 10
activation_energy = 14.3E3
one_over_T0 = 0.003354
[]
[rate_Anorthite]
type = GeochemistryKineticRate
kinetic_species_name = Anorthite
intrinsic_rate_constant = 1.0E-13
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Calcite]
type = GeochemistryKineticRate
kinetic_species_name = Calcite
intrinsic_rate_constant = 1.0E-10
multiply_by_mass = true
area_quantity = 10
activation_energy = 23.5E3
one_over_T0 = 0.003354
[]
[rate_Chalcedony]
type = GeochemistryKineticRate
kinetic_species_name = Chalcedony
intrinsic_rate_constant = 1.0E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Clinochl-7A]
type = GeochemistryKineticRate
kinetic_species_name = Clinochl-7A
intrinsic_rate_constant = 1.0E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 88.0E3
one_over_T0 = 0.003354
[]
[rate_Illite]
type = GeochemistryKineticRate
kinetic_species_name = Illite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 29E3
one_over_T0 = 0.003354
[]
[rate_K-feldspar]
type = GeochemistryKineticRate
kinetic_species_name = K-feldspar
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 38E3
one_over_T0 = 0.003354
[]
[rate_Kaolinite]
type = GeochemistryKineticRate
kinetic_species_name = Kaolinite
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 22.2E3
one_over_T0 = 0.003354
[]
[rate_Quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Paragonite]
type = GeochemistryKineticRate
kinetic_species_name = Paragonite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Phlogopite]
type = GeochemistryKineticRate
kinetic_species_name = Phlogopite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Laumontite]
type = GeochemistryKineticRate
kinetic_species_name = Laumontite
intrinsic_rate_constant = 1.0E-15
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Zoisite]
type = GeochemistryKineticRate
kinetic_species_name = Zoisite
intrinsic_rate_constant = 1E-16
multiply_by_mass = true
area_quantity = 10
activation_energy = 66.1E3
one_over_T0 = 0.003354
[]
[definition]
type = GeochemicalModelDefinition
database_file = '../../../../geochemistry/database/moose_geochemdb.json'
basis_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
remove_all_extrapolated_secondary_species = true
kinetic_minerals = 'Albite Anhydrite Anorthite Calcite Chalcedony Clinochl-7A Illite K-feldspar Kaolinite Quartz Paragonite Phlogopite Zoisite Laumontite'
kinetic_rate_descriptions = 'rate_Albite rate_Anhydrite rate_Anorthite rate_Calcite rate_Chalcedony rate_Clinochl-7A rate_Illite rate_K-feldspar rate_Kaolinite rate_Quartz rate_Paragonite rate_Phlogopite rate_Zoisite rate_Laumontite'
[]
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = 'Cl-'
constraint_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
# Following numbers are from water_3_out.csv
constraint_value = ' 0.99999999549877 8.0204734722945e-07 0.0001319920398478 2.8097346859027e-05 7.7328020546464e-05 2.874602030221e-05 0.00027284654762868 4.4715524787497e-12 0.0002253530818877 1.0385772502298e-05 0.00012427759434288'
constraint_meaning = 'kg_solvent_water free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration bulk_composition free_concentration free_concentration'
constraint_unit = ' kg molal molal molal molal molal molal molal moles molal molal'
initial_temperature = 70
temperature = 70
close_system_at_time = 1E20 # keep the free molalities specified above for all time
kinetic_species_name = ' Albite Anorthite K-feldspar Quartz Phlogopite Paragonite Calcite Anhydrite Chalcedony Illite Kaolinite Clinochl-7A Zoisite Laumontite'
kinetic_species_initial_value = '4.324073236492E+02 4.631370307325E+01 2.685015418378E+02 7.720095013956E+02 1.235192062541E+01 7.545461404965E-01 4.234651808835E-04 4.000485907930E-04 4.407616361072E+00 1.342524904876E+01 1.004823151125E+00 4.728132387707E-01 7.326007326007E-01 4.818116116598E-01'
kinetic_species_unit = ' moles moles moles moles moles moles moles moles moles moles moles moles moles moles'
evaluate_kinetic_rates_always = true # otherwise will easily "run out" of dissolving species
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
execute_console_output_on = ''
[]
[Executioner]
type = Transient
[TimeStepper]
type = FunctionDT
function = 'max(1E6, 0.3 * t)'
[]
end_time = 4E11
[]
[GlobalParams]
point = '0 0 0'
[]
[Postprocessors]
[temperature]
type = PointValue
variable = 'solution_temperature'
[]
[cm3_Albite]
type = PointValue
variable = 'free_cm3_Albite'
[]
[cm3_Anhydrite]
type = PointValue
variable = 'free_cm3_Anhydrite'
[]
[cm3_Anorthite]
type = PointValue
variable = 'free_cm3_Anorthite'
[]
[cm3_Calcite]
type = PointValue
variable = 'free_cm3_Calcite'
[]
[cm3_Chalcedony]
type = PointValue
variable = 'free_cm3_Chalcedony'
[]
[cm3_Clinochl-7A]
type = PointValue
variable = 'free_cm3_Clinochl-7A'
[]
[cm3_Illite]
type = PointValue
variable = 'free_cm3_Illite'
[]
[cm3_K-feldspar]
type = PointValue
variable = 'free_cm3_K-feldspar'
[]
[cm3_Kaolinite]
type = PointValue
variable = 'free_cm3_Kaolinite'
[]
[cm3_Quartz]
type = PointValue
variable = 'free_cm3_Quartz'
[]
[cm3_Paragonite]
type = PointValue
variable = 'free_cm3_Paragonite'
[]
[cm3_Phlogopite]
type = PointValue
variable = 'free_cm3_Phlogopite'
[]
[cm3_Zoisite]
type = PointValue
variable = 'free_cm3_Zoisite'
[]
[cm3_Laumontite]
type = PointValue
variable = 'free_cm3_Laumontite'
[]
[cm3_mineral]
type = LinearCombinationPostprocessor
pp_names = 'cm3_Albite cm3_Anhydrite cm3_Anorthite cm3_Calcite cm3_Chalcedony cm3_Clinochl-7A cm3_Illite cm3_K-feldspar cm3_Kaolinite cm3_Quartz cm3_Paragonite cm3_Phlogopite cm3_Zoisite cm3_Laumontite'
pp_coefs = '1 1 1 1 1 1 1 1 1 1 1 1 1 1'
[]
[pH]
type = PointValue
variable = 'pH'
[]
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/kinetics/quartz_dissolution.i)
# Example of quartz dissolution.
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
constraint_species = "H2O H+ Cl- SiO2(aq)"
constraint_value = " 1.0 1E-10 1E-10 1E-9"
constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
constraint_unit = " kg moles moles molal"
initial_temperature = 100.0
temperature = 100.0
kinetic_species_name = Quartz
kinetic_species_initial_value = 5
kinetic_species_unit = kg
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
stoichiometric_ionic_str_using_Cl_only = true # for comparison with GWB
execute_console_output_on = '' # only CSV output for this example
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1.728E-10 # 2.0E-15mol/s/cm^2 = 1.728E-10mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O SiO2(aq) H+ Cl-"
kinetic_minerals = "Quartz"
kinetic_rate_descriptions = "rate_quartz"
piecewise_linear_interpolation = true # for comparison with GWB
[]
[]
[Functions]
[timestepper]
type = PiecewiseLinear
x = '0 0.5 3'
y = '0.01 0.05 0.1'
[]
[]
[Executioner]
type = Transient
[TimeStepper]
type = FunctionDT
function = timestepper
[]
end_time = 5.0
[]
[AuxVariables]
[diss]
[]
[]
[AuxKernels]
[diss]
type = ParsedAux
args = moles_Quartz
function = '83.216414271 - moles_Quartz'
variable = diss
[]
[]
[Postprocessors]
[dissolved_moles]
type = PointValue
point = '0 0 0'
variable = diss
[]
[]
[Outputs]
csv = true
[]
(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_geochemistry.i)
# Simulates geochemistry in the aquifer. This input file may be run in standalone fashion but it does not do anything of interest. To simulate something interesting, run the porous_flow.i simulation which couples to this input file using MultiApps.
# This file receives pf_rate_H2O, pf_rate_Na, pf_rate_Cl, pf_rate_SiO2 and temperature as AuxVariables from porous_flow.i.
# The pf_rate quantities are kg/s changes of fluid-component mass at each node, but the geochemistry module expects rates-of-changes of moles at every node. Secondly, since this input file considers just 1 litre of aqueous solution at every node, the nodal_void_volume is used to convert pf_rate_* into rate_*_per_1l, which is measured in mol/s/1_litre_of_aqueous_solution.
# This file sends massfrac_Na, massfrac_Cl and massfrac_SiO2 to porous_flow.i. These are computed from the corresponding transported_* quantities.
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 14 # for better resolution, use 56 or 112
ny = 8 # for better resolution, use 32 or 64
xmin = -70
xmax = 70
ymin = -40
ymax = 40
[]
[]
[GlobalParams]
point = '0 0 0'
reactor = reactor
[]
[SpatialReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
constraint_species = "H2O Na+ Cl- SiO2(aq)"
# ASSUME that 1 litre of solution contains:
constraint_value = " 1.0 0.1 0.1 0.000555052386"
constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
constraint_unit = " kg moles moles molal"
initial_temperature = 50.0
kinetic_species_name = QuartzLike
# Per 1 litre (1000cm^3) of aqueous solution (1kg of solvent water), there is 9000cm^3 of QuartzLike, which means the initial porosity is 0.1.
kinetic_species_initial_value = 9000
kinetic_species_unit = cm3
temperature = temperature
source_species_names = 'H2O Na+ Cl- SiO2(aq)'
source_species_rates = 'rate_H2O_per_1l rate_Na_per_1l rate_Cl_per_1l rate_SiO2_per_1l'
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
add_aux_pH = false # there is no H+ in this system
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
execute_console_output_on = ''
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = QuartzLike
intrinsic_rate_constant = 1.0E-2
multiply_by_mass = true
area_quantity = 1
activation_energy = 72800.0
[]
[definition]
type = GeochemicalModelDefinition
database_file = "small_database.json"
basis_species = "H2O SiO2(aq) Na+ Cl-"
kinetic_minerals = "QuartzLike"
kinetic_rate_descriptions = "rate_quartz"
[]
[nodal_void_volume_uo]
type = NodalVoidVolume
porosity = porosity
execute_on = 'initial timestep_end' # "initial" means this is evaluated properly for the first timestep
[]
[]
[Executioner]
type = Transient
dt = 1E5
end_time = 7.76E6 # 90 days
[]
[AuxVariables]
[temperature]
initial_condition = 50.0
[]
[porosity]
initial_condition = 0.1
[]
[nodal_void_volume]
[]
[pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_Na] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_Cl] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_SiO2] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[rate_H2O_per_1l] # rate per 1 litre of aqueous solution that we consider at each node
[]
[rate_Na_per_1l]
[]
[rate_Cl_per_1l]
[]
[rate_SiO2_per_1l]
[]
[transported_H2O]
[]
[transported_Na]
[]
[transported_Cl]
[]
[transported_SiO2]
[]
[transported_mass]
[]
[massfrac_Na]
[]
[massfrac_Cl]
[]
[massfrac_SiO2]
[]
[massfrac_H2O]
[]
[]
[AuxKernels]
[porosity]
type = ParsedAux
args = free_cm3_QuartzLike
function = '1000.0 / (1000.0 + free_cm3_QuartzLike)'
variable = porosity
execute_on = 'timestep_end'
[]
[nodal_void_volume_auxk]
type = NodalVoidVolumeAux
variable = nodal_void_volume
nodal_void_volume_uo = nodal_void_volume_uo
execute_on = 'initial timestep_end' # "initial" to ensure it is properly evaluated for the first timestep
[]
[rate_H2O_per_1l_auxk]
type = ParsedAux
args = 'pf_rate_H2O nodal_void_volume'
variable = rate_H2O_per_1l
# pf_rate = change in kg at every node
# pf_rate * 1000 / molar_mass_in_g_per_mole = change in moles at every node
# pf_rate * 1000 / molar_mass / (nodal_void_volume_in_m^3 * 1000) = change in moles per litre of aqueous solution
function = 'pf_rate_H2O / 18.0152 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Na_per_1l]
type = ParsedAux
args = 'pf_rate_Na nodal_void_volume'
variable = rate_Na_per_1l
function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Cl_per_1l]
type = ParsedAux
args = 'pf_rate_Cl nodal_void_volume'
variable = rate_Cl_per_1l
function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_SiO2_per_1l]
type = ParsedAux
args = 'pf_rate_SiO2 nodal_void_volume'
variable = rate_SiO2_per_1l
function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[transported_H2O_auxk]
type = GeochemistryQuantityAux
variable = transported_H2O
species = H2O
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_Na]
type = GeochemistryQuantityAux
variable = transported_Na
species = Na+
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_Cl]
type = GeochemistryQuantityAux
variable = transported_Cl
species = Cl-
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_SiO2]
type = GeochemistryQuantityAux
variable = transported_SiO2
species = 'SiO2(aq)'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_mass_auxk]
type = ParsedAux
args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
variable = transported_mass
function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
execute_on = 'timestep_end'
[]
[massfrac_H2O]
type = ParsedAux
args = 'transported_H2O transported_mass'
variable = massfrac_H2O
function = 'transported_H2O * 18.0152 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Na]
type = ParsedAux
args = 'transported_Na transported_mass'
variable = massfrac_Na
function = 'transported_Na * 22.9898 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Cl]
type = ParsedAux
args = 'transported_Cl transported_mass'
variable = massfrac_Cl
function = 'transported_Cl * 35.453 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_SiO2]
type = ParsedAux
args = 'transported_SiO2 transported_mass'
variable = massfrac_SiO2
function = 'transported_SiO2 * 60.0843 / transported_mass'
execute_on = 'timestep_end'
[]
[]
[Postprocessors]
[cm3_quartz]
type = PointValue
variable = free_cm3_QuartzLike
[]
[porosity]
type = PointValue
variable = porosity
[]
[solution_temperature]
type = PointValue
variable = solution_temperature
[]
[massfrac_H2O]
type = PointValue
variable = massfrac_H2O
[]
[massfrac_Na]
type = PointValue
variable = massfrac_Na
[]
[massfrac_Cl]
type = PointValue
variable = massfrac_Cl
[]
[massfrac_SiO2]
type = PointValue
variable = massfrac_SiO2
[]
[]
[Outputs]
exodus = true
csv = true
[]
(modules/combined/examples/geochem-porous_flow/forge/natural_reservoir.i)
# Simulation to assess natural changes in the reservoir. Recall that water_60_to_220degC has provided a stable mineral assemblage that is in agreement with XRD observations, and a water at equilibrium with that assemblage. However, Stuart Simmons suggested including Laumontite and Zoisite into the simulation, and they were not included in water_60_to_220degC since they are more stable than Anorthite, so Anorthite completely dissolves when equilibrium is assumed. Here, all minerals suggested by Stuart Simmons are added to the system and kinetics are used to determine the time scales of the mineral changes. The initial water composition is the reservoir water from water_60_to_220degC.
# The initial mole numbers of the kinetic species are chosen to be such that:
# - the mass fractions are: Albite 0.44; Anorthite 0.05; K-feldspar 0.29; Quartz 0.18, Phlgoptite 0.02 and Illite 0.02 with trace amounts of the remaining minerals. These are similar to that measured in bulk X-ray diffraction results of 10 samples from well 58-32, assuming that "plagioclase feldspar" consists of Albite and Anorthite in the ratio 9:1, and that Biotite is Phlogoptite. The trace amounts of each mineral are necessary because of the way the kinetics works: precipitation rate is proportional to mineral-species mass, so without any mass, no precipitation is possible. Precisely:
# - it is assumed that water_60_to_220degC consists of 1 litre of water (there is 1kg of solvent water) and that the porosity is 0.01, so the amount of rock should be 99000cm^3
# - the cm^3 of the trace minerals Calcite and Anhydrite is exactly given by water_60_to_220degC (0.016 and 0.018 respectively)
# - see initial_kinetic_moles.xlsx for the remaining mole numbers
# The results depend on the kinetic rates used and these are recognised to be poorly constrained by experiment
[UserObjects]
[rate_Albite]
type = GeochemistryKineticRate
kinetic_species_name = Albite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 69.8E3
one_over_T0 = 0.003354
[]
[rate_Anhydrite]
type = GeochemistryKineticRate
kinetic_species_name = Anhydrite
intrinsic_rate_constant = 1.0E-7
multiply_by_mass = true
area_quantity = 10
activation_energy = 14.3E3
one_over_T0 = 0.003354
[]
[rate_Anorthite]
type = GeochemistryKineticRate
kinetic_species_name = Anorthite
intrinsic_rate_constant = 1.0E-13
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Calcite]
type = GeochemistryKineticRate
kinetic_species_name = Calcite
intrinsic_rate_constant = 1.0E-10
multiply_by_mass = true
area_quantity = 10
activation_energy = 23.5E3
one_over_T0 = 0.003354
[]
[rate_Chalcedony]
type = GeochemistryKineticRate
kinetic_species_name = Chalcedony
intrinsic_rate_constant = 1.0E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Clinochl-7A]
type = GeochemistryKineticRate
kinetic_species_name = Clinochl-7A
intrinsic_rate_constant = 1.0E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 88.0E3
one_over_T0 = 0.003354
[]
[rate_Illite]
type = GeochemistryKineticRate
kinetic_species_name = Illite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 29E3
one_over_T0 = 0.003354
[]
[rate_K-feldspar]
type = GeochemistryKineticRate
kinetic_species_name = K-feldspar
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 38E3
one_over_T0 = 0.003354
[]
[rate_Kaolinite]
type = GeochemistryKineticRate
kinetic_species_name = Kaolinite
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 22.2E3
one_over_T0 = 0.003354
[]
[rate_Quartz]
type = GeochemistryKineticRate
kinetic_species_name = Quartz
intrinsic_rate_constant = 1E-18
multiply_by_mass = true
area_quantity = 10
activation_energy = 90.1E3
one_over_T0 = 0.003354
[]
[rate_Paragonite]
type = GeochemistryKineticRate
kinetic_species_name = Paragonite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Phlogopite]
type = GeochemistryKineticRate
kinetic_species_name = Phlogopite
intrinsic_rate_constant = 1E-17
multiply_by_mass = true
area_quantity = 10
activation_energy = 22E3
one_over_T0 = 0.003354
[]
[rate_Laumontite]
type = GeochemistryKineticRate
kinetic_species_name = Laumontite
intrinsic_rate_constant = 1.0E-15
multiply_by_mass = true
area_quantity = 10
activation_energy = 17.8E3
one_over_T0 = 0.003354
[]
[rate_Zoisite]
type = GeochemistryKineticRate
kinetic_species_name = Zoisite
intrinsic_rate_constant = 1E-16
multiply_by_mass = true
area_quantity = 10
activation_energy = 66.1E3
one_over_T0 = 0.003354
[]
[definition]
type = GeochemicalModelDefinition
database_file = '../../../../geochemistry/database/moose_geochemdb.json'
basis_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
remove_all_extrapolated_secondary_species = true
kinetic_minerals = 'Albite Anhydrite Anorthite Calcite Chalcedony Clinochl-7A Illite K-feldspar Kaolinite Quartz Paragonite Phlogopite Zoisite Laumontite'
kinetic_rate_descriptions = 'rate_Albite rate_Anhydrite rate_Anorthite rate_Calcite rate_Chalcedony rate_Clinochl-7A rate_Illite rate_K-feldspar rate_Kaolinite rate_Quartz rate_Paragonite rate_Phlogopite rate_Zoisite rate_Laumontite'
[]
[]
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = 'Cl-'
constraint_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
# Following numbers are from water_60_to_220degC_out.csv
constraint_value = ' 1.0006383866109 9.5165072498215e-07 0.100020379171 0.0059389061065 0.011570884507621 4.6626763057447e-06 0.0045110404925255 5.8096968688789e-17 0.13500708594394 6.6523540147676e-05 7.7361407898089e-05'
constraint_meaning = 'kg_solvent_water free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration bulk_composition free_concentration free_concentration'
constraint_unit = ' kg molal molal molal molal molal molal molal moles molal molal'
initial_temperature = 220
temperature = 220
kinetic_species_name = ' Albite Anorthite K-feldspar Quartz Phlogopite Paragonite Calcite Anhydrite Chalcedony Illite Kaolinite Clinochl-7A Zoisite Laumontite'
kinetic_species_initial_value = '4.324073236492E+02 4.631370307325E+01 2.685015418378E+02 7.720095013956E+02 1.235192062541E+01 7.545461404965E-01 4.234651808835E-04 4.000485907930E-04 4.407616361072E+00 1.342524904876E+01 1.004823151125E+00 4.728132387707E-01 7.326007326007E-01 4.818116116598E-01'
kinetic_species_unit = ' moles moles moles moles moles moles moles moles moles moles moles moles moles moles'
evaluate_kinetic_rates_always = true # otherwise will easily "run out" of dissolving species
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
execute_console_output_on = ''
[]
[Executioner]
type = Transient
[TimeStepper]
type = FunctionDT
function = 'max(1E2, 0.1 * t)'
[]
end_time = 4E11
[]
[GlobalParams]
point = '0 0 0'
[]
[Postprocessors]
[cm3_Albite]
type = PointValue
variable = 'free_cm3_Albite'
[]
[cm3_Anhydrite]
type = PointValue
variable = 'free_cm3_Anhydrite'
[]
[cm3_Anorthite]
type = PointValue
variable = 'free_cm3_Anorthite'
[]
[cm3_Calcite]
type = PointValue
variable = 'free_cm3_Calcite'
[]
[cm3_Chalcedony]
type = PointValue
variable = 'free_cm3_Chalcedony'
[]
[cm3_Clinochl-7A]
type = PointValue
variable = 'free_cm3_Clinochl-7A'
[]
[cm3_Illite]
type = PointValue
variable = 'free_cm3_Illite'
[]
[cm3_K-feldspar]
type = PointValue
variable = 'free_cm3_K-feldspar'
[]
[cm3_Kaolinite]
type = PointValue
variable = 'free_cm3_Kaolinite'
[]
[cm3_Quartz]
type = PointValue
variable = 'free_cm3_Quartz'
[]
[cm3_Paragonite]
type = PointValue
variable = 'free_cm3_Paragonite'
[]
[cm3_Phlogopite]
type = PointValue
variable = 'free_cm3_Phlogopite'
[]
[cm3_Zoisite]
type = PointValue
variable = 'free_cm3_Zoisite'
[]
[cm3_Laumontite]
type = PointValue
variable = 'free_cm3_Laumontite'
[]
[cm3_mineral]
type = LinearCombinationPostprocessor
pp_names = 'cm3_Albite cm3_Anhydrite cm3_Anorthite cm3_Calcite cm3_Chalcedony cm3_Clinochl-7A cm3_Illite cm3_K-feldspar cm3_Kaolinite cm3_Quartz cm3_Paragonite cm3_Phlogopite cm3_Zoisite cm3_Laumontite'
pp_coefs = '1 1 1 1 1 1 1 1 1 1 1 1 1 1'
[]
[pH]
type = PointValue
variable = 'pH'
[]
[kg_solvent_H2O]
type = PointValue
variable = 'kg_solvent_H2O'
[]
[]
[Outputs]
csv = true
[]
(modules/geochemistry/test/tests/kinetics/kinetic_albite.i)
# Example of kinetically-controlled dissolution of albite into an acidic solution
[TimeDependentReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
constraint_species = "H2O H+ Cl- Na+ SiO2(aq) Al+++"
constraint_value = " 1.0 -1.5 0.1 0.1 1E-6 1E-6"
constraint_meaning = "kg_solvent_water log10activity bulk_composition bulk_composition free_concentration free_concentration"
constraint_unit = " kg dimensionless moles moles molal molal"
initial_temperature = 70.0
temperature = 70.0
kinetic_species_name = Albite
kinetic_species_initial_value = 250
kinetic_species_unit = g
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
stoichiometric_ionic_str_using_Cl_only = true # for comparison with GWB
execute_console_output_on = '' # only CSV output for this example
[]
[UserObjects]
[rate_albite]
type = GeochemistryKineticRate
kinetic_species_name = Albite
intrinsic_rate_constant = 5.4432E-8 # 6.3E-13mol/s/cm^2 = 5.4432E-8mol/day/cm^2
multiply_by_mass = true
area_quantity = 1000
promoting_species_names = "H+"
promoting_species_indices = "1.0"
[]
[definition]
type = GeochemicalModelDefinition
database_file = "../../../database/moose_geochemdb.json"
basis_species = "H2O H+ Cl- Na+ SiO2(aq) Al+++"
kinetic_minerals = "Albite"
kinetic_rate_descriptions = "rate_albite"
[]
[]
[Executioner]
type = Transient
dt = 5
end_time = 30 # measured in days
[]
[AuxVariables]
[mole_change_albite]
[]
[]
[AuxKernels]
[mole_change_albite]
type = ParsedAux
args = moles_Albite
function = 'moles_Albite - 0.953387'
variable = mole_change_albite
[]
[]
[Postprocessors]
[mole_change_Albite]
type = PointValue
point = '0 0 0'
variable = "mole_change_albite"
[]
[]
[Outputs]
csv = true
[]
(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_un_quartz_geochemistry.i)
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 56
ny = 32
xmin = -70
xmax = 70
ymin = -40
ymax = 40
[]
[]
[GlobalParams]
point = '0 0 0'
reactor = reactor
[]
[SpatialReactionSolver]
model_definition = definition
geochemistry_reactor_name = reactor
charge_balance_species = "Cl-"
constraint_species = "H2O Na+ Cl- SiO2(aq)"
# ASSUME that 1 litre of solution contains:
constraint_value = " 1.0 0.1 0.1 0.00172249633"
constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
constraint_unit = " kg moles moles molal"
initial_temperature = 50.0
kinetic_species_name = QuartzUnlike
# Per 1 litre (1000cm^3) of aqueous solution (1kg of solvent water), there is 9000cm^3 of QuartzUnlike, which means the initial porosity is 0.1.
kinetic_species_initial_value = 9000
kinetic_species_unit = cm3
temperature = temperature
source_species_names = 'H2O Na+ Cl- SiO2(aq)'
source_species_rates = 'rate_H2O_per_1l rate_Na_per_1l rate_Cl_per_1l rate_SiO2_per_1l'
ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
add_aux_pH = false # there is no H+ in this system
evaluate_kinetic_rates_always = true # implicit time-marching used for stability
execute_console_output_on = '' # only CSV and exodus output used in this example
[]
[UserObjects]
[rate_quartz]
type = GeochemistryKineticRate
kinetic_species_name = QuartzUnlike
intrinsic_rate_constant = 1.0E-2
multiply_by_mass = true
area_quantity = 1
activation_energy = 72800.0
[]
[definition]
type = GeochemicalModelDefinition
database_file = "small_database.json"
basis_species = "H2O SiO2(aq) Na+ Cl-"
kinetic_minerals = "QuartzUnlike"
kinetic_rate_descriptions = "rate_quartz"
[]
[]
[Executioner]
type = Transient
dt = 1E5
end_time = 7.76E6 # 90 days
[]
[AuxVariables]
[temperature]
initial_condition = 50.0
[]
[nodal_volume]
[]
[porosity]
[]
[nodal_void_volume]
[]
[pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_Na] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_Cl] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[pf_rate_SiO2] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
[]
[rate_H2O_per_1l] # rate per 1 litre of aqueous solution that we consider at each node
[]
[rate_Na_per_1l]
[]
[rate_Cl_per_1l]
[]
[rate_SiO2_per_1l]
[]
[transported_H2O]
[]
[transported_Na]
[]
[transported_Cl]
[]
[transported_SiO2]
[]
[transported_mass]
[]
[massfrac_Na]
[]
[massfrac_Cl]
[]
[massfrac_SiO2]
[]
[massfrac_H2O]
[]
[]
[AuxKernels]
[nodal_volume] # TODO: change this hard-coded version once PR is merged
type = FunctionAux
variable = nodal_volume
function = 'if(abs(x) = 70 & abs(y) = 40, 2.5, if(abs(x) = 70 | abs(y) = 40, 5, 10))'
execute_on = 'initial'
[]
[porosity]
type = ParsedAux
args = free_cm3_QuartzUnlike
function = '1000.0 / (1000.0 + free_cm3_QuartzUnlike)'
variable = porosity
execute_on = 'timestep_begin timestep_end'
[]
[nodal_void_volume]
type = ParsedAux
args = 'porosity nodal_volume'
variable = nodal_void_volume
function = 'porosity * nodal_volume'
execute_on = 'timestep_begin'
[]
[rate_H2O_per_1l]
type = ParsedAux
args = 'pf_rate_H2O nodal_void_volume'
variable = rate_H2O_per_1l
# pf_rate = change in kg at every node
# pf_rate * 1000 / molar_mass_in_g_per_mole = change in moles at every node
# pf_rate * 1000 / molar_mass / (nodal_void_volume_in_m^3 * 1000) = change in moles per litre of aqueous solution
function = 'pf_rate_H2O / 18.0152 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Na_per_1l]
type = ParsedAux
args = 'pf_rate_Na nodal_void_volume'
variable = rate_Na_per_1l
function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_Cl_per_1l]
type = ParsedAux
args = 'pf_rate_Cl nodal_void_volume'
variable = rate_Cl_per_1l
function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[rate_SiO2_per_1l]
type = ParsedAux
args = 'pf_rate_SiO2 nodal_void_volume'
variable = rate_SiO2_per_1l
function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
execute_on = 'timestep_begin'
[]
[transported_H2O]
type = GeochemistryQuantityAux
variable = transported_H2O
species = H2O
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_Na]
type = GeochemistryQuantityAux
variable = transported_Na
species = Na+
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_Cl]
type = GeochemistryQuantityAux
variable = transported_Cl
species = Cl-
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_SiO2]
type = GeochemistryQuantityAux
variable = transported_SiO2
species = 'SiO2(aq)'
quantity = transported_moles_in_original_basis
execute_on = 'timestep_end'
[]
[transported_mass]
type = ParsedAux
args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
variable = transported_mass
function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
execute_on = 'timestep_end'
[]
[massfrac_H2O]
type = ParsedAux
args = 'transported_H2O transported_mass'
variable = massfrac_H2O
function = 'transported_H2O * 18.0152 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Na]
type = ParsedAux
args = 'transported_Na transported_mass'
variable = massfrac_Na
function = 'transported_Na * 22.9898 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_Cl]
type = ParsedAux
args = 'transported_Cl transported_mass'
variable = massfrac_Cl
function = 'transported_Cl * 35.453 / transported_mass'
execute_on = 'timestep_end'
[]
[massfrac_SiO2]
type = ParsedAux
args = 'transported_SiO2 transported_mass'
variable = massfrac_SiO2
function = 'transported_SiO2 * 60.0843 / transported_mass'
execute_on = 'timestep_end'
[]
[]
[Postprocessors]
[cm3_quartz]
type = PointValue
variable = free_cm3_QuartzUnlike
[]
[porosity]
type = PointValue
variable = porosity
[]
[solution_temperature]
type = PointValue
variable = solution_temperature
[]
[massfrac_H2O]
type = PointValue
variable = massfrac_H2O
[]
[massfrac_Na]
type = PointValue
variable = massfrac_Na
[]
[massfrac_Cl]
type = PointValue
variable = massfrac_Cl
[]
[massfrac_SiO2]
type = PointValue
variable = massfrac_SiO2
[]
[]
[Outputs]
exodus = true
csv = true
[]