AddSpatialReactionSolverAction Class Reference

Action that sets up a spatial reaction solver. More...

#include <AddSpatialReactionSolverAction.h>

Inheritance diagram for AddSpatialReactionSolverAction:

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	AddSpatialReactionSolverAction (const InputParameters &parameters)
virtual void	act () override
void	timedAct ()
virtual void	addRelationshipManagers (Moose::RelationshipManagerType when_type)
MooseObjectName	uniqueActionName () const
const std::string &	specificTaskName () const
const std::set< std::string > &	getAllTasks () const
void	appendTask (const std::string &task)
MooseApp &	getMooseApp () const
const std::string &	type () const
const std::string &	name () const
std::string	typeAndName () const
MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const
MooseObjectName	uniqueName () const
const InputParameters &	parameters () const
const hit::Node *	getHitNode () const
bool	hasBase () const
const std::string &	getBase () const
const T &	getParam (const std::string &name) const
std::vector< std::pair< T1, T2 > >	getParam (const std::string &param1, const std::string &param2) const
const T *	queryParam (const std::string &name) const
const T &	getRenamedParam (const std::string &old_name, const std::string &new_name) const
T	getCheckedPointerParam (const std::string &name, const std::string &error_string="") const
bool	isParamValid (const std::string &name) const
bool	isParamSetByUser (const std::string &name) const
void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const
void	paramError (const std::string &param, Args... args) const
void	paramWarning (const std::string &param, Args... args) const
void	paramWarning (const std::string &param, Args... args) const
void	paramInfo (const std::string &param, Args... args) const
std::string	messagePrefix (const bool hit_prefix=true) const
std::string	errorPrefix (const std::string &) const
void	mooseError (Args &&... args) const
void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const
void	mooseErrorNonPrefixed (Args &&... args) const
void	mooseWarning (Args &&... args) const
void	mooseWarning (Args &&... args) const
void	mooseWarningNonPrefixed (Args &&... args) const
void	mooseWarningNonPrefixed (Args &&... args) const
void	mooseDeprecated (Args &&... args) const
void	mooseDeprecated (Args &&... args) const
void	mooseDeprecatedNoTrace (Args &&... args) const
void	mooseInfo (Args &&... args) const
void	callMooseError (std::string msg, const bool with_prefix, const hit::Node *node=nullptr, const bool show_trace=true) const
std::string	getDataFileName (const std::string &param) const
std::string	getDataFileNameByName (const std::string &relative_path) const
std::string	getDataFilePath (const std::string &relative_path) const
PerfGraph &	perfGraph ()
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

Static Public Member Functions
static InputParameters	validParams ()
static void	callMooseError (MooseApp *const app, const InputParameters &params, std::string msg, const bool with_prefix, const hit::Node *node, const bool show_trace=true)

Public Attributes
	usingCombinedWarningSolutionWarnings
const ConsoleStream	_console

Static Public Attributes
static const std::string	unique_action_name_param
static const std::string	type_param
static const std::string	name_param
static const std::string	unique_name_param
static const std::string	app_param
static const std::string	moose_base_param
static const std::string	kokkos_object_param
static constexpr auto	SYSTEM
static constexpr auto	NAME

Protected Member Functions
void	addAuxSpecies (const std::string &var_name, const std::string &species_name, const std::string &unit)
	Adds AuxVariable and AuxKernel that will record species concentrations.
bool	addRelationshipManagers (Moose::RelationshipManagerType when_type, const InputParameters &moose_object_pars)
void	associateWithParameter (const std::string &param_name, InputParameters &params) const
void	associateWithParameter (const InputParameters &from_params, const std::string &param_name, InputParameters &params) const
const T &	getMeshProperty (const std::string &data_name, const std::string &prefix)
const T &	getMeshProperty (const std::string &data_name)
bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const
bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const
bool	hasMeshProperty (const std::string &data_name) const
bool	hasMeshProperty (const std::string &data_name) const
std::string	meshPropertyName (const std::string &data_name) const
PerfID	registerTimedSection (const std::string &section_name, const unsigned int level) const
PerfID	registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const
std::string	timedSectionName (const std::string &section_name) const
void	flagInvalidSolutionInternal (const InvalidSolutionID invalid_solution_id) const
InvalidSolutionID	registerInvalidSolutionInternal (const std::string &message, const bool warning) const

Static Protected Member Functions
static std::string	meshPropertyName (const std::string &data_name, const std::string &prefix)

Protected Attributes
std::string	_registered_identifier
std::string	_specific_task_name
std::set< std::string >	_all_tasks
ActionWarehouse &	_awh
const std::string &	_current_task
std::shared_ptr< MooseMesh > &	_mesh
std::shared_ptr< MooseMesh > &	_displaced_mesh
std::shared_ptr< FEProblemBase > &	_problem
PerfID	_act_timer
MooseApp &	_app
Factory &	_factory
ActionFactory &	_action_factory
const std::string &	_type
const std::string &	_name
const InputParameters &	_pars
MooseApp &	_pg_moose_app
const std::string	_prefix
const Parallel::Communicator &	_communicator

Private Member Functions
bool	addRelationshipManager (Moose::RelationshipManagerType input_rm_type, const InputParameters &moose_object_pars, std::string rm_name, Moose::RelationshipManagerType rm_type, Moose::RelationshipManagerInputParameterCallback rm_input_parameter_func, Moose::RMSystemType sys_type=Moose::RMSystemType::NONE)
virtual std::string	meshPropertyPrefix (const std::string &data_name) const
const RestartableDataValue &	getMeshPropertyInternal (const std::string &data_name, const std::string &prefix) const
void	mooseErrorInternal (Args &&... args) const

Static Private Member Functions
static const hit::Node *	getHitNode (const InputParameters &params)
static std::string	messagePrefix (const InputParameters &params, const bool hit_prefix)

Private Attributes
const ParallelParamObject &	_parent
MooseApp &	_meta_data_app
const MooseObject *const	_meta_data_object
const MooseBase &	_si_moose_base
const FEProblemBase *	_si_problem

Detailed Description

Action that sets up a spatial reaction solver.

Definition at line 17 of file AddSpatialReactionSolverAction.h.

Constructor & Destructor Documentation

AddSpatialReactionSolverAction()

AddSpatialReactionSolverAction::AddSpatialReactionSolverAction

(

const InputParameters &

parameters

)

Definition at line 35 of file AddSpatialReactionSolverAction.C.

  : AddGeochemistrySolverAction(params)
{
}

Member Function Documentation

act()

void AddSpatialReactionSolverAction::act ( )

overridevirtual

Reimplemented from AddGeochemistrySolverAction.

Definition at line 41 of file AddSpatialReactionSolverAction.C.

{
  // create Output and Aux objects
  AddGeochemistrySolverAction::act();
 
  // Create a "solve=false" FEProblem, if appropriate
  if (_current_task == "create_problem")
  {
    const std::string class_name = "FEProblem";
    InputParameters params = _factory.getValidParams(class_name);
    params.set<MooseMesh *>("mesh") = _mesh.get();
    params.set<bool>("use_nonlinear") = true;
    params.set<bool>("solve") = getParam<bool>("include_moose_solve");
    _problem = _factory.create<FEProblemBase>(class_name, "Problem", params);
    _problem->setKernelCoverageCheck(getParam<bool>("include_moose_solve")
                                         ? FEProblemBase::CoverageCheckMode::TRUE
                                         : FEProblemBase::CoverageCheckMode::FALSE);
  }
  else if (_current_task == "add_geochemistry_reactor")
  {
    const std::string class_name = "GeochemistrySpatialReactor";
    auto params = _factory.getValidParams(class_name);
    // Only pass parameters that were supplied to this action
 
    // Block and Boundary params
    if (isParamValid("block"))
      params.set<std::vector<SubdomainName>>("block") =
          getParam<std::vector<SubdomainName>>("block");
    if (isParamValid("boundary"))
      params.set<std::vector<BoundaryName>>("boundary") =
          getParam<std::vector<BoundaryName>>("boundary");
 
    // GeochemistryReactorBase::sharedParams
    if (isParamValid("swap_out_of_basis"))
      params.set<std::vector<std::string>>("swap_out_of_basis") =
          getParam<std::vector<std::string>>("swap_out_of_basis");
    if (isParamValid("swap_into_basis"))
      params.set<std::vector<std::string>>("swap_into_basis") =
          getParam<std::vector<std::string>>("swap_into_basis");
    params.set<MultiMooseEnum>("constraint_meaning") =
        getParam<MultiMooseEnum>("constraint_meaning");
    params.set<std::vector<std::string>>("constraint_species") =
        getParam<std::vector<std::string>>("constraint_species");
    params.set<std::vector<Real>>("constraint_value") =
        getParam<std::vector<Real>>("constraint_value");
    params.set<MultiMooseEnum>("constraint_unit") = getParam<MultiMooseEnum>("constraint_unit");
    params.set<Real>("max_ionic_strength") = getParam<Real>("max_ionic_strength");
    params.set<unsigned>("extra_iterations_to_make_consistent") =
        getParam<unsigned>("extra_iterations_to_make_consistent");
    params.set<std::string>("charge_balance_species") =
        getParam<std::string>("charge_balance_species");
    if (isParamValid("prevent_precipitation"))
      params.set<std::vector<std::string>>("prevent_precipitation") =
          getParam<std::vector<std::string>>("prevent_precipitation");
    params.set<Real>("abs_tol") = getParam<Real>("abs_tol");
    params.set<Real>("rel_tol") = getParam<Real>("rel_tol");
    params.set<Real>("min_initial_molality") = getParam<Real>("min_initial_molality");
    params.set<unsigned>("max_iter") = getParam<unsigned>("max_iter");
    params.set<Real>("max_initial_residual") = getParam<Real>("max_initial_residual");
    params.set<Real>("swap_threshold") = getParam<Real>("swap_threshold");
    params.set<unsigned>("max_swaps_allowed") = getParam<unsigned>("max_swaps_allowed");
    params.set<unsigned>("ramp_max_ionic_strength_initial") =
        getParam<unsigned>("ramp_max_ionic_strength_initial");
    params.set<bool>("ionic_str_using_basis_only") = getParam<bool>("ionic_str_using_basis_only");
    params.set<bool>("stoichiometric_ionic_str_using_Cl_only") =
        getParam<bool>("stoichiometric_ionic_str_using_Cl_only");
 
    // GeochemistryReactorBase non-shared params
    params.set<UserObjectName>("model_definition") = getParam<UserObjectName>("model_definition");
    params.set<Real>("stoichiometry_tolerance") = getParam<Real>("stoichiometry_tolerance");
 
    // GeochemistrySpatialReactor::sharedParams
    params.set<unsigned>("ramp_max_ionic_strength_subsequent") =
        getParam<unsigned>("ramp_max_ionic_strength_subsequent");
    params.set<Real>("initial_temperature") = getParam<Real>("initial_temperature");
    params.applySpecificParameters(parameters(), {"temperature"});
    params.set<Real>("close_system_at_time") = getParam<Real>("close_system_at_time");
    if (isParamValid("remove_fixed_activity_name"))
      params.set<std::vector<std::string>>("remove_fixed_activity_name") =
          getParam<std::vector<std::string>>("remove_fixed_activity_name");
    if (isParamValid("remove_fixed_activity_time"))
      params.set<std::vector<Real>>("remove_fixed_activity_time") =
          getParam<std::vector<Real>>("remove_fixed_activity_time");
    if (isParamValid("source_species_names"))
      params.set<std::vector<std::string>>("source_species_names") =
          getParam<std::vector<std::string>>("source_species_names");
    if (isParamValid("source_species_rates"))
      params.applySpecificParameters(parameters(), {"source_species_rates"});
    if (isParamValid("controlled_activity_name"))
      params.set<std::vector<std::string>>("controlled_activity_name") =
          getParam<std::vector<std::string>>("controlled_activity_name");
    if (isParamValid("controlled_activity_value"))
      params.applySpecificParameters(parameters(), {"controlled_activity_value"});
    params.set<bool>("evaluate_kinetic_rates_always") =
        getParam<bool>("evaluate_kinetic_rates_always");
    if (isParamValid("kinetic_species_name"))
      params.set<std::vector<std::string>>("kinetic_species_name") =
          getParam<std::vector<std::string>>("kinetic_species_name");
    if (isParamValid("kinetic_species_initial_value"))
      params.set<std::vector<Real>>("kinetic_species_initial_value") =
          getParam<std::vector<Real>>("kinetic_species_initial_value");
    if (isParamValid("kinetic_species_unit"))
      params.set<MultiMooseEnum>("kinetic_species_unit") =
          getParam<MultiMooseEnum>("kinetic_species_unit");
    params.set<bool>("adaptive_timestepping") = getParam<bool>("adaptive_timestepping");
    params.set<Real>("dt_min") = getParam<Real>("dt_min");
    params.set<Real>("dt_dec") = getParam<Real>("dt_dec");
    params.set<Real>("dt_inc") = getParam<Real>("dt_inc");
    params.set<ExecFlagEnum>("execute_on") = {EXEC_TIMESTEP_END};
    _problem->addUserObject(
        class_name, getParam<UserObjectName>("geochemistry_reactor_name"), params);
  }
}

addAuxSpecies()

void AddGeochemistrySolverAction::addAuxSpecies ( const std::string &  var_name, const std::string &  species_name, const std::string &  unit  )

protectedinherited

Adds AuxVariable and AuxKernel that will record species concentrations.

Parameters

var_name	AuxVariable name
species_name	Species name
unit	Unit choice: defined in GeochemistryQuantityAux

Definition at line 255 of file AddGeochemistrySolverAction.C.

{
  // add AuxVariable
  auto var_params = _factory.getValidParams("MooseVariable");
  _problem->addAuxVariable("MooseVariable", var_name, var_params);
  // add AuxKernel
  const std::string class_name = "GeochemistryQuantityAux";
  auto params = _factory.getValidParams(class_name);
  params.set<std::string>("species") = species_name;
  params.set<MooseEnum>("quantity") = quantity;
  params.set<UserObjectName>("reactor") = getParam<UserObjectName>("geochemistry_reactor_name");
  params.set<AuxVariableName>("variable") = var_name;
  params.set<ExecFlagEnum>("execute_on") = EXEC_TIMESTEP_END;
  _problem->addAuxKernel(class_name, var_name, params);
}

Referenced by AddGeochemistrySolverAction::act().

validParams()

InputParameters AddSpatialReactionSolverAction::validParams ( )

static

Definition at line 23 of file AddSpatialReactionSolverAction.C.

{
  InputParameters params = AddGeochemistrySolverAction::validParams();
  params += GeochemistrySpatialReactor::sharedParams();
  params.addClassDescription(
      "Action that sets up a spatially-dependent reaction solver.  This creates creates a "
      "spatial geochemistry solver, and adds AuxVariables corresonding to the molalities, "
      "etc");
 
  return params;
}

---

The documentation for this class was generated from the following files:

• geochemistry/include/actions/AddSpatialReactionSolverAction.h
• geochemistry/src/actions/AddSpatialReactionSolverAction.C