GeochemistryConsoleOutput

This Output writes information to the console regarding the geochemical system (defined by the geochemistry_reactor) at a particular point that is defined by a NearestNodeNumber UserObject. It is quite verbose since it provides information about molalities, free masses, bulk compositions, surface characteristics and Nernst information for all relevant species, as well as descriptive characteristics such as temperature, pH, and ionic strength. It should therefore be used with caution otherwise your std::out will rapidly fill up, but it is useful for understanding and debugging models.

Usually this Output is added using Actions such as the TimeIndependentReactionSolver and the TimeDependentReactionSolver.

Advanced users may wish to add these objects manually to their input files. Here is an example:

[Outputs]
  [specially_added]
    type = GeochemistryConsoleOutput
    geochemistry_reactor = reactor_name
    precision = 8 # 8 digits of precision
    mol_cutoff = 1E-8 # species with molality or mole-number lower than this are not outputted
    solver_info = true
    nearest_node_number_UO = nearest_node
    execute_on = 'final' # just output at the end of the simulation
  []
[]

Input Parameters

geochemistry_reactorThe name of the GeochemistryReactor UserObject
C++ Type:UserObjectName
Controllable:No
Description:The name of the GeochemistryReactor UserObject
nearest_node_number_UOThe NearestNodeNumber UserObject that defines the physical point at which to query the GeochemistryReactor
C++ Type:UserObjectName
Controllable:No
Description:The NearestNodeNumber UserObject that defines the physical point at which to query the GeochemistryReactor

Required Parameters

additional_execute_onThe list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, FAILED, CUSTOM, ALWAYS.
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, FAILED, CUSTOM, ALWAYS
Controllable:No
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, FAILED, CUSTOM, ALWAYS.
end_stepTime step at which this output object stop operating
C++ Type:int
Controllable:No
Description:Time step at which this output object stop operating
execute_onINITIAL TIMESTEP_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, FAILED, CUSTOM, ALWAYS.
Default:INITIAL TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, FAILED, CUSTOM, ALWAYS
Controllable:No
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, FAILED, CUSTOM, ALWAYS.
mol_cutoff1e-40Information regarding species with molalities less than this amount will not be outputted
Default:1e-40
C++ Type:double
Controllable:No
Description:Information regarding species with molalities less than this amount will not be outputted
precision4Precision for printing values
Default:4
C++ Type:unsigned int
Controllable:No
Description:Precision for printing values
solver_infoFalsePrint information (to the console) from the solver including residuals, swaps, etc
Default:False
C++ Type:bool
Controllable:No
Description:Print information (to the console) from the solver including residuals, swaps, etc
start_stepTime step at which this output object begins to operate
C++ Type:int
Controllable:No
Description:Time step at which this output object begins to operate
stoichiometry_tolerance1e-06if abs(any stoichiometric coefficient) < stoi_tol then it is set to zero, and so will not appear in the output
Default:1e-06
C++ Type:double
Controllable:No
Description:if abs(any stoichiometric coefficient) < stoi_tol then it is set to zero, and so will not appear in the output
use_displacedFalseEnable/disable the use of the displaced mesh for outputting
Default:False
C++ Type:bool
Controllable:No
Description:Enable/disable the use of the displaced mesh for outputting

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.

Advanced Parameters

end_timeTime at which this output object stop operating
C++ Type:double
Controllable:No
Description:Time at which this output object stop operating
interval1The interval at which time steps are output to the solution file
Default:1
C++ Type:unsigned int
Controllable:No
Description:The interval at which time steps are output to the solution file
start_timeTime at which this output object begins to operate
C++ Type:double
Controllable:No
Description:Time at which this output object begins to operate
sync_onlyFalseOnly export results at sync times
Default:False
C++ Type:bool
Controllable:No
Description:Only export results at sync times
sync_timesTimes at which the output and solution is forced to occur
C++ Type:std::vector<double>
Controllable:No
Description:Times at which the output and solution is forced to occur
time_tolerance1e-14Time tolerance utilized checking start and end times
Default:1e-14
C++ Type:double
Controllable:No
Description:Time tolerance utilized checking start and end times

Timing Parameters

Input Files

(modules/geochemistry/test/tests/equilibrium_models/HCl_no_action.i)
(modules/geochemistry/test/tests/time_dependent_reactions/simple_no_action.i)
(modules/geochemistry/test/tests/geochemistry_console_output/console.i)

(modules/geochemistry/test/tests/geochemistry_console_output/console.i)

# An example of manually adding a GeochemistryConsoleOutput
[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor_name
  charge_balance_species = "Cl-"
  constraint_species = "H2O H+ Cl- Fe+++"
  constraint_value = "  1.0 1.0E-2 1.3E-2 1.0E-3"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition bulk_composition"
  constraint_unit = "kg moles moles moles"
  ramp_max_ionic_strength_initial = 0
  ramp_max_ionic_strength_subsequent = 1 # so can see the solver_info in the GeochemistryConsoleOutput
  kinetic_species_name = "Fe(OH)3(ppd)_nosorb"
  kinetic_species_initial_value = "1.0E-6"
  kinetic_species_unit = moles
  execute_console_output_on = 'final' # can compare with the specially_added one, below
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../database/ferric_hydroxide_sorption.json"
    basis_species = "H2O H+ Cl- Fe+++"
    kinetic_minerals = "Fe(OH)3(ppd)_nosorb"
  []
  [nearest_node]
    type = NearestNodeNumberUO
    point = '0 0 0' # in this case there is no spatial dependence, so the point is rather irrelevant
  []
[]

[Executioner]
  type = Steady
[]

[Outputs]
  [specially_added]
    type = GeochemistryConsoleOutput
    geochemistry_reactor = reactor_name
    precision = 8 # 8 digits of precision
    mol_cutoff = 1E-8 # species with molality or mole-number lower than this are not outputted
    solver_info = true
    nearest_node_number_UO = nearest_node
    execute_on = 'final' # just output at the end of the simulation
  []
[]

(modules/geochemistry/test/tests/equilibrium_models/HCl_no_action.i)

# This is an example of an input file that does not utilize an action.  Its functionality is the same as HCl.i
# This solves for molalities in a system just containing HCl
[GlobalParams]
  point = '0 0 0'
[]

[Mesh]
  type = GeneratedMesh
  dim = 1
  nx= 1
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [u]
    type = Diffusion
    variable = u
  []
[]

[AuxVariables]
  [solution_temperature]
  []
  [kg_solvent_H2O]
  []
  [activity_H2O]
  []
  [bulk_moles_H2O]
  []
  [pH]
  []
  [molal_H+]
  []
  [molal_Cl-]
  []
  [molal_HCl]
  []
  [molal_OH-]
  []
  [mg_per_kg_H+]
  []
  [mg_per_kg_Cl-]
  []
  [mg_per_kg_HCl]
  []
  [mg_per_kg_OH-]
  []
  [activity_H+]
  []
  [activity_Cl-]
  []
  [activity_HCl]
  []
  [activity_OH-]
  []
  [bulk_moles_H+]
  []
  [bulk_moles_Cl-]
  []
  [bulk_moles_HCl]
  []
  [bulk_moles_OH-]
  []
[]

[AuxKernels]
  [solution_temperature]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = solution_temperature
    quantity = temperature
  []
  [kg_solvent_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = kg_solvent_H2O
    quantity = molal
  []
  [activity_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = activity_H2O
    quantity = activity
  []
  [bulk_moles_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = bulk_moles_H2O
    quantity = bulk_moles
  []
  [pH]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = pH
    quantity = neglog10a
  []
  [molal_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'molal_H+'
    quantity = molal
  []
  [molal_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'molal_Cl-'
    quantity = molal
  []
  [molal_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'molal_HCl'
    quantity = molal
  []
  [molal_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'molal_OH-'
    quantity = molal
  []
  [mg_per_kg_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'mg_per_kg_H+'
    quantity = mg_per_kg
  []
  [mg_per_kg_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'mg_per_kg_Cl-'
    quantity = mg_per_kg
  []
  [mg_per_kg_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'mg_per_kg_HCl'
    quantity = mg_per_kg
  []
  [mg_per_kg_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'mg_per_kg_OH-'
    quantity = mg_per_kg
  []
  [activity_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'activity_H+'
    quantity = activity
  []
  [activity_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'activity_Cl-'
    quantity = activity
  []
  [activity_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'activity_HCl'
    quantity = activity
  []
  [activity_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'activity_OH-'
    quantity = activity
  []
  [bulk_moles_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'bulk_moles_H+'
    quantity = bulk_moles
  []
  [bulk_moles_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'bulk_moles_Cl-'
    quantity = bulk_moles
  []
  [bulk_moles_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'bulk_moles_HCl'
    quantity = bulk_moles
  []
  [bulk_moles_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'bulk_moles_OH-'
    quantity = bulk_moles
  []
[]

[Postprocessors]
  [pH]
    type = PointValue
    variable = 'pH'
  []
  [solvent_mass]
    type = PointValue
    variable = 'kg_solvent_H2O'
  []
  [molal_Cl-]
    type = PointValue
    variable = 'molal_Cl-'
  []
  [mg_per_kg_HCl]
    type = PointValue
    variable = 'mg_per_kg_HCl'
  []
  [activity_OH-]
    type = PointValue
    variable = 'activity_OH-'
  []
  [bulk_H+]
    type = PointValue
    variable = 'bulk_moles_H+'
  []
  [temperature]
    type = PointValue
    variable = 'solution_temperature'
  []
[]

[Executioner]
  type = Steady
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl-"
    piecewise_linear_interpolation = true # to reproduce the GWB result
  []
  [reactor]
    type = GeochemistryTimeDependentReactor
    model_definition = definition
    charge_balance_species = "Cl-"
    constraint_species = "H2O              H+            Cl-"
    constraint_value = "  1.0              -2            1E-2"
    constraint_meaning = "kg_solvent_water log10activity bulk_composition"
    constraint_unit = "   kg               dimensionless moles"
    ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
    abs_tol = 1E-15
  []
  [nnn]
    type = NearestNodeNumberUO
  []
[]

[Outputs]
  csv = true
  [console_output]
    type = GeochemistryConsoleOutput
    geochemistry_reactor = reactor
    nearest_node_number_UO = nnn
    solver_info = true
    execute_on = initial
  []
[]

(modules/geochemistry/test/tests/time_dependent_reactions/simple_no_action.i)

# This example is simple.i but without using an Action
# Simple example of time-dependent reaction path.
# This example involves an HCl solution that is initialized at pH=2, then the pH is controlled via controlled_activity, and finally HCl is titrated into the solution
[GlobalParams]
  point = '0 0 0'
[]

[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [u]
    type = Diffusion
    variable = u
  []
[]

[AuxVariables]
  [act_H+]
  []
  [solution_temperature]
  []
  [kg_solvent_H2O]
  []
  [activity_H2O]
  []
  [bulk_moles_H2O]
  []
  [pH]
  []
  [molal_H+]
  []
  [molal_Cl-]
  []
  [molal_HCl]
  []
  [molal_OH-]
  []
  [mg_per_kg_H+]
  []
  [mg_per_kg_Cl-]
  []
  [mg_per_kg_HCl]
  []
  [mg_per_kg_OH-]
  []
  [activity_H+]
  []
  [activity_Cl-]
  []
  [activity_HCl]
  []
  [activity_OH-]
  []
  [bulk_moles_H+]
  []
  [bulk_moles_Cl-]
  []
  [bulk_moles_HCl]
  []
  [bulk_moles_OH-]
  []
[]

[AuxKernels]
  [act_H+]
    type = FunctionAux
    variable = act_H+
    function = '10^(-2 - t)'
    execute_on = timestep_begin
  []
  [solution_temperature]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = solution_temperature
    quantity = temperature
  []
  [kg_solvent_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = kg_solvent_H2O
    quantity = molal
  []
  [activity_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = activity_H2O
    quantity = activity
  []
  [bulk_moles_H2O]
    type = GeochemistryQuantityAux
    species = 'H2O'
    reactor = reactor
    variable = bulk_moles_H2O
    quantity = bulk_moles
  []
  [pH]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = pH
    quantity = neglog10a
  []
  [molal_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'molal_H+'
    quantity = molal
  []
  [molal_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'molal_Cl-'
    quantity = molal
  []
  [molal_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'molal_HCl'
    quantity = molal
  []
  [molal_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'molal_OH-'
    quantity = molal
  []
  [mg_per_kg_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'mg_per_kg_H+'
    quantity = mg_per_kg
  []
  [mg_per_kg_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'mg_per_kg_Cl-'
    quantity = mg_per_kg
  []
  [mg_per_kg_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'mg_per_kg_HCl'
    quantity = mg_per_kg
  []
  [mg_per_kg_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'mg_per_kg_OH-'
    quantity = mg_per_kg
  []
  [activity_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'activity_H+'
    quantity = activity
  []
  [activity_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'activity_Cl-'
    quantity = activity
  []
  [activity_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'activity_HCl'
    quantity = activity
  []
  [activity_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'activity_OH-'
    quantity = activity
  []
  [bulk_moles_H+]
    type = GeochemistryQuantityAux
    species = 'H+'
    reactor = reactor
    variable = 'bulk_moles_H+'
    quantity = bulk_moles
  []
  [bulk_moles_Cl-]
    type = GeochemistryQuantityAux
    species = 'Cl-'
    reactor = reactor
    variable = 'bulk_moles_Cl-'
    quantity = bulk_moles
  []
  [bulk_moles_HCl]
    type = GeochemistryQuantityAux
    species = 'HCl'
    reactor = reactor
    variable = 'bulk_moles_HCl'
    quantity = bulk_moles
  []
  [bulk_moles_OH-]
    type = GeochemistryQuantityAux
    species = 'OH-'
    reactor = reactor
    variable = 'bulk_moles_OH-'
    quantity = bulk_moles
  []
[]

[Postprocessors]
  [pH]
    type = PointValue
    variable = 'pH'
  []
  [solvent_mass]
    type = PointValue
    variable = 'kg_solvent_H2O'
  []
  [molal_Cl-]
    type = PointValue
    variable = 'molal_Cl-'
  []
  [mg_per_kg_HCl]
    type = PointValue
    variable = 'mg_per_kg_HCl'
  []
  [activity_OH-]
    type = PointValue
    variable = 'activity_OH-'
  []
  [bulk_H+]
    type = PointValue
    variable = 'bulk_moles_H+'
  []
  [temperature]
    type = PointValue
    variable = 'solution_temperature'
  []
[]

[Executioner]
  type = Transient
  dt = 1
  end_time = 10
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl-"
  []
  [reactor]
    type = GeochemistryTimeDependentReactor
    model_definition = definition
    charge_balance_species = "Cl-"
    constraint_species = "H2O              H+            Cl-"
    constraint_value = "  1.0              -2            1E-2"
    constraint_meaning = "kg_solvent_water log10activity bulk_composition"
    constraint_unit = "   kg               dimensionless moles"
    ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping

# close the system at time = 0
    close_system_at_time = 0

# control pH.  This sets pH = 2 + t (see the act_H+ AuxKernel)
    controlled_activity_name = 'H+'
    controlled_activity_value = 'act_H+'

# remove the constraint on H+ activity at time = 5, when, from the previous time-step, pH = 2 + 4 = 6
    remove_fixed_activity_name = 'H+'
    remove_fixed_activity_time = 5

# add 1E-5 moles of HCl every second of the simulation: this has no impact before time = 5 when the fixed-activity constraint it turned off, but then, molality_H+ ~ 1E-6 + 1E-4 * (t - 4), so
# time, approx_pH
# 5, -log10(1E-4) = 4
# 10, -log10(6E-4) = 3.2
    source_species_names = 'HCl'
    source_species_rates = '1E-4'
  []
  [nnn]
    type = NearestNodeNumberUO
  []
[]

[Outputs]
  csv = true
  file_base = simple_out
  [console_output]
    type = GeochemistryConsoleOutput
    geochemistry_reactor = reactor
    nearest_node_number_UO = nnn
    solver_info = true
    execute_on = 'final'
  []
[]

(modules/geochemistry/test/tests/geochemistry_console_output/console.i)

# An example of manually adding a GeochemistryConsoleOutput
[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor_name
  charge_balance_species = "Cl-"
  constraint_species = "H2O H+ Cl- Fe+++"
  constraint_value = "  1.0 1.0E-2 1.3E-2 1.0E-3"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition bulk_composition"
  constraint_unit = "kg moles moles moles"
  ramp_max_ionic_strength_initial = 0
  ramp_max_ionic_strength_subsequent = 1 # so can see the solver_info in the GeochemistryConsoleOutput
  kinetic_species_name = "Fe(OH)3(ppd)_nosorb"
  kinetic_species_initial_value = "1.0E-6"
  kinetic_species_unit = moles
  execute_console_output_on = 'final' # can compare with the specially_added one, below
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../database/ferric_hydroxide_sorption.json"
    basis_species = "H2O H+ Cl- Fe+++"
    kinetic_minerals = "Fe(OH)3(ppd)_nosorb"
  []
  [nearest_node]
    type = NearestNodeNumberUO
    point = '0 0 0' # in this case there is no spatial dependence, so the point is rather irrelevant
  []
[]

[Executioner]
  type = Steady
[]

[Outputs]
  [specially_added]
    type = GeochemistryConsoleOutput
    geochemistry_reactor = reactor_name
    precision = 8 # 8 digits of precision
    mol_cutoff = 1E-8 # species with molality or mole-number lower than this are not outputted
    solver_info = true
    nearest_node_number_UO = nearest_node
    execute_on = 'final' # just output at the end of the simulation
  []
[]

Input Parameters
Input Files

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