User object that parses a geochemical database file, and only retains information relevant to the current geochemical model. More...

#include <GeochemicalModelDefinition.h>

Inheritance diagram for GeochemicalModelDefinition:

[legend]

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	GeochemicalModelDefinition (const InputParameters &parameters)

virtual void	initialize () override final

virtual void	execute () override final

virtual void	finalize () override final

const ModelGeochemicalDatabase &	getDatabase () const
	provides a reference to the pertinent geochemical database held by this object More...

const PertinentGeochemicalSystem &	getPertinentGeochemicalSystem () const
	provides a reference to the PertinentGeochemicalSystem of this object More...

const GeochemicalDatabaseReader &	getOriginalFullDatabase () const
	provides a reference to the full database file used by this object More...

SubProblem &	getSubProblem () const

bool	shouldDuplicateInitialExecution () const

virtual Real	spatialValue (const Point &) const

virtual const std::vector< Point >	spatialPoints () const

void	gatherSum (T &value)

void	gatherMax (T &value)

void	gatherMin (T &value)

void	gatherProxyValueMax (T1 &proxy, T2 &value)

void	gatherProxyValueMin (T1 &proxy, T2 &value)

void	setPrimaryThreadCopy (UserObject *primary)

UserObject *	primaryThreadCopy ()

std::set< UserObjectName >	getDependObjects () const

virtual bool	needThreadedCopy () const

const std::set< std::string > &	getRequestedItems () override

const std::set< std::string > &	getSuppliedItems () override

unsigned int	systemNumber () const

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

std::shared_ptr< const MooseObject >	getSharedPtr () const

MooseApp &	getMooseApp () const

const std::string &	type () const

virtual const std::string &	name () const

std::string	typeAndName () const

std::string	errorPrefix (const std::string &error_type) const

void	callMooseError (std::string msg, const bool with_prefix) const

MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const

const InputParameters &	parameters () const

MooseObjectName	uniqueName () 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 &nm) const

void	paramError (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

void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const

void	mooseError (Args &&... args) const

void	mooseErrorNonPrefixed (Args &&... args) const

void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseInfo (Args &&... args) 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

virtual void	initialSetup ()

virtual void	timestepSetup ()

virtual void	jacobianSetup ()

virtual void	residualSetup ()

virtual void	customSetup (const ExecFlagType &)

const ExecFlagEnum &	getExecuteOnEnum () const

UserObjectName	getUserObjectName (const std::string &param_name) const

const T &	getUserObject (const std::string &param_name, bool is_dependency=true) const

const T &	getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const

const UserObject &	getUserObjectBase (const std::string &param_name, bool is_dependency=true) const

const UserObject &	getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const

const std::vector< MooseVariableScalar *> &	getCoupledMooseScalarVars ()

const std::set< TagID > &	getScalarVariableCoupleableVectorTags () const

const std::set< TagID > &	getScalarVariableCoupleableMatrixTags () const

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, const unsigned int state=0)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name, MaterialData &material_data)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name)

std::pair< const MaterialProperty< T > *, std::set< SubdomainID > >	getBlockMaterialProperty (const MaterialPropertyName &name)

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialProperty (const std::string &name)

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialProperty ()

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialPropertyByName (const std::string &prop_name)

const MaterialProperty< T > &	getZeroMaterialProperty (Ts... args)

std::set< SubdomainID >	getMaterialPropertyBlocks (const std::string &name)

std::vector< SubdomainName >	getMaterialPropertyBlockNames (const std::string &name)

std::set< BoundaryID >	getMaterialPropertyBoundaryIDs (const std::string &name)

std::vector< BoundaryName >	getMaterialPropertyBoundaryNames (const std::string &name)

void	checkBlockAndBoundaryCompatibility (std::shared_ptr< MaterialBase > discrete)

std::unordered_map< SubdomainID, std::vector< MaterialBase *> >	buildRequiredMaterials (bool allow_stateful=true)

void	statefulPropertiesAllowed (bool)

bool	getMaterialPropertyCalled () const

virtual const std::unordered_set< unsigned int > &	getMatPropDependencies () const

virtual void	resolveOptionalProperties ()

const GenericMaterialProperty< T, is_ad > &	getPossiblyConstantGenericMaterialPropertyByName (const MaterialPropertyName &prop_name, MaterialData &material_data, const unsigned int state)

bool	isImplicit ()

Moose::StateArg	determineState () const

virtual void	threadJoin (const UserObject &) override

virtual void	threadJoin (const UserObject &) override

virtual void	subdomainSetup () override

virtual void	subdomainSetup () override

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

const GenericOptionalMaterialProperty< T, is_ad > &	getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const GenericOptionalMaterialProperty< T, is_ad > &	getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalMaterialProperty< T > &	getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalMaterialProperty< T > &	getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalADMaterialProperty< T > &	getOptionalADMaterialProperty (const std::string &name)

const OptionalADMaterialProperty< T > &	getOptionalADMaterialProperty (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOld (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOld (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOlder (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOlder (const std::string &name)

MaterialBase &	getMaterial (const std::string &name)

MaterialBase &	getMaterial (const std::string &name)

MaterialBase &	getMaterialByName (const std::string &name, bool no_warn=false)

MaterialBase &	getMaterialByName (const std::string &name, bool no_warn=false)

bool	hasMaterialProperty (const std::string &name)

bool	hasMaterialProperty (const std::string &name)

bool	hasMaterialPropertyByName (const std::string &name)

bool	hasMaterialPropertyByName (const std::string &name)

bool	hasADMaterialProperty (const std::string &name)

bool	hasADMaterialProperty (const std::string &name)

bool	hasADMaterialPropertyByName (const std::string &name)

bool	hasADMaterialPropertyByName (const std::string &name)

bool	hasGenericMaterialProperty (const std::string &name)

bool	hasGenericMaterialProperty (const std::string &name)

bool	hasGenericMaterialPropertyByName (const std::string &name)

bool	hasGenericMaterialPropertyByName (const std::string &name)

const Function &	getFunction (const std::string &name) const

const Function &	getFunctionByName (const FunctionName &name) const

bool	hasFunction (const std::string &param_name) const

bool	hasFunctionByName (const FunctionName &name) const

bool	isDefaultPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessor (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessorByName (const PostprocessorName &name) const

std::size_t	coupledPostprocessors (const std::string &param_name) const

const PostprocessorName &	getPostprocessorName (const std::string &param_name, const unsigned int index=0) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name) const

const VectorPostprocessorName &	getVectorPostprocessorName (const std::string &param_name) const

T &	getSampler (const std::string &name)

Sampler &	getSampler (const std::string &name)

T &	getSamplerByName (const SamplerName &name)

Sampler &	getSamplerByName (const SamplerName &name)

virtual void	meshChanged ()

virtual void	meshDisplaced ()

PerfGraph &	perfGraph ()

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

const Distribution &	getDistribution (const std::string &name) const

const T &	getDistribution (const std::string &name) const

const Distribution &	getDistribution (const std::string &name) const

const T &	getDistribution (const std::string &name) const

const Distribution &	getDistributionByName (const DistributionName &name) const

const T &	getDistributionByName (const std::string &name) const

const Distribution &	getDistributionByName (const DistributionName &name) const

const T &	getDistributionByName (const std::string &name) const

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	sort (typename std::vector< T > &vector)

static void	sortDFS (typename std::vector< T > &vector)

static void	cyclicDependencyError (CyclicDependencyException< T2 > &e, const std::string &header)

Public Attributes
const ConsoleStream	_console

Static Public Attributes
static constexpr PropertyValue::id_type	default_property_id

static constexpr PropertyValue::id_type	zero_property_id

static constexpr auto	SYSTEM

static constexpr auto	NAME

Protected Member Functions
virtual void	addPostprocessorDependencyHelper (const PostprocessorName &name) const override

virtual void	addVectorPostprocessorDependencyHelper (const VectorPostprocessorName &name) const override

virtual void	addUserObjectDependencyHelper (const UserObject &uo) const override

void	addReporterDependencyHelper (const ReporterName &reporter_name) override

const ReporterName &	getReporterName (const std::string &param_name) const

T &	declareRestartableData (const std::string &data_name, Args &&... args)

ManagedValue< T >	declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

const T &	getRestartableData (const std::string &data_name) const

T &	declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

T &	declareRecoverableData (const std::string &data_name, Args &&... args)

T &	declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)

T &	declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)

std::string	restartableName (const std::string &data_name) 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

bool	isCoupledScalar (const std::string &var_name, unsigned int i=0) const

unsigned int	coupledScalarComponents (const std::string &var_name) const

unsigned int	coupledScalar (const std::string &var_name, unsigned int comp=0) const

libMesh::Order	coupledScalarOrder (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarValue (const std::string &var_name, unsigned int comp=0) const

const ADVariableValue &	adCoupledScalarValue (const std::string &var_name, unsigned int comp=0) const

const GenericVariableValue< is_ad > &	coupledGenericScalarValue (const std::string &var_name, unsigned int comp=0) const

const GenericVariableValue< false > &	coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const

const GenericVariableValue< true > &	coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const

const VariableValue &	coupledVectorTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const

const VariableValue &	coupledMatrixTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const

const VariableValue &	coupledScalarValueOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarValueOlder (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDot (const std::string &var_name, unsigned int comp=0) const

const ADVariableValue &	adCoupledScalarDot (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDot (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDotOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDu (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDotDu (const std::string &var_name, unsigned int comp=0) const

const MooseVariableScalar *	getScalarVar (const std::string &var_name, unsigned int comp) const

virtual void	checkMaterialProperty (const std::string &name, const unsigned int state)

void	markMatPropRequested (const std::string &)

MaterialPropertyName	getMaterialPropertyName (const std::string &name) const

void	checkExecutionStage ()

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

const GenericMaterialProperty< T, is_ad > *	defaultGenericMaterialProperty (const std::string &name)

const GenericMaterialProperty< T, is_ad > *	defaultGenericMaterialProperty (const std::string &name)

const MaterialProperty< T > *	defaultMaterialProperty (const std::string &name)

const MaterialProperty< T > *	defaultMaterialProperty (const std::string &name)

const ADMaterialProperty< T > *	defaultADMaterialProperty (const std::string &name)

const ADMaterialProperty< T > *	defaultADMaterialProperty (const std::string &name)

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

Protected Attributes
SubProblem &	_subproblem

FEProblemBase &	_fe_problem

SystemBase &	_sys

const THREAD_ID	_tid

Assembly &	_assembly

const Moose::CoordinateSystemType &	_coord_sys

const bool	_duplicate_initial_execution

std::set< std::string >	_depend_uo

const bool &	_enabled

MooseApp &	_app

const std::string	_type

const std::string	_name

const InputParameters &	_pars

Factory &	_factory

ActionFactory &	_action_factory

const ExecFlagEnum &	_execute_enum

const ExecFlagType &	_current_execute_flag

MooseApp &	_restartable_app

const std::string	_restartable_system_name

const THREAD_ID	_restartable_tid

const bool	_restartable_read_only

FEProblemBase &	_mci_feproblem

FEProblemBase &	_mdi_feproblem

MooseApp &	_pg_moose_app

const std::string	_prefix

FEProblemBase &	_sc_fe_problem

const THREAD_ID	_sc_tid

const Real &	_real_zero

const VariableValue &	_scalar_zero

const Point &	_point_zero

const InputParameters &	_mi_params

const std::string	_mi_name

const MooseObjectName	_mi_moose_object_name

FEProblemBase &	_mi_feproblem

SubProblem &	_mi_subproblem

const THREAD_ID	_mi_tid

const Moose::MaterialDataType	_material_data_type

MaterialData &	_material_data

bool	_stateful_allowed

bool	_get_material_property_called

std::vector< std::unique_ptr< PropertyValue > >	_default_properties

std::unordered_set< unsigned int >	_material_property_dependencies

const MaterialPropertyName	_get_suffix

const bool	_use_interpolated_state

const InputParameters &	_ti_params

FEProblemBase &	_ti_feproblem

bool	_is_implicit

Real &	_t

const Real &	_t_old

int &	_t_step

Real &	_dt

Real &	_dt_old

bool	_is_transient

const Parallel::Communicator &	_communicator

Static Protected Attributes
static const std::string	_interpolated_old

static const std::string	_interpolated_older

Private Attributes
const GeochemicalDatabaseReader	_db

PertinentGeochemicalSystem	_model

Detailed Description

User object that parses a geochemical database file, and only retains information relevant to the current geochemical model.

Definition at line 19 of file GeochemicalModelDefinition.h.

Constructor & Destructor Documentation

◆ GeochemicalModelDefinition()

GeochemicalModelDefinition::GeochemicalModelDefinition ( const InputParameters & parameters )

Definition at line 104 of file GeochemicalModelDefinition.C.

   : GeneralUserObject(parameters),
     _db(getParam<FileName>("database_file"),
         getParam<bool>("reexpress_free_electron"),
         getParam<bool>("piecewise_linear_interpolation"),
         getParam<bool>("remove_all_extrapolated_secondary_species")),
     _model(_db,
            getParam<std::vector<std::string>>("basis_species"),
            getParam<std::vector<std::string>>("equilibrium_minerals"),
            getParam<std::vector<std::string>>("equilibrium_gases"),
            getParam<std::vector<std::string>>("kinetic_minerals"),
            getParam<std::vector<std::string>>("kinetic_redox"),
            getParam<std::vector<std::string>>("kinetic_surface_species"),
            getParam<std::string>("redox_oxygen"),
            getParam<std::string>("redox_electron"))
 {
   for (const auto & kr : getParam<std::vector<UserObjectName>>("kinetic_rate_descriptions"))
     _model.addKineticRate(getUserObjectByName<GeochemistryKineticRate>(kr).getRateDescription());
 }

Member Function Documentation

◆ execute()

void GeochemicalModelDefinition::execute ( )

finaloverridevirtual

Implements GeneralUserObject.

Definition at line 130 of file GeochemicalModelDefinition.C.

131 {

132 }

◆ finalize()

void GeochemicalModelDefinition::finalize ( )

finaloverridevirtual

Implements GeneralUserObject.

Definition at line 135 of file GeochemicalModelDefinition.C.

136 {

137 }

◆ getDatabase()

const ModelGeochemicalDatabase & GeochemicalModelDefinition::getDatabase ( ) const

provides a reference to the pertinent geochemical database held by this object

Definition at line 140 of file GeochemicalModelDefinition.C.

Referenced by AddGeochemistrySolverAction::act().

 {
   return _model.modelGeochemicalDatabase();
 }

◆ getOriginalFullDatabase()

const GeochemicalDatabaseReader & GeochemicalModelDefinition::getOriginalFullDatabase ( ) const

provides a reference to the full database file used by this object

Definition at line 152 of file GeochemicalModelDefinition.C.

 {
   return _db;
 }

◆ getPertinentGeochemicalSystem()

const PertinentGeochemicalSystem & GeochemicalModelDefinition::getPertinentGeochemicalSystem ( ) const

provides a reference to the PertinentGeochemicalSystem of this object

Definition at line 146 of file GeochemicalModelDefinition.C.

 {
   return _model;
 }

◆ initialize()

void GeochemicalModelDefinition::initialize ( )

finaloverridevirtual

Implements GeneralUserObject.

Definition at line 125 of file GeochemicalModelDefinition.C.

126 {

127 }

◆ validParams()

InputParameters GeochemicalModelDefinition::validParams ( )

static

Definition at line 16 of file GeochemicalModelDefinition.C.

 {
   InputParameters params = GeneralUserObject::validParams();
   params.addRequiredParam<FileName>("database_file", "The name of the geochemical database file");
   params.addParam<bool>(
       "reexpress_free_electron",
       true,
       "If true then if: (1) the 'free electron' appears in the database file; and (2) its "
       "equilibrium reaction includes O2(g); and (3) O2(g) is a gas; and (4) O2(g)'s equilibrium "
       "reaction is O2(g)=O2(eq); and (5) O2(aq) exists as a basis species in the database file; "
       "then reexpress the free electron's equilibrium reaction in terms of O2(aq).  Note that if "
       "you choose 'reexpress_free_electron=false' and these other 5 conditions are true, then the "
       "'free electron' will not be available as a secondary species");
   params.addParam<bool>(
       "piecewise_linear_interpolation",
       false,
       "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");
   params.addRequiredParam<std::vector<std::string>>(
       "basis_species",
       "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).");
   params.addParam<std::vector<std::string>>(
       "equilibrium_minerals",
       {},
       "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");
   params.addParam<std::vector<std::string>>(
       "equilibrium_gases",
       {},
       "A list of gases that are in equilibrium with the aqueous solution and can have their "
       "fugacities fixed, at least for some time and spatial location.  All members of this list "
       "must be in the 'gas' section of the database file");
   params.addParam<std::vector<std::string>>(
       "kinetic_minerals",
       {},
       "A list of minerals whose dynamics are governed by a rate law.  These are not in equilibrium "
       "with the aqueous solution.  All members of this list must be in the 'minerals' section of "
       "the database "
       "file.");
   params.addParam<std::vector<std::string>>(
       "kinetic_redox",
       {},
       "A list alternative oxidation states (eg Fe+++) whose dynamics are governed by a rate law.  "
       "These are not in equilibrium with the aqueous solution.  All members of this list must be "
       "in the "
       "'redox couples' section of the database file.");
   params.addParam<std::vector<std::string>>(
       "kinetic_surface_species",
       {},
       "A list surface sorbing species whose dynamics are governed by a rate law.  These are not in "
       "equilibrium with the aqueous solution.  All members of this list must be in the 'surface "
       "species' section of the database file.");
   params.addParam<std::string>(
       "redox_oxygen",
       "O2(aq)",
       "The name of the oxygen species that appears in redox reactions.  For redox pairs that are "
       "in disequilibrium to be correctly recorded, and hence their Nernst potentials to be "
       "computed easily, redox_oxygen must be a basis species and it must appear in the reaction "
       "for each redox pair");
   params.addParam<std::string>(
       "redox_electron",
       "e-",
       "The name of the free electron.  For redox pairs that are in disequilibrium to be correctly "
       "recorded, and hence their Nernst potentials to be computed eqsily, the equilibrium reaction "
       "for redox_electron must involve redox_oxygen, and the basis species must be chosen to that "
       "redox_electron is an equilibrium species");
   params.addParam<std::vector<UserObjectName>>(
       "kinetic_rate_descriptions",
       {},
       "A list of GeochemistryKineticRate UserObject names that define the kinetic rates.  If a "
       "kinetic species has no rate prescribed to it, its reaction rate will be zero");
   params.addParam<bool>(
       "remove_all_extrapolated_secondary_species",
       false,
       "After reading the database file, immediately remove all secondary species that have "
       "extrapolated equilibrium constants.  Sometimes these extrapolations are completely crazy "
       "and those secondary species greatly impact the results");
 
   params.addClassDescription("User object that parses a geochemical database file, and only "
                              "retains information relevant to the current geochemical model");
 
   return params;
 }

Member Data Documentation

◆ _db

const GeochemicalDatabaseReader GeochemicalModelDefinition::_db

private

Definition at line 40 of file GeochemicalModelDefinition.h.

Referenced by getOriginalFullDatabase().

◆ _model

PertinentGeochemicalSystem GeochemicalModelDefinition::_model

private

Definition at line 41 of file GeochemicalModelDefinition.h.

Referenced by GeochemicalModelDefinition(), getDatabase(), and getPertinentGeochemicalSystem().

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

geochemistry/include/userobjects/GeochemicalModelDefinition.h
geochemistry/src/userobjects/GeochemicalModelDefinition.C

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GeochemicalModelDefinition()

Member Function Documentation

◆ execute()

◆ finalize()

◆ getDatabase()

◆ getOriginalFullDatabase()

◆ getPertinentGeochemicalSystem()

◆ initialize()

◆ validParams()

Member Data Documentation

◆ _db

◆ _model