Theory

Usage

Development

GeochemistryQuantityAux

This AuxKernel is used to extract information from the GeochemistryReactor that underlies geochemistry models.

A large number of AuxVariables and GeochemistryQuantityAux Kernels are often added automatically using the geochemistry actions, for instance TimeDependentReactionSolver. However, if users wish to add their own manually, an example (that adds an AuxVariable to measure pH) is

[AuxVariables<<<{"href": "../../syntax/AuxVariables/index.html"}>>>]
  [the_aux]
  []
[]

[AuxKernels<<<{"href": "../../syntax/AuxKernels/index.html"}>>>]
  [the_aux]
    type = GeochemistryQuantityAux<<<{"description": "Extracts information from the Reactor and records it in the AuxVariable", "href": "GeochemistryQuantityAux.html"}>>>
    species<<<{"description": "Species name"}>>> = 'H+'
    reactor<<<{"description": "The name of the Geochemistry*Reactor user object."}>>> = geochemistry_reactor
    variable<<<{"description": "The name of the variable that this object applies to"}>>> = the_aux
    quantity<<<{"description": "Type of quantity to output.  These are available for non-kinetic species: activity (which equals fugacity for gases); bulk moles (this will be zero if the species is not in the basis); neglog10a = -log10(activity); transported_moles_in_original_basis (will throw an error if species is not in original basis).  These are available only for non-kinetic non-minerals: molal = mol(species)/kg(solvent_water); mg_per_kg = mg(species)/kg(solvent_water).  These are available only for minerals: free_mg = free mg; free_cm3 = free cubic-centimeters; moles_dumped = moles dumped when special dump and flow-through modes are active.  These are available for minerals that host sorbing sites: surface_charge (C/m^2); surface_potential (V).  These are available for kinetic species: kinetic_moles; kinetic_additions (-dt * rate = mole increment in kinetic species for this timestep).  If quantity=temperature, then the 'species' is ignored and the AuxVariable will record the aqueous solution temperature in degC"}>>> = neglog10a
  []
[]
(moose/modules/geochemistry/test/tests/geochemistry_quantity_aux/neglog10a.i)

Input Parameters

  • reactorThe name of the Geochemistry*Reactor user object.

    C++ Type:UserObjectName

    Controllable:No

    Description:The name of the Geochemistry*Reactor user object.

  • speciesSpecies name

    C++ Type:std::string

    Controllable:Yes

    Description:Species name

  • variableThe name of the variable that this object applies to

    C++ Type:AuxVariableName

    Unit:(no unit assumed)

    Controllable:No

    Description:The name of the variable that this object applies to

Required Parameters

  • blockThe list of blocks (ids or names) that this object will be applied

    C++ Type:std::vector<SubdomainName>

    Controllable:No

    Description:The list of blocks (ids or names) that this object will be applied

  • boundaryThe list of boundaries (ids or names) from the mesh where this object applies

    C++ Type:std::vector<BoundaryName>

    Controllable:No

    Description:The list of boundaries (ids or names) from the mesh where this object applies

  • check_boundary_restrictedTrueWhether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh

    Default:True

    C++ Type:bool

    Controllable:No

    Description:Whether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh

  • execute_onLINEAR TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.

    Default:LINEAR TIMESTEP_END

    C++ Type:ExecFlagEnum

    Options:NONE, INITIAL, LINEAR, LINEAR_CONVERGENCE, NONLINEAR, NONLINEAR_CONVERGENCE, POSTCHECK, TIMESTEP_END, TIMESTEP_BEGIN, MULTIAPP_FIXED_POINT_END, MULTIAPP_FIXED_POINT_BEGIN, MULTIAPP_FIXED_POINT_CONVERGENCE, FINAL, CUSTOM, PRE_DISPLACE

    Controllable:No

    Description:The list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.

  • quantitymolalType of quantity to output. These are available for non-kinetic species: activity (which equals fugacity for gases); bulk moles (this will be zero if the species is not in the basis); neglog10a = -log10(activity); transported_moles_in_original_basis (will throw an error if species is not in original basis). These are available only for non-kinetic non-minerals: molal = mol(species)/kg(solvent_water); mg_per_kg = mg(species)/kg(solvent_water). These are available only for minerals: free_mg = free mg; free_cm3 = free cubic-centimeters; moles_dumped = moles dumped when special dump and flow-through modes are active. These are available for minerals that host sorbing sites: surface_charge (C/m^2); surface_potential (V). These are available for kinetic species: kinetic_moles; kinetic_additions (-dt * rate = mole increment in kinetic species for this timestep). If quantity=temperature, then the 'species' is ignored and the AuxVariable will record the aqueous solution temperature in degC

    Default:molal

    C++ Type:MooseEnum

    Options:molal, mg_per_kg, free_mg, free_cm3, neglog10a, activity, bulk_moles, surface_charge, surface_potential, temperature, kinetic_moles, kinetic_additions, moles_dumped, transported_moles_in_original_basis

    Controllable:No

    Description:Type of quantity to output. These are available for non-kinetic species: activity (which equals fugacity for gases); bulk moles (this will be zero if the species is not in the basis); neglog10a = -log10(activity); transported_moles_in_original_basis (will throw an error if species is not in original basis). These are available only for non-kinetic non-minerals: molal = mol(species)/kg(solvent_water); mg_per_kg = mg(species)/kg(solvent_water). These are available only for minerals: free_mg = free mg; free_cm3 = free cubic-centimeters; moles_dumped = moles dumped when special dump and flow-through modes are active. These are available for minerals that host sorbing sites: surface_charge (C/m^2); surface_potential (V). These are available for kinetic species: kinetic_moles; kinetic_additions (-dt * rate = mole increment in kinetic species for this timestep). If quantity=temperature, then the 'species' is ignored and the AuxVariable will record the aqueous solution temperature in degC

Optional Parameters

  • control_tagsAdds user-defined labels for accessing object parameters via control logic.

    C++ Type:std::vector<std::string>

    Controllable:No

    Description:Adds user-defined labels for accessing object parameters via control logic.

  • enableTrueSet the enabled status of the MooseObject.

    Default:True

    C++ Type:bool

    Controllable:Yes

    Description:Set the enabled status of the MooseObject.

  • seed0The seed for the master random number generator

    Default:0

    C++ Type:unsigned int

    Controllable:No

    Description:The seed for the master random number generator

  • use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

  • prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.

    C++ Type:MaterialPropertyName

    Unit:(no unit assumed)

    Controllable:No

    Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.

  • use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

Material Property Retrieval Parameters