Base class that controls the spatio-temporal solution of geochemistry reactions. More...

#include <GeochemistryReactorBase.h>

Inheritance diagram for GeochemistryReactorBase:

Public Types
enum	TEST_TYPE

typedef DataFileName	DataFileParameterType

Public Member Functions
	GeochemistryReactorBase (const InputParameters &parameters)

virtual void	initialize () override

virtual void	threadJoin (const UserObject &) override

virtual void	finalize () override

virtual void	execute () override

virtual const GeochemicalSystem &	getGeochemicalSystem (dof_id_type node_id) const =0

virtual const std::stringstream &	getSolverOutput (dof_id_type node_id) const =0

virtual unsigned	getSolverIterations (dof_id_type node_id) const =0

virtual Real	getSolverResidual (dof_id_type node_id) const =0

virtual const DenseVector< Real > &	getMoleAdditions (dof_id_type node_id) const =0

virtual Real	getMolesDumped (dof_id_type node_id, const std::string &species) const =0

const PertinentGeochemicalSystem &	getPertinentGeochemicalSystem () const
	returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase More...

virtual void	subdomainSetup () override

bool	isUniqueNodeExecute ()

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< SubdomainName > &	blocks () const

unsigned int	numBlocks () const

virtual const std::set< SubdomainID > &	blockIDs () const

unsigned int	blocksMaxDimension () const

bool	hasBlocks (const SubdomainName &name) const

bool	hasBlocks (const std::vector< SubdomainName > &names) const

bool	hasBlocks (const std::set< SubdomainName > &names) const

bool	hasBlocks (SubdomainID id) const

bool	hasBlocks (const std::vector< SubdomainID > &ids) const

bool	hasBlocks (const std::set< SubdomainID > &ids) const

bool	isBlockSubset (const std::set< SubdomainID > &ids) const

bool	isBlockSubset (const std::vector< SubdomainID > &ids) const

bool	hasBlockMaterialProperty (const std::string &prop_name)

const std::set< SubdomainID > &	meshBlockIDs () const

virtual bool	blockRestricted () const

virtual void	checkVariable (const MooseVariableFieldBase &variable) const

virtual const std::set< BoundaryID > &	boundaryIDs () const

const std::vector< BoundaryName > &	boundaryNames () const

unsigned int	numBoundaryIDs () const

bool	hasBoundary (const BoundaryName &name) const

bool	hasBoundary (const std::vector< BoundaryName > &names) const

bool	hasBoundary (const BoundaryID &id) const

bool	hasBoundary (const std::vector< BoundaryID > &ids, TEST_TYPE type=ALL) const

bool	hasBoundary (const std::set< BoundaryID > &ids, TEST_TYPE type=ALL) const

bool	isBoundarySubset (const std::set< BoundaryID > &ids) const

bool	isBoundarySubset (const std::vector< BoundaryID > &ids) const

bool	hasBoundaryMaterialProperty (const std::string &prop_name) const

virtual bool	boundaryRestricted () const

const std::set< BoundaryID > &	meshBoundaryIDs () const

virtual bool	checkVariableBoundaryIntegrity () const

virtual const VariableValue &	coupledValueByName (const std::string &var_name)

virtual const ArrayVariableValue &	coupledArrayValueByName (const std::string &var_name)

const std::unordered_map< std::string, std::vector< MooseVariableFieldBase *> > &	getCoupledVars () const

const std::vector< MooseVariableFieldBase *> &	getCoupledMooseVars () const

const std::vector< MooseVariable *> &	getCoupledStandardMooseVars () const

const std::vector< VectorMooseVariable *> &	getCoupledVectorMooseVars () const

const std::vector< ArrayMooseVariable *> &	getCoupledArrayMooseVars () const

void	addFEVariableCoupleableVectorTag (TagID tag)

void	addFEVariableCoupleableMatrixTag (TagID tag)

std::set< TagID > &	getFEVariableCoupleableVectorTags ()

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

std::set< TagID > &	getFEVariableCoupleableMatrixTags ()

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

auto &	getWritableCoupledVariables () const

bool	hasWritableCoupledVariables () const

const ADVariableValue *	getADDefaultValue (const std::string &var_name) const

const ADVectorVariableValue *	getADDefaultVectorValue (const std::string &var_name) const

const ADVariableGradient &	getADDefaultGradient () const

const ADVectorVariableGradient &	getADDefaultVectorGradient () const

const ADVariableSecond &	getADDefaultSecond () const

const ADVectorVariableCurl &	getADDefaultCurl () const

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

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

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

const std::set< MooseVariableFieldBase *> &	getMooseVariableDependencies () const

std::set< MooseVariableFieldBase *>	checkAllVariables (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_omit={})

std::set< MooseVariableFieldBase *>	checkVariables (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_check)

void	addMooseVariableDependency (MooseVariableFieldBase *var)

void	addMooseVariableDependency (const std::vector< MooseVariableFieldBase * > &vars)

bool	isImplicit ()

Moose::StateArg	determineState () const

void	setRandomResetFrequency (ExecFlagType exec_flag)

unsigned long	getRandomLong () const

Real	getRandomReal () const

unsigned int	getSeed (std::size_t id)

unsigned int	getMasterSeed () const

bool	isNodal () const

ExecFlagType	getResetOnTime () const

void	setRandomDataPointer (RandomData *random_data)

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 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	sharedParams ()
	contains params that are shared with AddGeochemistrySolverAction and its children More...

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)

static bool	restricted (const std::set< BoundaryID > &ids)

Public Attributes
	ALL

	ANY

const ConsoleStream	_console

Static Public Attributes
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

virtual bool	hasBlockMaterialPropertyHelper (const std::string &prop_name)

void	initializeBlockRestrictable (const MooseObject *moose_object)

Moose::CoordinateSystemType	getBlockCoordSystem ()

bool	hasBoundaryMaterialPropertyHelper (const std::string &prop_name) const

virtual void	coupledCallback (const std::string &, bool) const

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

virtual bool	isCoupledConstant (const std::string &var_name) const

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

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

std::vector< VariableName >	coupledNames (const std::string &var_name) const

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

std::vector< unsigned int >	coupledIndices (const std::string &var_name) const

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

std::vector< const VariableValue *>	coupledValues (const std::string &var_name) const

std::vector< const VectorVariableValue *>	coupledVectorValues (const std::string &var_name) const

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

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

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

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

const GenericVectorVariableValue< false > &	coupledGenericVectorValue (const std::string &var_name, unsigned int comp) const

const GenericVectorVariableValue< true > &	coupledGenericVectorValue (const std::string &var_name, unsigned int comp) const

std::vector< const GenericVariableValue< is_ad > *>	coupledGenericValues (const std::string &var_name) const

std::vector< const GenericVariableValue< false > *>	coupledGenericValues (const std::string &var_name) const

std::vector< const GenericVariableValue< true > *>	coupledGenericValues (const std::string &var_name) const

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

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

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

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

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

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

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

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

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

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

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

std::vector< const ADVariableValue *>	adCoupledValues (const std::string &var_name) const

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

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

std::vector< const ADVectorVariableValue *>	adCoupledVectorValues (const std::string &var_name) const

virtual const VariableValue &	coupledVectorTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const

virtual const VariableValue &	coupledVectorTagValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

std::vector< const VariableValue *>	coupledVectorTagValues (const std::string &var_names, TagID tag) const

std::vector< const VariableValue *>	coupledVectorTagValues (const std::string &var_names, const std::string &tag_name) const

virtual const ArrayVariableValue &	coupledVectorTagArrayValue (const std::string &var_names, TagID tag, unsigned int index=0) const

virtual const ArrayVariableValue &	coupledVectorTagArrayValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

std::vector< const ArrayVariableValue *>	coupledVectorTagArrayValues (const std::string &var_names, TagID tag) const

std::vector< const ArrayVariableValue *>	coupledVectorTagArrayValues (const std::string &var_names, const std::string &tag_name) const

virtual const VariableGradient &	coupledVectorTagGradient (const std::string &var_names, TagID tag, unsigned int index=0) const

virtual const VariableGradient &	coupledVectorTagGradient (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

std::vector< const VariableGradient *>	coupledVectorTagGradients (const std::string &var_names, TagID tag) const

std::vector< const VariableGradient *>	coupledVectorTagGradients (const std::string &var_names, const std::string &tag_name) const

virtual const ArrayVariableGradient &	coupledVectorTagArrayGradient (const std::string &var_names, TagID tag, unsigned int index=0) const

virtual const ArrayVariableGradient &	coupledVectorTagArrayGradient (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

std::vector< const ArrayVariableGradient *>	coupledVectorTagArrayGradients (const std::string &var_names, TagID tag) const

std::vector< const ArrayVariableGradient *>	coupledVectorTagArrayGradients (const std::string &var_names, const std::string &tag_name) const

virtual const VariableValue &	coupledVectorTagDofValue (const std::string &var_name, TagID tag, unsigned int index=0) const

virtual const VariableValue &	coupledVectorTagDofValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

const ArrayVariableValue &	coupledVectorTagArrayDofValue (const std::string &var_name, const std::string &tag_name, unsigned int comp=0) const

std::vector< const VariableValue *>	coupledVectorTagDofValues (const std::string &var_names, TagID tag) const

std::vector< const VariableValue *>	coupledVectorTagDofValues (const std::string &var_names, const std::string &tag_name) const

virtual const VariableValue &	coupledMatrixTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const

virtual const VariableValue &	coupledMatrixTagValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const

std::vector< const VariableValue *>	coupledMatrixTagValues (const std::string &var_names, TagID tag) const

std::vector< const VariableValue *>	coupledMatrixTagValues (const std::string &var_names, const std::string &tag_name) const

virtual const VectorVariableValue &	coupledVectorValue (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayValue (const std::string &var_name, unsigned int comp=0) const

std::vector< const ArrayVariableValue *>	coupledArrayValues (const std::string &var_name) const

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

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

void	checkWritableVar (MooseWritableVariable *var)

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

std::vector< const VariableValue *>	coupledValuesOld (const std::string &var_name) const

std::vector< const VectorVariableValue *>	coupledVectorValuesOld (const std::string &var_name) const

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

std::vector< const VariableValue *>	coupledValuesOlder (const std::string &var_name) const

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

virtual const VectorVariableValue &	coupledVectorValueOld (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableValue &	coupledVectorValueOlder (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayValueOld (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayValueOlder (const std::string &var_name, unsigned int comp=0) const

virtual const VariableGradient &	coupledGradient (const std::string &var_name, unsigned int comp=0) const

std::vector< const VariableGradient *>	coupledGradients (const std::string &var_name) const

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

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

std::vector< const ADVariableGradient *>	adCoupledGradients (const std::string &var_name) const

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

const GenericVariableGradient< false > &	coupledGenericGradient (const std::string &var_name, unsigned int comp) const

const GenericVariableGradient< true > &	coupledGenericGradient (const std::string &var_name, unsigned int comp) const

std::vector< const GenericVariableGradient< is_ad > *>	coupledGenericGradients (const std::string &var_name) const

std::vector< const GenericVariableGradient< false > *>	coupledGenericGradients (const std::string &var_name) const

std::vector< const GenericVariableGradient< true > *>	coupledGenericGradients (const std::string &var_name) const

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

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

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

virtual const VariableGradient &	coupledGradientOld (const std::string &var_name, unsigned int comp=0) const

std::vector< const VariableGradient *>	coupledGradientsOld (const std::string &var_name) const

virtual const VariableGradient &	coupledGradientOlder (const std::string &var_name, unsigned int comp=0) const

virtual const VariableGradient &	coupledGradientPreviousNL (const std::string &var_name, unsigned int comp=0) const

virtual const VariableGradient &	coupledGradientDot (const std::string &var_name, unsigned int comp=0) const

virtual const VariableGradient &	coupledGradientDotDot (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableGradient &	coupledVectorGradient (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableGradient &	coupledVectorGradientOld (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableGradient &	coupledVectorGradientOlder (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableGradient &	coupledArrayGradient (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableGradient &	coupledArrayGradientOld (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableGradient &	coupledArrayGradientOlder (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableGradient &	coupledArrayGradientDot (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableCurl &	coupledCurl (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableCurl &	coupledCurlOld (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableCurl &	coupledCurlOlder (const std::string &var_name, unsigned int comp=0) const

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

virtual const VectorVariableDivergence &	coupledDiv (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableDivergence &	coupledDivOld (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableDivergence &	coupledDivOlder (const std::string &var_name, unsigned int comp=0) const

virtual const VariableSecond &	coupledSecond (const std::string &var_name, unsigned int comp=0) const

virtual const VariableSecond &	coupledSecondOld (const std::string &var_name, unsigned int comp=0) const

virtual const VariableSecond &	coupledSecondOlder (const std::string &var_name, unsigned int comp=0) const

virtual const VariableSecond &	coupledSecondPreviousNL (const std::string &var_name, unsigned int comp=0) const

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

std::vector< const VariableValue *>	coupledDots (const std::string &var_name) const

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

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

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

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

std::vector< const ADVariableValue *>	adCoupledDots (const std::string &var_name) const

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

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

virtual const VectorVariableValue &	coupledVectorDot (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableValue &	coupledVectorDotDot (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableValue &	coupledVectorDotOld (const std::string &var_name, unsigned int comp=0) const

virtual const VectorVariableValue &	coupledVectorDotDotOld (const std::string &var_name, unsigned int comp=0) const

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

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

virtual const ArrayVariableValue &	coupledArrayDot (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayDotDot (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayDotOld (const std::string &var_name, unsigned int comp=0) const

virtual const ArrayVariableValue &	coupledArrayDotDotOld (const std::string &var_name, unsigned int comp=0) const

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

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

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

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

const Moose::ADType< T >::type &	adCoupledNodalValue (const std::string &var_name, unsigned int comp=0) const

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

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

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

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

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

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

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

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

std::vector< const VariableValue *>	coupledAllDofValues (const std::string &var_name) const

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

std::vector< const VariableValue *>	coupledAllDofValuesOld (const std::string &var_name) const

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

std::vector< const VariableValue *>	coupledAllDofValuesOlder (const std::string &var_name) const

virtual const ArrayVariableValue &	coupledArrayDofValues (const std::string &var_name, unsigned int comp=0) const

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

const ADVariableValue &	adZeroValue () const

const ADVariableGradient &	adZeroGradient () const

const ADVariableSecond &	adZeroSecond () const

const GenericVariableValue< is_ad > &	genericZeroValue ()

const GenericVariableValue< false > &	genericZeroValue ()

const GenericVariableValue< true > &	genericZeroValue ()

const GenericVariableGradient< is_ad > &	genericZeroGradient ()

const GenericVariableGradient< false > &	genericZeroGradient ()

const GenericVariableGradient< true > &	genericZeroGradient ()

const GenericVariableSecond< is_ad > &	genericZeroSecond ()

const GenericVariableSecond< false > &	genericZeroSecond ()

const GenericVariableSecond< true > &	genericZeroSecond ()

bool	checkVar (const std::string &var_name, unsigned int comp=0, unsigned int comp_bound=0) const

const MooseVariableFieldBase *	getFEVar (const std::string &var_name, unsigned int comp) const

const MooseVariableFieldBase *	getFieldVar (const std::string &var_name, unsigned int comp) const

MooseVariableFieldBase *	getFieldVar (const std::string &var_name, unsigned int comp)

const T *	getVarHelper (const std::string &var_name, unsigned int comp) const

T *	getVarHelper (const std::string &var_name, unsigned int comp)

MooseVariable *	getVar (const std::string &var_name, unsigned int comp)

const MooseVariable *	getVar (const std::string &var_name, unsigned int comp) const

VectorMooseVariable *	getVectorVar (const std::string &var_name, unsigned int comp)

const VectorMooseVariable *	getVectorVar (const std::string &var_name, unsigned int comp) const

ArrayMooseVariable *	getArrayVar (const std::string &var_name, unsigned int comp)

const ArrayMooseVariable *	getArrayVar (const std::string &var_name, unsigned int comp) const

void	validateExecutionerType (const std::string &name, const std::string &fn_name) const

std::vector< T >	coupledVectorHelper (const std::string &var_name, const Func &func) 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

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

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

Protected Attributes
const unsigned	_num_my_nodes
	Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is handled) More...

ModelGeochemicalDatabase	_mgd
	my copy of the underlying ModelGeochemicalDatabase More...

const PertinentGeochemicalSystem &	_pgs
	Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase. More...

const unsigned	_num_basis
	number of basis species More...

const unsigned	_num_eqm
	number of equilibrium species More...

const Real	_initial_max_ionic_str
	Initial value of maximum ionic strength. More...

GeochemistryIonicStrength	_is
	The ionic strength calculator. More...

GeochemistryActivityCoefficientsDebyeHuckel	_gac
	The activity calculator. More...

const unsigned	_max_swaps_allowed
	Maximum number of swaps allowed during a single solve. More...

GeochemistrySpeciesSwapper	_swapper
	The species swapper. More...

const Real	_small_molality
	A small value of molality. More...

std::vector< std::stringstream >	_solver_output
	The solver output at each node. More...

std::vector< unsigned >	_tot_iter
	Number of iterations used by the solver at each node. More...

std::vector< Real >	_abs_residual
	L1norm of the solver residual at each node. More...

MooseMesh &	_mesh

const unsigned int	_qp

const Node *const &	_current_node

const bool &	_unique_node_execute

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

const MaterialData *	_blk_material_data

const InputParameters &	_c_parameters

const std::string &	_c_name

const std::string &	_c_type

FEProblemBase &	_c_fe_problem

const SystemBase *const	_c_sys

std::unordered_map< std::string, std::vector< MooseVariableFieldBase *> >	_coupled_vars

std::vector< MooseVariableFieldBase *>	_coupled_moose_vars

std::vector< MooseVariable *>	_coupled_standard_moose_vars

std::vector< VectorMooseVariable *>	_coupled_vector_moose_vars

std::vector< ArrayMooseVariable *>	_coupled_array_moose_vars

std::vector< MooseVariableFV< Real > *>	_coupled_standard_fv_moose_vars

std::vector< MooseLinearVariableFV< Real > *>	_coupled_standard_linear_fv_moose_vars

const std::unordered_map< std::string, std::string > &	_new_to_deprecated_coupled_vars

bool	_c_nodal

bool	_c_is_implicit

const bool	_c_allow_element_to_nodal_coupling

THREAD_ID	_c_tid

std::unordered_map< std::string, std::vector< std::unique_ptr< VariableValue > > >	_default_value

std::unordered_map< std::string, std::unique_ptr< MooseArray< ADReal > > >	_ad_default_value

std::unordered_map< std::string, std::unique_ptr< VectorVariableValue > >	_default_vector_value

std::unordered_map< std::string, std::unique_ptr< ArrayVariableValue > >	_default_array_value

std::unordered_map< std::string, std::unique_ptr< MooseArray< ADRealVectorValue > > >	_ad_default_vector_value

VariableValue	_default_value_zero

VariableGradient	_default_gradient

MooseArray< ADRealVectorValue >	_ad_default_gradient

MooseArray< ADRealTensorValue >	_ad_default_vector_gradient

VariableSecond	_default_second

MooseArray< ADRealTensorValue >	_ad_default_second

MooseArray< ADRealVectorValue >	_ad_default_curl

const VariableValue &	_zero

const VariablePhiValue &	_phi_zero

const MooseArray< ADReal > &	_ad_zero

const VariableGradient &	_grad_zero

const MooseArray< ADRealVectorValue > &	_ad_grad_zero

const VariablePhiGradient &	_grad_phi_zero

const VariableSecond &	_second_zero

const MooseArray< ADRealTensorValue > &	_ad_second_zero

const VariablePhiSecond &	_second_phi_zero

const VectorVariableValue &	_vector_zero

const VectorVariableCurl &	_vector_curl_zero

VectorVariableValue	_default_vector_value_zero

VectorVariableGradient	_default_vector_gradient

VectorVariableCurl	_default_vector_curl

VectorVariableDivergence	_default_div

ArrayVariableValue	_default_array_value_zero

ArrayVariableGradient	_default_array_gradient

bool	_coupleable_neighbor

FEProblemBase &	_sc_fe_problem

const THREAD_ID	_sc_tid

const Real &	_real_zero

const VariableValue &	_scalar_zero

const Point &	_point_zero

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

Detailed Description

Base class that controls the spatio-temporal solution of geochemistry reactions.

Definition at line 19 of file GeochemistryReactorBase.h.

Constructor & Destructor Documentation

◆ GeochemistryReactorBase()

GeochemistryReactorBase::GeochemistryReactorBase ( const InputParameters & parameters )

Definition at line 173 of file GeochemistryReactorBase.C.

   : NodalUserObject(parameters),
     _num_my_nodes(_subproblem.mesh().getMesh().n_local_nodes()),
     _mgd(getUserObject<GeochemicalModelDefinition>("model_definition").getDatabase()),
     _pgs(getUserObject<GeochemicalModelDefinition>("model_definition")
              .getPertinentGeochemicalSystem()),
     _num_basis(_mgd.basis_species_name.size()),
     _num_eqm(_mgd.eqm_species_name.size()),
     _initial_max_ionic_str(getParam<Real>("max_ionic_strength") /
                            (1.0 + getParam<unsigned>("ramp_max_ionic_strength_initial"))),
     _is(_initial_max_ionic_str,
         _initial_max_ionic_str,
         getParam<bool>("ionic_str_using_basis_only"),
         getParam<bool>("stoichiometric_ionic_str_using_Cl_only")),
     _gac(_is,
          getUserObject<GeochemicalModelDefinition>("model_definition").getOriginalFullDatabase()),
     _max_swaps_allowed(getParam<unsigned>("max_swaps_allowed")),
     _swapper(_num_basis, getParam<Real>("stoichiometry_tolerance")),
     _small_molality(getParam<Real>("swap_threshold") * getParam<Real>("abs_tol")),
     _solver_output(_num_my_nodes),
     _tot_iter(_num_my_nodes, 0),
     _abs_residual(_num_my_nodes, 0.0)
 {
 }

Member Function Documentation

◆ execute()

virtual void GeochemistryReactorBase::execute ( )

inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 30 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeIndependentReactor::execute().

30 {}

◆ finalize()

virtual void GeochemistryReactorBase::finalize ( )

inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 29 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeIndependentReactor::finalize(), GeochemistryTimeDependentReactor::finalize(), and GeochemistrySpatialReactor::finalize().

29 {}

◆ getGeochemicalSystem()

virtual const GeochemicalSystem& GeochemistryReactorBase::getGeochemicalSystem ( dof_id_type node_id ) const

pure virtual

Returns: a reference to the equilibrium geochemical system at the given node

Parameters

node_id the ID of the node

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryQuantityAux::computeValue(), and GeochemistryConsoleOutput::output().

◆ getMoleAdditions()

virtual const DenseVector<Real>& GeochemistryReactorBase::getMoleAdditions ( dof_id_type node_id ) const

pure virtual

Returns: the mole additions (the first num_basis of these are additions to the bulk composition of the equilibrium system, the last num_kin of these are -dt*kinetic_reaction_rate, ie dt*dissolution_rate) at the specified node_id

Parameters

node_id the node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryQuantityAux::computeValue(), and GeochemistryConsoleOutput::output().

◆ getMolesDumped()

virtual Real GeochemistryReactorBase::getMolesDumped	(	dof_id_type	node_id,
		const std::string &	species
	)		const

pure virtual

Returns: the moles dumped of the given species at the specified node_id

Parameters

species	the name of the species
node_id	the node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryQuantityAux::computeValue().

◆ getPertinentGeochemicalSystem()

const PertinentGeochemicalSystem& GeochemistryReactorBase::getPertinentGeochemicalSystem ( ) const

inline

returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase

Definition at line 73 of file GeochemistryReactorBase.h.

Referenced by GeochemistryQuantityAux::computeValue(), GeochemistryQuantityAux::GeochemistryQuantityAux(), and GeochemistryConsoleOutput::output().

73 { return _pgs; };

GeochemistryReactorBase::_pgs

const PertinentGeochemicalSystem & _pgs

Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

Definition: GeochemistryReactorBase.h:81

◆ getSolverIterations()

virtual unsigned GeochemistryReactorBase::getSolverIterations ( dof_id_type node_id ) const

pure virtual

Returns: the total number of iterations used by the most recent solve at the specified node_id

Parameters

node_id the node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ getSolverOutput()

virtual const std::stringstream& GeochemistryReactorBase::getSolverOutput ( dof_id_type node_id ) const

pure virtual

Returns: a reference to the most recent solver output (containing iteration info, swap info, residuals, etc) at the specified node_id

Parameters

node_id the node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ getSolverResidual()

virtual Real GeochemistryReactorBase::getSolverResidual ( dof_id_type node_id ) const

pure virtual

Returns: the L1norm of the residual at the end of the most recent solve at the specified node_id

Parameters

node_id the node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ initialize()

virtual void GeochemistryReactorBase::initialize ( )

inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 27 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeIndependentReactor::initialize(), GeochemistrySpatialReactor::initialize(), and GeochemistryTimeDependentReactor::initialize().

27 {}

◆ sharedParams()

InputParameters GeochemistryReactorBase::sharedParams ( )

static

contains params that are shared with AddGeochemistrySolverAction and its children

Definition at line 13 of file GeochemistryReactorBase.C.

Referenced by AddGeochemistrySolverAction::validParams(), and validParams().

 {
   InputParameters params = emptyInputParameters();
   params.addParam<std::vector<std::string>>(
       "swap_out_of_basis",
       {},
       "Species that should be removed from the model_definition's basis and be replaced with the "
       "swap_into_basis species");
   params.addParam<std::vector<std::string>>(
       "swap_into_basis",
       {},
       "Species that should be removed from the model_definition's equilibrium species list and "
       "added to the basis.  There must be the same number of species in swap_out_of_basis and "
       "swap_into_basis.  These swaps are performed before any other computations during the "
       "initial problem setup. 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");
   MultiMooseEnum constraint_user_meaning(
       "kg_solvent_water bulk_composition bulk_composition_with_kinetic free_concentration "
       "free_mineral activity log10activity fugacity log10fugacity");
   params.addRequiredParam<MultiMooseEnum>(
       "constraint_meaning",
       constraint_user_meaning,
       "Meanings of the numerical values given in constraint_value.  kg_solvent_water: can only be "
       "applied to H2O and units must be kg.  bulk_composition: can be applied to all non-gas "
       "species, and represents the total amount of the basis species contained as free species as "
       "well as the amount found in secondary species but not in kinetic species, and units must be "
       "moles or mass (kg, g, etc).  bulk_composition_with_kinetic: can be applied to all non-gas "
       "species, and represents the total amount of the basis species contained as free species as "
       "well as the amount found in secondary species and in kinetic species, and units must be "
       "moles or mass (kg, g, etc).  free_concentration: can be applied to all basis species that "
       "are not gas and not H2O and not mineral, and represents the total amount of the basis "
       "species existing freely (not as secondary species) within the solution, and units must be "
       "molal or mass_per_kg_solvent.  free_mineral: can be applied to all mineral basis species, "
       "and represents the total amount of the mineral existing freely (precipitated) within the "
       "solution, and units must be moles, mass or cm3.  activity and log10activity: can be applied "
       "to basis species that are not gas and not mineral and not sorbing sites, and represents the "
       "activity of the basis species (recall pH = -log10activity), and units must be "
       "dimensionless.  fugacity and log10fugacity: can be applied to gases, and units must be "
       "dimensionless");
   MultiMooseEnum constraint_unit("dimensionless moles molal kg g mg ug kg_per_kg_solvent "
                                  "g_per_kg_solvent mg_per_kg_solvent ug_per_kg_solvent cm3");
   params.addRequiredParam<MultiMooseEnum>(
       "constraint_unit",
       constraint_unit,
       "Units of the numerical values given in constraint_value.  Dimensionless: should only be "
       "used for activity or fugacity constraints.  Moles: mole number.  Molal: moles per kg "
       "solvent water.  kg: kilograms.  g: grams.  mg: milligrams.  ug: micrograms.  "
       "kg_per_kg_solvent: kilograms per kg solvent water.  g_per_kg_solvent: grams per kg solvent "
       "water.  mg_per_kg_solvent: milligrams per kg solvent water.  ug_per_kg_solvent: micrograms "
       "per kg solvent water.  cm3: cubic centimeters");
   params.addRequiredParam<std::vector<std::string>>(
       "constraint_species",
       "Names of the species that have their values fixed to constraint_value with meaning "
       "constraint_meaning.  All basis species (after swap_into_basis and swap_out_of_basis) must "
       "be provided with exactly one constraint.  These constraints are used to compute the "
       "configuration during the initial problem setup, and in time-dependent simulations they may "
       "be modified as time progresses.");
   params.addRequiredParam<std::vector<Real>>(
       "constraint_value", "Numerical value of the containts on constraint_species");
   params.addRangeCheckedParam<Real>(
       "max_ionic_strength", 3.0, "max_ionic_strength >= 0.0", "Maximum value of ionic strength");
   params.addParam<unsigned>(
       "extra_iterations_to_make_consistent",
       0,
       "Extra iterations to make the molalities, activities, etc, consistent "
       "before commencing the Newton process to find the aqueous configuration");
   params.addRequiredParam<std::string>(
       "charge_balance_species",
       "Charge balance will be enforced on this basis species.  This means that its bulk mole "
       "number may be changed from the initial value you provide in order to ensure charge "
       "neutrality.  After the initial swaps have been performed, this must be in the basis, and it "
       "must be provided with a bulk_composition constraint_meaning.");
   params.addParam<std::vector<std::string>>(
       "prevent_precipitation",
       {},
       "Mineral species in this list will be prevented from precipitating, irrespective of their "
       "saturation index (unless they are initially in the basis)");
   params.addParam<Real>(
       "abs_tol",
       1E-10,
       "If the residual of the algebraic system (measured in mol) is lower than this value, the "
       "Newton process (that finds the aqueous configuration) is deemed to have converged");
   params.addParam<Real>("rel_tol",
                         1E-200,
                         "If the residual of the algebraic system (measured in mol) is lower than "
                         "this value times the initial residual, the Newton process (that finds the "
                         "aqueous configuration) is deemed to have converged");
   params.addRangeCheckedParam<Real>("min_initial_molality",
                                     1E-20,
                                     "min_initial_molality > 0.0",
                                     "Minimum value of the initial-guess molality used in the "
                                     "Newton process to find the aqueous configuration");
   params.addParam<unsigned>(
       "max_iter",
       100,
       "Maximum number of Newton iterations allowed when finding the aqueous configuration");
   params.addParam<Real>(
       "max_initial_residual",
       1E3,
       "Attempt to alter the initial-guess molalities so that the initial residual for the Newton "
       "process (that finds the aqueous configuration) is less than this number of moles");
   params.addRangeCheckedParam<Real>(
       "swap_threshold",
       0.1,
       "swap_threshold >= 0.0",
       "If the molality of a basis species in the algebraic system falls below swap_threshold * "
       "abs_tol then it is swapped out of the basis.  The dimensions of swap_threshold are "
       "1/kg(solvent water)");
   params.addParam<unsigned>(
       "max_swaps_allowed",
       20,
       "Maximum number of swaps allowed during a single attempt at finding the aqueous "
       "configuration.  Usually only a handful of swaps are used: this parameter prevents endless "
       "cyclic swapping that prevents the algorithm from progressing");
   params.addParam<unsigned>(
       "ramp_max_ionic_strength_initial",
       20,
       "The number of iterations over which to progressively increase the maximum ionic strength "
       "(from zero to max_ionic_strength) during the initial equilibration.  Increasing this can "
       "help in convergence of the Newton process, at the cost of spending more time finding the "
       "aqueous configuration.");
   params.addParam<bool>(
       "ionic_str_using_basis_only",
       false,
       "If set to true, ionic strength and stoichiometric ionic strength will be computed using "
       "only the basis molalities, ignoring molalities of equilibrium species.  Since basis "
       "molality is usually greater than equilibrium molality, and the whole Debye-Huckel concept "
       "of activity coefficients depending on ionic strength is only approximate in practice, "
       "setting this parameter true often results in a reasonable approximation.  It can aid in "
       "convergence since it eliminates problems associated with unphysical huge equilibrium "
       "molalities that can occur during Newton iteration to the solution");
   params.addParam<bool>("stoichiometric_ionic_str_using_Cl_only",
                         false,
                         "If set to true, the stoichiometric ionic strength will be set equal to "
                         "Cl- molality (or max_ionic_strength if the Cl- molality is too "
                         "big).  This flag overrides ionic_str_using_basis_molality_only");
   return params;
 }

◆ threadJoin()

virtual void GeochemistryReactorBase::threadJoin ( const UserObject & )

inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor.

Definition at line 28 of file GeochemistryReactorBase.h.

28 {}

◆ validParams()

InputParameters GeochemistryReactorBase::validParams ( )

static

Definition at line 154 of file GeochemistryReactorBase.C.

Referenced by GeochemistryTimeIndependentReactor::validParams(), GeochemistrySpatialReactor::validParams(), and GeochemistryTimeDependentReactor::validParams().

 {
   InputParameters params = NodalUserObject::validParams();
   params += GeochemistryReactorBase::sharedParams();
 
   params.addRequiredParam<UserObjectName>(
       "model_definition", "The name of the GeochemicalModelDefinition user object.");
   params.addRangeCheckedParam<Real>(
       "stoichiometry_tolerance",
       1E-6,
       "stoichiometry_tolerance >= 0.0",
       "Swapping involves inverting matrices via a singular value decomposition. During this "
       "process: (1) if abs(singular value) < stoi_tol * L1norm(singular values), then the "
       "matrix is deemed singular (so the basis swap is deemed invalid); (2) if abs(any "
       "stoichiometric coefficient) < stoi_tol then it is set to zero.");
   params.addClassDescription("Base class for UserObject to solve geochemistry reactions");
   return params;
 }

Member Data Documentation

◆ _abs_residual

std::vector<Real> GeochemistryReactorBase::_abs_residual

protected

L1norm of the solver residual at each node.

Definition at line 103 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::execute(), GeochemistrySpatialReactor::execute(), GeochemistryTimeIndependentReactor::getSolverResidual(), GeochemistryTimeDependentReactor::getSolverResidual(), GeochemistrySpatialReactor::getSolverResidual(), GeochemistryTimeIndependentReactor::initialSetup(), GeochemistryTimeDependentReactor::initialSetup(), GeochemistrySpatialReactor::initialSetup(), GeochemistryTimeDependentReactor::postSolveExchanger(), and GeochemistrySpatialReactor::threadJoin().

◆ _gac

GeochemistryActivityCoefficientsDebyeHuckel GeochemistryReactorBase::_gac

protected

The activity calculator.

Definition at line 91 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _initial_max_ionic_str

const Real GeochemistryReactorBase::_initial_max_ionic_str

protected

Initial value of maximum ionic strength.

Definition at line 87 of file GeochemistryReactorBase.h.

◆ _is

GeochemistryIonicStrength GeochemistryReactorBase::_is

protected

The ionic strength calculator.

Definition at line 89 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _max_swaps_allowed

const unsigned GeochemistryReactorBase::_max_swaps_allowed

protected

Maximum number of swaps allowed during a single solve.

Definition at line 93 of file GeochemistryReactorBase.h.

◆ _mgd

ModelGeochemicalDatabase GeochemistryReactorBase::_mgd

protected

my copy of the underlying ModelGeochemicalDatabase

Definition at line 79 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::execute(), GeochemistrySpatialReactor::GeochemistrySpatialReactor(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), GeochemistryTimeDependentReactor::newTemperature(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), GeochemistryTimeDependentReactor::preSolveDump(), and GeochemistryTimeDependentReactor::preSolveFlush().

◆ _num_basis

const unsigned GeochemistryReactorBase::_num_basis

protected

number of basis species

Definition at line 83 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::execute(), GeochemistrySpatialReactor::execute(), GeochemistryTimeIndependentReactor::initialSetup(), GeochemistryTimeDependentReactor::newTemperature(), GeochemistryTimeDependentReactor::postSolveExchanger(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), GeochemistryTimeDependentReactor::preSolveDump(), GeochemistryTimeDependentReactor::preSolveFlush(), and GeochemistryTimeDependentReactor::removeCurrentSpecies().

◆ _num_eqm

const unsigned GeochemistryReactorBase::_num_eqm

protected

number of equilibrium species

Definition at line 85 of file GeochemistryReactorBase.h.

◆ _num_my_nodes

const unsigned GeochemistryReactorBase::_num_my_nodes

protected

Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is handled)

Definition at line 73 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::buildMyNodeNumber(), GeochemistrySpatialReactor::GeochemistrySpatialReactor(), GeochemistrySpatialReactor::initialize(), GeochemistryTimeIndependentReactor::initialSetup(), GeochemistryTimeDependentReactor::initialSetup(), GeochemistrySpatialReactor::initialSetup(), and GeochemistrySpatialReactor::threadJoin().

◆ _pgs

const PertinentGeochemicalSystem& GeochemistryReactorBase::_pgs

protected

Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

Definition at line 81 of file GeochemistryReactorBase.h.

Referenced by getPertinentGeochemicalSystem().

◆ _small_molality

const Real GeochemistryReactorBase::_small_molality

protected

A small value of molality.

Definition at line 97 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::postSolveFlowThrough().

◆ _solver_output

std::vector<std::stringstream> GeochemistryReactorBase::_solver_output

protected

The solver output at each node.

Definition at line 99 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::execute(), GeochemistrySpatialReactor::execute(), GeochemistryTimeIndependentReactor::getSolverOutput(), GeochemistryTimeDependentReactor::getSolverOutput(), GeochemistrySpatialReactor::getSolverOutput(), GeochemistryTimeIndependentReactor::initialSetup(), GeochemistryTimeDependentReactor::initialSetup(), GeochemistrySpatialReactor::initialSetup(), GeochemistryTimeDependentReactor::postSolveExchanger(), and GeochemistrySpatialReactor::threadJoin().

◆ _swapper

GeochemistrySpeciesSwapper GeochemistryReactorBase::_swapper

protected

The species swapper.

Definition at line 95 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _tot_iter

std::vector<unsigned> GeochemistryReactorBase::_tot_iter

protected

Number of iterations used by the solver at each node.

Definition at line 101 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::execute(), GeochemistrySpatialReactor::execute(), GeochemistryTimeIndependentReactor::getSolverIterations(), GeochemistryTimeDependentReactor::getSolverIterations(), GeochemistrySpatialReactor::getSolverIterations(), GeochemistryTimeIndependentReactor::initialSetup(), GeochemistryTimeDependentReactor::initialSetup(), GeochemistrySpatialReactor::initialSetup(), GeochemistryTimeDependentReactor::postSolveExchanger(), and GeochemistrySpatialReactor::threadJoin().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GeochemistryReactorBase()

Member Function Documentation

◆ execute()

◆ finalize()

◆ getGeochemicalSystem()

◆ getMoleAdditions()

◆ getMolesDumped()

◆ getPertinentGeochemicalSystem()

◆ getSolverIterations()

◆ getSolverOutput()

◆ getSolverResidual()

◆ initialize()

◆ sharedParams()

◆ threadJoin()

◆ validParams()

Member Data Documentation

◆ _abs_residual

◆ _gac

◆ _initial_max_ionic_str

◆ _is

◆ _max_swaps_allowed

◆ _mgd

◆ _num_basis

◆ _num_eqm

◆ _num_my_nodes

◆ _pgs

◆ _small_molality

◆ _solver_output

◆ _swapper

◆ _tot_iter