GeochemicalModelInterrogator

Usually this Output is added using the GeochemicalModelInterrogator action. The purpose of this Output is to output balanced reactions and equilibrium constants, activity ratios, equilibrium temperature, etc, depending on the interrogation option. If a invalid swap is defined through the swap_into_basis and swap_out_of_basis options, the simulation will exit with an explanatory error message.

An example of outputting equilibrium reactions (interrogation = reaction) for different choices of basis components is

# Outputs equilibrium reactions fo Clinoptil-Ca for various different basis species, along with log10(K)
[GeochemicalModelInterrogator<<<{"href": "../../syntax/GeochemicalModelInterrogator/index.html"}>>>]
  model_definition<<<{"description": "The name of the GeochemicalModelDefinition user object"}>>> = definition
  swap_out_of_basis<<<{"description": "Species that should be removed from the model_definition's basis and be replaced with the swap_into_basis species.  There must be the same number of species in swap_out_of_basis and swap_into_basis.  If this list contains more than one species, the swapping is performed one-by-one, starting with the first pair (swap_out_of_basis[0] and swap_into_basis[0]), then the next pair, etc"}>>> = "Al+++     SiO2(aq) H+"
  swap_into_basis<<<{"description": "Species that should be removed from the model_definition's equilibrium species list and added to the basis"}>>> = "  Muscovite Quartz   OH-"
  equilibrium_species<<<{"description": "Only output results for this equilibrium species.  If not provided, results for all equilibrium species will be outputted"}>>> = "Clinoptil-Ca"
[]

[UserObjects<<<{"href": "../../syntax/UserObjects/index.html"}>>>]
  [definition]
    type = GeochemicalModelDefinition<<<{"description": "User object that parses a geochemical database file, and only retains information relevant to the current geochemical model", "href": "../userobjects/GeochemicalModelDefinition.html"}>>>
    database_file<<<{"description": "The name of the geochemical database file"}>>> = "../../../database/moose_geochemdb.json"
    basis_species<<<{"description": "A list of basis components relevant to the aqueous-equilibrium problem. H2O must appear first in this list.  These components must be chosen from the 'basis species' in the database, the sorbing sites (if any) and the decoupled redox states that are in disequilibrium (if any)."}>>> = "H2O Ca++ Al+++ SiO2(aq) H+ K+"
    equilibrium_minerals<<<{"description": "A list of minerals that are in equilibrium with the aqueous solution.  All members of this list must be in the 'minerals' section of the database file"}>>> = "Clinoptil-Ca Muscovite Quartz"
    piecewise_linear_interpolation<<<{"description": "If true then use a piecewise-linear interpolation of logK and Debye-Huckel parameters, regardless of the interpolation type specified in the database file.  This can be useful for comparing with results using other geochemistry software"}>>> = true # to get exact logK at 25degC with no best-fit interpolation
  []
[]

An example of outputting activity ratios/products (interrogation = activity) is

# Output activity ratios for reactions involving muscovite
[GeochemicalModelInterrogator<<<{"href": "../../syntax/GeochemicalModelInterrogator/index.html"}>>>]
  model_definition<<<{"description": "The name of the GeochemicalModelDefinition user object"}>>> = definition
  swap_out_of_basis<<<{"description": "Species that should be removed from the model_definition's basis and be replaced with the swap_into_basis species.  There must be the same number of species in swap_out_of_basis and swap_into_basis.  If this list contains more than one species, the swapping is performed one-by-one, starting with the first pair (swap_out_of_basis[0] and swap_into_basis[0]), then the next pair, etc"}>>> = "Al+++"
  swap_into_basis<<<{"description": "Species that should be removed from the model_definition's equilibrium species list and added to the basis"}>>> = "  Kaolinite"
  activity_species<<<{"description": "Species that are provided numerical values of activity (or fugacity for gases) in the activity_value input"}>>> = "H2O"
  activity_values<<<{"description": "Numerical values for the activity (or fugacity) for the species in the activity_species list.  These are activity values, not log10(activity)."}>>> = "1.0"
  equilibrium_species<<<{"description": "Only output results for this equilibrium species.  If not provided, results for all equilibrium species will be outputted"}>>> = Muscovite
  interrogation<<<{"description": "Type of interrogation to perform.  reaction: Output equilibrium species reactions and log10K.  activity: determine activity products at equilibrium.  eqm_temperature: determine temperature to ensure equilibrium"}>>> = activity
[]

[UserObjects<<<{"href": "../../syntax/UserObjects/index.html"}>>>]
  [definition]
    type = GeochemicalModelDefinition<<<{"description": "User object that parses a geochemical database file, and only retains information relevant to the current geochemical model", "href": "../userobjects/GeochemicalModelDefinition.html"}>>>
    database_file<<<{"description": "The name of the geochemical database file"}>>> = "../../../database/moose_geochemdb.json"
    basis_species<<<{"description": "A list of basis components relevant to the aqueous-equilibrium problem. H2O must appear first in this list.  These components must be chosen from the 'basis species' in the database, the sorbing sites (if any) and the decoupled redox states that are in disequilibrium (if any)."}>>> = "H2O K+ Al+++ SiO2(aq) H+"
    equilibrium_minerals<<<{"description": "A list of minerals that are in equilibrium with the aqueous solution.  All members of this list must be in the 'minerals' section of the database file"}>>> = "Muscovite Kaolinite"
    piecewise_linear_interpolation<<<{"description": "If true then use a piecewise-linear interpolation of logK and Debye-Huckel parameters, regardless of the interpolation type specified in the database file.  This can be useful for comparing with results using other geochemistry software"}>>> = true # to get exact logK at 25degC with no best-fit interpolation
  []
[]

An example of computing temperature (interrogation = eqm_temperature) at equilibrium is

# Find temperature at equilibrium for reactions involving gypsum
[GeochemicalModelInterrogator<<<{"href": "../../syntax/GeochemicalModelInterrogator/index.html"}>>>]
  model_definition<<<{"description": "The name of the GeochemicalModelDefinition user object"}>>> = definition
  swap_out_of_basis<<<{"description": "Species that should be removed from the model_definition's basis and be replaced with the swap_into_basis species.  There must be the same number of species in swap_out_of_basis and swap_into_basis.  If this list contains more than one species, the swapping is performed one-by-one, starting with the first pair (swap_out_of_basis[0] and swap_into_basis[0]), then the next pair, etc"}>>> = "Ca++"
  swap_into_basis<<<{"description": "Species that should be removed from the model_definition's equilibrium species list and added to the basis"}>>> = "  Anhydrite"
  activity_species<<<{"description": "Species that are provided numerical values of activity (or fugacity for gases) in the activity_value input"}>>> = "H2O"
  activity_values<<<{"description": "Numerical values for the activity (or fugacity) for the species in the activity_species list.  These are activity values, not log10(activity)."}>>> = "1.0"
  temperature<<<{"description": "Equilibrium constants will be computed at this temperature [degC].  This is ignored if interrogation=eqm_temperature."}>>> = 25
  equilibrium_species<<<{"description": "Only output results for this equilibrium species.  If not provided, results for all equilibrium species will be outputted"}>>> = Gypsum
  interrogation<<<{"description": "Type of interrogation to perform.  reaction: Output equilibrium species reactions and log10K.  activity: determine activity products at equilibrium.  eqm_temperature: determine temperature to ensure equilibrium"}>>> = eqm_temperature
[]

[UserObjects<<<{"href": "../../syntax/UserObjects/index.html"}>>>]
  [definition]
    type = GeochemicalModelDefinition<<<{"description": "User object that parses a geochemical database file, and only retains information relevant to the current geochemical model", "href": "../userobjects/GeochemicalModelDefinition.html"}>>>
    database_file<<<{"description": "The name of the geochemical database file"}>>> = "../../../database/moose_geochemdb.json"
    basis_species<<<{"description": "A list of basis components relevant to the aqueous-equilibrium problem. H2O must appear first in this list.  These components must be chosen from the 'basis species' in the database, the sorbing sites (if any) and the decoupled redox states that are in disequilibrium (if any)."}>>> = "H2O Ca++ SO4--"
    equilibrium_minerals<<<{"description": "A list of minerals that are in equilibrium with the aqueous solution.  All members of this list must be in the 'minerals' section of the database file"}>>> = "Gypsum Anhydrite"
  []
[]

An example of outputting pH and pe (interrogation = activity) at equilibrium is

# Compute pH values for an equilibrium reaction involving the mineral hematite
[GeochemicalModelInterrogator<<<{"href": "../../syntax/GeochemicalModelInterrogator/index.html"}>>>]
  model_definition<<<{"description": "The name of the GeochemicalModelDefinition user object"}>>> = definition
  equilibrium_species<<<{"description": "Only output results for this equilibrium species.  If not provided, results for all equilibrium species will be outputted"}>>> = Hematite
  activity_species<<<{"description": "Species that are provided numerical values of activity (or fugacity for gases) in the activity_value input"}>>> = 'H2O Fe++'
  activity_values<<<{"description": "Numerical values for the activity (or fugacity) for the species in the activity_species list.  These are activity values, not log10(activity)."}>>> = '1 1E-10'
  interrogation<<<{"description": "Type of interrogation to perform.  reaction: Output equilibrium species reactions and log10K.  activity: determine activity products at equilibrium.  eqm_temperature: determine temperature to ensure equilibrium"}>>> = activity
[]

[UserObjects<<<{"href": "../../syntax/UserObjects/index.html"}>>>]
  [definition]
    type = GeochemicalModelDefinition<<<{"description": "User object that parses a geochemical database file, and only retains information relevant to the current geochemical model", "href": "../userobjects/GeochemicalModelDefinition.html"}>>>
    database_file<<<{"description": "The name of the geochemical database file"}>>> = "../../../database/moose_geochemdb.json"
    basis_species<<<{"description": "A list of basis components relevant to the aqueous-equilibrium problem. H2O must appear first in this list.  These components must be chosen from the 'basis species' in the database, the sorbing sites (if any) and the decoupled redox states that are in disequilibrium (if any)."}>>> = "H2O Fe++ H+ O2(aq)"
    equilibrium_minerals<<<{"description": "A list of minerals that are in equilibrium with the aqueous solution.  All members of this list must be in the 'minerals' section of the database file"}>>> = "Hematite"
    piecewise_linear_interpolation<<<{"description": "If true then use a piecewise-linear interpolation of logK and Debye-Huckel parameters, regardless of the interpolation type specified in the database file.  This can be useful for comparing with results using other geochemistry software"}>>> = true # to get exact logK at 25degC with no best-fit interpolation
  []
[]