Class that controls the space-dependent and time-dependent geochemistry reactions. More...

#include <GeochemistrySpatialReactor.h>

Inheritance diagram for GeochemistrySpatialReactor:

Public Types
enum	TEST_TYPE

typedef DataFileName	DataFileParameterType

Public Member Functions
	GeochemistrySpatialReactor (const InputParameters &parameters)

virtual void	initialize () override

virtual void	finalize () override
	the main-thread information is used to set the other-thread information in finalize() More...

virtual void	threadJoin (const UserObject &uo) override

virtual void	initialSetup () override

virtual void	execute () override

virtual void	meshChanged () override

virtual const GeochemicalSystem &	getGeochemicalSystem (dof_id_type node_id) const override

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

virtual unsigned	getSolverIterations (dof_id_type node_id) const override

virtual Real	getSolverResidual (dof_id_type node_id) const override

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

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

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	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	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 ()
	params that are shared with AddTimeDependentReactionSolverAction 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
void	buildMyNodeNumber ()
	Build the _my_node_number map. More...

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 Real	_initial_temperature
	Initial equilibration temperature. More...

const VariableValue &	_temperature
	Temperature specified by user. More...

const unsigned	_num_kin
	Number of kinetic species. More...

std::vector< ModelGeochemicalDatabase >	_mgd_at_node
	ModelGeochemicalDatabase at each node. More...

std::vector< GeochemicalSystem >	_egs_at_node
	GeochemicalSystem at each node. More...

GeochemicalSystem	_egs_copy
	GeochemicalSystem into which the nodal GeochemicalSystem is copied to enable recovery during adaptive timestepping. More...

GeochemicalSolver	_solver
	The solver. More...

const Real	_close_system_at_time
	Defines the time at which to close the system. More...

bool	_closed_system
	Whether the system has been closed. More...

const std::vector< std::string >	_source_species_names
	Names of the source species. More...

const unsigned	_num_source_species
	Number of source species. More...

std::vector< const VariableValue * >	_source_species_rates
	Rates of the source species. More...

const std::vector< std::string >	_remove_fixed_activity_name
	Names of species to remove the fixed activity or fugacity constraint from. More...

const std::vector< Real >	_remove_fixed_activity_time
	Times at which to remove the fixed activity or fugacity from the species in _remove_fixed_activity_name. More...

const unsigned	_num_removed_fixed
	Number of elements in the vector _remove_fixed_activity_name;. More...

std::vector< std::vector< bool > >	_removed_fixed_activity
	Whether the activity or activity constraint has been removed at each node. More...

const std::vector< std::string >	_controlled_activity_species_names
	Names of the species with controlled activity or fugacity. More...

const unsigned	_num_controlled_activity
	Number of species with controlled activity or fugacity. More...

std::vector< const VariableValue * >	_controlled_activity_species_values
	Activity or fugacity of the species with controlled activity or fugacity. More...

DenseVector< Real >	_mole_rates
	Rate of mole additions. More...

std::vector< DenseVector< Real > >	_mole_additions
	Moles of each basis species added at each node at the current timestep, along with kinetic rates. More...

std::vector< DenseMatrix< Real > >	_dmole_additions
	Derivative of moles_added. More...

const unsigned	_ramp_subsequent
	the ramp_max_ionic_strength to use during time-stepping More...

std::unordered_map< dof_id_type, unsigned >	_my_node_number
	_my_node_number[_current_node->id()] = node number used in this object that corresponds to _current_node->id() More...

std::vector< bool >	_execute_done
	whether execute has been called using this thread More...

const bool	_adaptive_timestepping
	Whether to use adaptive timestepping at the nodes. More...

const Real	_dt_min
	minimum value of dt allowed during adpative timestepping. This is set to a large number if _adaptive_timestepping = false so that if any solve ever fails, this class will throw a mooseException More...

const Real	_dt_dec
	value to multiply dt my in the case of a failed solve More...

const Real	_dt_inc
	value to multiply dt my in the case of a successful solve More...

unsigned	_nthreads
	number of threads used to execute this UserObject More...

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

Class that controls the space-dependent and time-dependent geochemistry reactions.

Definition at line 18 of file GeochemistrySpatialReactor.h.

Constructor & Destructor Documentation

◆ GeochemistrySpatialReactor()

GeochemistrySpatialReactor::GeochemistrySpatialReactor ( const InputParameters & parameters )

Definition at line 128 of file GeochemistrySpatialReactor.C.

   : GeochemistryReactorBase(parameters),
     _initial_temperature(getParam<Real>("initial_temperature")),
     _temperature(coupledValue("temperature")),
     _num_kin(_mgd.kin_species_name.size()),
     // NOTE: initialize _mgd_at_node before the swaps are performed
     _mgd_at_node(_num_my_nodes, _mgd),
     _egs_at_node(),
     // NOTE: the following implements the swaps in _mgd
     _egs_copy(_mgd,
               _gac,
               _is,
               _swapper,
               getParam<std::vector<std::string>>("swap_out_of_basis"),
               getParam<std::vector<std::string>>("swap_into_basis"),
               getParam<std::string>("charge_balance_species"),
               getParam<std::vector<std::string>>("constraint_species"),
               getParam<std::vector<Real>>("constraint_value"),
               getParam<MultiMooseEnum>("constraint_unit"),
               getParam<MultiMooseEnum>("constraint_meaning"),
               _initial_temperature,
               getParam<unsigned>("extra_iterations_to_make_consistent"),
               getParam<Real>("min_initial_molality"),
               getParam<std::vector<std::string>>("kinetic_species_name"),
               getParam<std::vector<Real>>("kinetic_species_initial_value"),
               getParam<MultiMooseEnum>("kinetic_species_unit")),
     _solver(_mgd.basis_species_name.size(),
             _mgd.kin_species_name.size(),
             _is,
             getParam<Real>("abs_tol"),
             getParam<Real>("rel_tol"),
             getParam<unsigned>("max_iter"),
             getParam<Real>("max_initial_residual"),
             _small_molality,
             _max_swaps_allowed,
             getParam<std::vector<std::string>>("prevent_precipitation"),
             getParam<Real>("max_ionic_strength"),
             getParam<unsigned>("ramp_max_ionic_strength_initial"),
             getParam<bool>("evaluate_kinetic_rates_always")),
     _close_system_at_time(getParam<Real>("close_system_at_time")),
     _closed_system(false),
     _source_species_names(getParam<std::vector<std::string>>("source_species_names")),
     _num_source_species(_source_species_names.size()),
     _source_species_rates(0),
     _remove_fixed_activity_name(getParam<std::vector<std::string>>("remove_fixed_activity_name")),
     _remove_fixed_activity_time(getParam<std::vector<Real>>("remove_fixed_activity_time")),
     _num_removed_fixed(_remove_fixed_activity_name.size()),
     _removed_fixed_activity(_num_my_nodes, std::vector<bool>(_num_removed_fixed, false)),
     _controlled_activity_species_names(
         getParam<std::vector<std::string>>("controlled_activity_name")),
     _num_controlled_activity(_controlled_activity_species_names.size()),
     _controlled_activity_species_values(0),
     _mole_rates(_num_basis + _num_kin),
     _mole_additions(_num_my_nodes, DenseVector<Real>(_num_basis + _num_kin)),
     _dmole_additions(_num_my_nodes,
                      DenseMatrix<Real>(_num_basis + _num_kin, _num_basis + _num_kin)),
     _ramp_subsequent(getParam<unsigned>("ramp_max_ionic_strength_subsequent")),
     _my_node_number(),
     _execute_done(_num_my_nodes, false),
     _adaptive_timestepping(getParam<bool>("adaptive_timestepping")),
     _dt_min(_adaptive_timestepping ? getParam<Real>("dt_min") : std::numeric_limits<Real>::max()),
     _dt_dec(getParam<Real>("dt_dec")),
     _dt_inc(getParam<Real>("dt_inc")),
     _nthreads(1)
 {
   // build _egs_at_node
   for (unsigned i = 0; i < _num_my_nodes; ++i)
     _egs_at_node.push_back(
         GeochemicalSystem(_mgd_at_node[i],
                           _gac,
                           _is,
                           _swapper,
                           getParam<std::vector<std::string>>("swap_out_of_basis"),
                           getParam<std::vector<std::string>>("swap_into_basis"),
                           getParam<std::string>("charge_balance_species"),
                           getParam<std::vector<std::string>>("constraint_species"),
                           getParam<std::vector<Real>>("constraint_value"),
                           getParam<MultiMooseEnum>("constraint_unit"),
                           getParam<MultiMooseEnum>("constraint_meaning"),
                           _initial_temperature,
                           getParam<unsigned>("extra_iterations_to_make_consistent"),
                           getParam<Real>("min_initial_molality"),
                           getParam<std::vector<std::string>>("kinetic_species_name"),
                           getParam<std::vector<Real>>("kinetic_species_initial_value"),
                           getParam<MultiMooseEnum>("kinetic_species_unit")));
 
   // check sources and set the rates
   if (coupledComponents("source_species_rates") != _num_source_species)
     paramError("source_species_names", "must have the same size as source_species_rates");
   for (unsigned i = 0; i < _num_source_species; ++i)
     _source_species_rates.push_back(&coupledValue("source_species_rates", i));
   for (unsigned i = 0; i < _num_source_species; ++i)
     if (!(_mgd.basis_species_index.count(_source_species_names[i]) == 1 ||
           _mgd.eqm_species_index.count(_source_species_names[i]) == 1 ||
           _mgd.kin_species_index.count(_source_species_names[i]) == 1))
       paramError("source_species_names",
                  "The name " + _source_species_names[i] +
                      " does not appear in the basis, equilibrium or kinetic species list");
 
   // check and set activity controllers
   for (unsigned i = 0; i < _num_removed_fixed; ++i)
   {
     if (_mgd.basis_species_index.count(_remove_fixed_activity_name[i]) == 0)
       paramError(
           "remove_fixed_activity_name",
           "The species ",
           _remove_fixed_activity_name[i],
           " is not in the basis, so cannot have its activity or fugacity constraint removed");
     else if (_num_my_nodes >
              0) // don't consider the silly (but possible) case that there are no nodes
     {
       const unsigned basis_ind = _mgd.basis_species_index.at(_remove_fixed_activity_name[i]);
       const GeochemicalSystem::ConstraintMeaningEnum cm =
           _egs_at_node[0].getConstraintMeaning()[basis_ind];
       if (!(cm == GeochemicalSystem::ConstraintMeaningEnum::ACTIVITY ||
             cm == GeochemicalSystem::ConstraintMeaningEnum::FUGACITY))
         paramError("remove_fixed_activity_name",
                    "The species ",
                    _remove_fixed_activity_name[i],
                    " is does not have an activity or fugacity constraint so cannot have such a "
                    "constraint removed");
     }
   }
   if (_num_removed_fixed != _remove_fixed_activity_time.size())
     paramError("remove_fixed_activity_name",
                "must be of the same size as remove_fixed_activity_time");
   if (coupledComponents("controlled_activity_value") != _num_controlled_activity)
     paramError("controlled_activity_name", "must have the same size as controlled_activity_value");
   for (unsigned i = 0; i < _num_controlled_activity; ++i)
     _controlled_activity_species_values.push_back(&coupledValue("controlled_activity_value", i));
 
   // record coupled variables
   const std::vector<MooseVariableFEBase *> & coupled_vars = getCoupledMooseVars();
   for (unsigned int i = 0; i < coupled_vars.size(); i++)
     addMooseVariableDependency(coupled_vars[i]);
 
   buildMyNodeNumber();
 }

Member Function Documentation

◆ buildMyNodeNumber()

void GeochemistrySpatialReactor::buildMyNodeNumber ( )

protected

Build the _my_node_number map.

Definition at line 268 of file GeochemistrySpatialReactor.C.

Referenced by GeochemistrySpatialReactor().

 {
   const MeshBase & msh = _subproblem.mesh().getMesh();
 
   // create the map from MOOSE's node numbering to the local node numbering (_my_node_number) used
   // by this object
   _my_node_number.clear();
   unsigned num_nodes_inserted = 0;
   for (const auto & node : as_range(msh.local_nodes_begin(), msh.local_nodes_end()))
   {
     if (_my_node_number.count(node->id()) == 0)
       _my_node_number[node->id()] = num_nodes_inserted;
     else
       mooseError(
           "GeochemistrySpatialReactor: something wrong with node numbering in buildMyNodeNumber");
     num_nodes_inserted += 1;
   }
   mooseAssert(
       _my_node_number.size() == _num_my_nodes,
       "GeochemistrySpatialReactor: something wrong with node numbering in buildMyNodeNumber");
 }

◆ execute()

void GeochemistrySpatialReactor::execute ( )

overridevirtual

Reimplemented from GeochemistryReactorBase.

Definition at line 317 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(_current_node->id()) == 0)
     mooseError(
         "GeochemistrySpatialReactor: something wrong with node numbering in buildMyNodeNumber");
   const unsigned my_node_number = _my_node_number.at(_current_node->id());
 
   const unsigned aux_comp_number = 0; // component number to use for AuxVariables
   const ModelGeochemicalDatabase & mgd_ref =
       _egs_at_node[my_node_number].getModelGeochemicalDatabase();
 
   // close system
   if (!_closed_system && _t >= _close_system_at_time)
     _egs_at_node[my_node_number].closeSystem();
 
   // remove fixed-activity constraints.
   for (unsigned i = 0; i < _num_removed_fixed; ++i)
   {
     if (!_removed_fixed_activity[my_node_number][i] && _t >= _remove_fixed_activity_time[i])
     {
       if (mgd_ref.basis_species_index.count(_remove_fixed_activity_name[i]))
         _egs_at_node[my_node_number].changeConstraintToBulk(
             mgd_ref.basis_species_index.at(_remove_fixed_activity_name[i]));
       _removed_fixed_activity[my_node_number][i] = true;
     }
   }
 
   // control activity
   for (unsigned ca = 0; ca < _num_controlled_activity; ++ca)
   {
     const std::vector<GeochemicalSystem::ConstraintMeaningEnum> & cm =
         _egs_at_node[my_node_number].getConstraintMeaning();
     if (mgd_ref.basis_species_index.count(_controlled_activity_species_names[ca]))
     {
       const unsigned basis_ind =
           mgd_ref.basis_species_index.at(_controlled_activity_species_names[ca]);
       if (cm[basis_ind] == GeochemicalSystem::ConstraintMeaningEnum::ACTIVITY ||
           cm[basis_ind] == GeochemicalSystem::ConstraintMeaningEnum::FUGACITY)
         _egs_at_node[my_node_number].setConstraintValue(
             basis_ind, (*_controlled_activity_species_values[ca])[aux_comp_number]);
     }
   }
 
   _solver.setRampMaxIonicStrength(_ramp_subsequent);
 
   Real temperature0 = _egs_at_node[my_node_number].getTemperature();
   const Real temperature_rate = (_temperature[aux_comp_number] - temperature0) / _dt;
 
   // record the system in case of solve failures using the copy-assignment operator of
   // GeochemicalSystem
   if (_adaptive_timestepping)
     _egs_copy = _egs_at_node[my_node_number];
 
   Real done_dt = 0.0;
   Real my_dt = _dt;
 
   // the following loop implements adaptive timestepping at the node
   while (done_dt < _dt)
   {
     // compute moles added in the current basis (the basis might change during adaptive
     // timestepping)
     _mole_rates.zero();
     for (unsigned i = 0; i < _num_source_species; ++i)
     {
       const Real this_rate = (*_source_species_rates[i])[aux_comp_number];
       if (mgd_ref.basis_species_index.count(_source_species_names[i]))
       {
         const unsigned basis_ind = mgd_ref.basis_species_index.at(_source_species_names[i]);
         _mole_rates(basis_ind) += this_rate;
       }
       else if (mgd_ref.eqm_species_index.count(_source_species_names[i]))
       {
         const unsigned eqm_j = mgd_ref.eqm_species_index.at(_source_species_names[i]);
         for (unsigned basis_ind = 0; basis_ind < _num_basis; ++basis_ind)
           _mole_rates(basis_ind) += mgd_ref.eqm_stoichiometry(eqm_j, basis_ind) * this_rate;
       }
       else
       {
         const unsigned kin_ind = mgd_ref.kin_species_index.at(_source_species_names[i]);
         _mole_rates(_num_basis + kin_ind) += this_rate;
       }
     }
 
     Real temperature = temperature0 + my_dt * temperature_rate;
     for (unsigned i = 0; i < _num_basis + _num_kin; ++i)
       _mole_additions[my_node_number](i) = my_dt * _mole_rates(i);
     _dmole_additions[my_node_number].zero();
 
     // set temperature, if needed
     if (temperature != _egs_at_node[my_node_number].getTemperature())
     {
       _egs_at_node[my_node_number].setTemperature(temperature);
       _egs_at_node[my_node_number].computeConsistentConfiguration();
     }
 
     // solve the geochemical system
     try
     {
       _solver.solveSystem(_egs_at_node[my_node_number],
                           _solver_output[my_node_number],
                           _tot_iter[my_node_number],
                           _abs_residual[my_node_number],
                           my_dt,
                           _mole_additions[my_node_number],
                           _dmole_additions[my_node_number]);
       done_dt += my_dt;
       if (done_dt < _dt)
       {
         temperature0 = _egs_at_node[my_node_number].getTemperature();
         _egs_copy =
             _egs_at_node[my_node_number]; // use the copy-assignment operator of GeochemicalSystem
       }
       my_dt *= _dt_inc;
     }
     catch (const MooseException & e)
     {
       // use the copy-assignment operator of GeochemicalSystem to restore to the original
       if (_adaptive_timestepping)
         _egs_at_node[my_node_number] = _egs_copy;
       my_dt *= _dt_dec;
       if (my_dt < _dt_min)
         mooseException(
             "Geochemistry solve failed with dt = ", my_dt, " at node: ", _current_node->get_info());
     }
 
     if (done_dt + my_dt > _dt)
       my_dt = _dt - done_dt; // avoid overstepping
   }
 
   _execute_done[my_node_number] = true;
 }

◆ finalize()

void GeochemistrySpatialReactor::finalize ( )

overridevirtual

the main-thread information is used to set the other-thread information in finalize()

Reimplemented from GeochemistryReactorBase.

Definition at line 473 of file GeochemistrySpatialReactor.C.

 {
   GeochemistryReactorBase::finalize();
   // if relevant, record that system is closed
   if (!_closed_system && _t >= _close_system_at_time)
     _closed_system = true;
   // ensure that the non-main threads have the main-thread's copy of _egs_at_node (and hence
   // _mgd_at_node) and _removed_fixed_activity, since the main-thread's copy has correctly gathered
   // all the information during threadJoin
   for (unsigned thrd = 1; thrd < _nthreads; ++thrd)
   {
     std::vector<GeochemistrySpatialReactor *> objects;
     _fe_problem.theWarehouse()
         .query()
         .condition<AttribSystem>("UserObject")
         .condition<AttribThread>(thrd)
         .condition<AttribName>(name())
         .queryInto(objects);
     mooseAssert(objects.size() == 1,
                 "GeochemistrySpatialReactor::finalize() failed to obtain a single thread copy of "
                 "the GeochemistrySpatialReactor");
     objects[0]->_removed_fixed_activity = _removed_fixed_activity;
     objects[0]->_egs_at_node = _egs_at_node;
     objects[0]->_closed_system = _closed_system;
   }
 }

◆ getGeochemicalSystem()

const GeochemicalSystem & GeochemistrySpatialReactor::getGeochemicalSystem ( dof_id_type node_id ) const

overridevirtual

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

Parameters

node_id the ID of the node

Implements GeochemistryReactorBase.

Definition at line 523 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(node_id) != 1)
     mooseError("GeochemistrySpatialReactor does not know about node ", node_id);
   return _egs_at_node[_my_node_number.at(node_id)];
 }

◆ getMoleAdditions()

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

overridevirtual

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

Implements GeochemistryReactorBase.

Definition at line 531 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(node_id) != 1)
     mooseError("GeochemistrySpatialReactor does not know about node ", node_id);
   return _mole_additions[_my_node_number.at(node_id)];
 }

◆ getMolesDumped()

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

overridevirtual

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

Implements GeochemistryReactorBase.

Definition at line 563 of file GeochemistrySpatialReactor.C.

 {
   return 0.0;
 }

◆ getPertinentGeochemicalSystem()

const PertinentGeochemicalSystem& GeochemistryReactorBase::getPertinentGeochemicalSystem ( ) const

inlineinherited

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()

unsigned GeochemistrySpatialReactor::getSolverIterations ( dof_id_type node_id ) const

overridevirtual

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

Parameters

node_id the node ID

Implements GeochemistryReactorBase.

Definition at line 547 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(node_id) != 1)
     mooseError("GeochemistrySpatialReactor does not know about node ", node_id);
   return _tot_iter[_my_node_number.at(node_id)];
 }

◆ getSolverOutput()

const std::stringstream & GeochemistrySpatialReactor::getSolverOutput ( dof_id_type node_id ) const

overridevirtual

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

Implements GeochemistryReactorBase.

Definition at line 539 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(node_id) != 1)
     mooseError("GeochemistrySpatialReactor does not know about node ", node_id);
   return _solver_output[_my_node_number.at(node_id)];
 }

◆ getSolverResidual()

Real GeochemistrySpatialReactor::getSolverResidual ( dof_id_type node_id ) const

overridevirtual

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

Implements GeochemistryReactorBase.

Definition at line 555 of file GeochemistrySpatialReactor.C.

 {
   if (_my_node_number.count(node_id) != 1)
     mooseError("GeochemistrySpatialReactor does not know about node ", node_id);
   return _abs_residual[_my_node_number.at(node_id)];
 }

◆ initialize()

void GeochemistrySpatialReactor::initialize ( )

overridevirtual

Reimplemented from GeochemistryReactorBase.

Definition at line 309 of file GeochemistrySpatialReactor.C.

 {
   GeochemistryReactorBase::initialize();
   _execute_done.assign(_num_my_nodes, false);
   _nthreads = 1;
 }

◆ initialSetup()

void GeochemistrySpatialReactor::initialSetup ( )

overridevirtual

Reimplemented from NodalUserObject.

Definition at line 291 of file GeochemistrySpatialReactor.C.

 {
   // Solve the geochemical system with its initial composition and with dt=0 so no kinetic additions
   for (unsigned i = 0; i < _num_my_nodes; ++i)
   {
     _mole_additions[i].zero();
     _dmole_additions[i].zero();
     _solver.solveSystem(_egs_at_node[i],
                         _solver_output[i],
                         _tot_iter[i],
                         _abs_residual[i],
                         0.0,
                         _mole_additions[i],
                         _dmole_additions[i]);
   }
 }

◆ meshChanged()

void GeochemistrySpatialReactor::meshChanged ( )

overridevirtual

Reimplemented from NodalUserObject.

Definition at line 501 of file GeochemistrySpatialReactor.C.

 {
   mooseError("GeochemistrySpatialReactor cannot yet handle adaptive meshing");
   /*
 Note to future coders:
 - have to rebuild _my_node_number.  _num_my_nodes has to be changed (so its not const anymore).
 The Action must not just execute_on = EXEC_INITIAL for NearestNodeNumberUO
 - have to populate the new nodes correctly.  This might be easiest if, at the start of execute,
 _egs_at_node was always populated using AuxVariables (probably a RequiredCoupledVar that is
 actually a ArrayVariableValue & (constructed with coupledArrayValue instead of just coupledValue)
 that record the kg_solvent_water, free molality, surface_pot_expr, etc.  That is use
 _egs_at_node[i].setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles with the
 values from the AuxVariables.  The reason for this design is that then MOOSE handles the
 interpolation of the AuxVariables to the newly-created nodes during mesh adaptivity.  The
 difficult thing is to figure out the variables at the new nodes.  Probably should copy the basis
 species, swap stuff, etc (_mgd_at_node) from the nearest original node to the newly-created node.
 And then solve the new system to allow basis swaps if appropriate.  This is a bit tricky, hence it
 hasn't yet been implemented.
   */
 }

◆ sharedParams()

InputParameters GeochemistrySpatialReactor::sharedParams ( )

static

params that are shared with AddTimeDependentReactionSolverAction

Definition at line 15 of file GeochemistrySpatialReactor.C.

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

 {
   InputParameters params = emptyInputParameters();
   params.addParam<unsigned>(
       "ramp_max_ionic_strength_subsequent",
       0,
       "The number of iterations over which to progressively increase the maximum ionic strength "
       "(from zero to max_ionic_strength) during time-stepping.  Unless a great deal occurs in each "
       "time step, this parameter can be set quite small");
   params.addParam<Real>("initial_temperature",
                         25,
                         "Temperature at which the initial system is equilibrated.  This is uniform "
                         "over the entire mesh.");
   params.addCoupledVar("temperature", 25, "Temperature");
   params.addParam<Real>("close_system_at_time",
                         0.0,
                         "Time at which to 'close' the entire spatial system, that is, change a "
                         "kg_solvent_water constraint to moles_bulk_water, and all free_molality "
                         "and free_moles_mineral_species to moles_bulk_species");
   params.addParam<std::vector<std::string>>(
       "remove_fixed_activity_name",
       {},
       "The name of the species that should have their activity or fugacity constraint removed at "
       "time given in remove_fixed_activity_time.  There should be an equal number of these names "
       "as times given in remove_fixed_activity_time.  Each of these must be in the basis and have "
       "an activity or fugacity constraint");
   params.addParam<std::vector<Real>>("remove_fixed_activity_time",
                                      {},
                                      "The times at which the species in remove_fixed_activity_name "
                                      "should have their activity or fugacity constraint removed.");
   params.addParam<std::vector<std::string>>(
       "source_species_names",
       {},
       "The name of the species that are added at rates given in source_species_rates.  There must "
       "be an equal number of these as source_species_rates.");
   params.addCoupledVar("source_species_rates",
                        "Rates, in mols/time_unit, of addition of the species with names given in "
                        "source_species_names.  A negative value corresponds to removing a species: "
                        "be careful that you don't cause negative mass problems!");
   params.addParam<std::vector<std::string>>(
       "controlled_activity_name",
       {},
       "The names of the species that have their activity or fugacity constrained.  There should be "
       "an equal number of these names as values given in controlled_activity_value.  NOTE: if "
       "these species are not in the basis, or they do not have an activity (or fugacity) "
       "constraint then their activity cannot be controlled: in this case MOOSE will ignore the "
       "value you prescribe in controlled_activity_value.");
   params.addCoupledVar("controlled_activity_value",
                        "Values of the activity or fugacity of the species in "
                        "controlled_activity_name list.  These should always be positive");
   params.addParam<bool>(
       "evaluate_kinetic_rates_always",
       true,
       "If true, then, evaluate the kinetic rates at every Newton step during the solve using the "
       "current values of molality, activity, etc (ie, implement an implicit solve).  If false, "
       "then evaluate the kinetic rates using the values of molality, activity, etc, at the start "
       "of the current time step (ie, implement an explicit solve)");
   params.addParam<std::vector<std::string>>(
       "kinetic_species_name",
       {},
       "Names of the kinetic species given initial values in kinetic_species_initial_value");
   params.addParam<std::vector<Real>>(
       "kinetic_species_initial_value",
       {},
       "Initial number of moles, mass or volume (depending on kinetic_species_unit) for each of the "
       "species named in kinetic_species_name");
   MultiMooseEnum kin_species_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.addParam<MultiMooseEnum>(
       "kinetic_species_unit",
       kin_species_unit,
       "Units of the numerical values given in kinetic_species_initial_value.  Moles: mole number.  "
       "kg: kilograms.  g: grams.  mg: milligrams.  ug: micrograms.  cm3: cubic centimeters");
   params.addParam<bool>("adaptive_timestepping",
                         false,
                         "Use adaptive timestepping at each node in an attempt to ensure "
                         "convergence of the solver.  Setting this parameter to false saves some "
                         "compute time because copying of datastructures is avoided");
   params.addParam<Real>(
       "dt_min",
       1E-10,
       "If, during adaptive timestepping at a node, the time-step fails below this value, "
       "MOOSE will give up trying to solve the geochemical system.  Optimally, you should set this "
       "value bearing abs_tol in mind because as dt changes, the initial value of the residual will "
       "also typically change.  For example, if you set dt_min very small relative to abs_tol MOOSE "
       "may think the system has converged just because dt is small.  Also, bear in mind your "
       "typical timestep size: if dt_min < 1E-16*typical_dt then you will run out of precision");
   params.addRangeCheckedParam<Real>(
       "dt_dec",
       0.5,
       "dt_dec >= 0 & dt_dec < 1.0",
       "If a geochemical solve fails, then 'adpative timestepping' at the node is initiated "
       "(assuming adaptive_timestepping = true): the time-step at the node is multiplied by this "
       "amount, and the solve process re-tried");
   params.addRangeCheckedParam<Real>(
       "dt_inc",
       1.1,
       "dt_inc >= 1.0",
       "If a geochemical solve suceeds during adpative timestepping at a node, then the time-step "
       "at the node is multiplied by this amount before performing the next adaptive timestep");
   return params;
 }

◆ threadJoin()

void GeochemistrySpatialReactor::threadJoin ( const UserObject & uo )

overridevirtual

Reimplemented from GeochemistryReactorBase.

Definition at line 450 of file GeochemistrySpatialReactor.C.

 {
   _nthreads += 1;
   const auto & gsr = static_cast<const GeochemistrySpatialReactor &>(uo);
   for (unsigned i = 0; i < _num_my_nodes; ++i)
   {
     if (!_execute_done[i] && gsr._execute_done[i])
     {
       _solver_output[i].str("");
       _solver_output[i] << gsr._solver_output[i].str();
       _tot_iter[i] = gsr._tot_iter[i];
       _abs_residual[i] = gsr._abs_residual[i];
       _mole_additions[i] = gsr._mole_additions[i];
       _egs_at_node[i] = gsr._egs_at_node[i];
       _removed_fixed_activity[i] = gsr._removed_fixed_activity[i];
       // _mgd_at_node does not need to be threadJoined, because _egs_at_node[i] =
       // gsr._egs_at_node[i] uses the copy-assignment operator to copy the data in
       // _egs_at_node[i]._mgd
     }
   }
 }

◆ validParams()

InputParameters GeochemistrySpatialReactor::validParams ( )

static

Definition at line 119 of file GeochemistrySpatialReactor.C.

 {
   InputParameters params = GeochemistryReactorBase::validParams();
   params += GeochemistrySpatialReactor::sharedParams();
   params.addClassDescription("UserObject that controls the space-dependent and time-dependent "
                              "geochemistry reaction processes");
   return params;
 }

Member Data Documentation

◆ _abs_residual

std::vector<Real> GeochemistryReactorBase::_abs_residual

protectedinherited

L1norm of the solver residual at each node.

Definition at line 103 of file GeochemistryReactorBase.h.

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

◆ _adaptive_timestepping

const bool GeochemistrySpatialReactor::_adaptive_timestepping

protected

Whether to use adaptive timestepping at the nodes.

Definition at line 95 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _close_system_at_time

const Real GeochemistrySpatialReactor::_close_system_at_time

protected

Defines the time at which to close the system.

Definition at line 59 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and finalize().

◆ _closed_system

bool GeochemistrySpatialReactor::_closed_system

protected

Whether the system has been closed.

Definition at line 61 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and finalize().

◆ _controlled_activity_species_names

const std::vector<std::string> GeochemistrySpatialReactor::_controlled_activity_species_names

protected

Names of the species with controlled activity or fugacity.

Definition at line 77 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _controlled_activity_species_values

std::vector<const VariableValue *> GeochemistrySpatialReactor::_controlled_activity_species_values

protected

Activity or fugacity of the species with controlled activity or fugacity.

Definition at line 81 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _dmole_additions

std::vector<DenseMatrix<Real> > GeochemistrySpatialReactor::_dmole_additions

protected

Derivative of moles_added.

Definition at line 87 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and initialSetup().

◆ _dt_dec

const Real GeochemistrySpatialReactor::_dt_dec

protected

value to multiply dt my in the case of a failed solve

Definition at line 99 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _dt_inc

const Real GeochemistrySpatialReactor::_dt_inc

protected

value to multiply dt my in the case of a successful solve

Definition at line 101 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _dt_min

const Real GeochemistrySpatialReactor::_dt_min

protected

minimum value of dt allowed during adpative timestepping. This is set to a large number if _adaptive_timestepping = false so that if any solve ever fails, this class will throw a mooseException

Definition at line 97 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _egs_at_node

std::vector<GeochemicalSystem> GeochemistrySpatialReactor::_egs_at_node

protected

GeochemicalSystem at each node.

Definition at line 53 of file GeochemistrySpatialReactor.h.

Referenced by execute(), finalize(), GeochemistrySpatialReactor(), getGeochemicalSystem(), initialSetup(), and threadJoin().

◆ _egs_copy

GeochemicalSystem GeochemistrySpatialReactor::_egs_copy

protected

GeochemicalSystem into which the nodal GeochemicalSystem is copied to enable recovery during adaptive timestepping.

Definition at line 55 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _execute_done

std::vector<bool> GeochemistrySpatialReactor::_execute_done

protected

whether execute has been called using this thread

Definition at line 93 of file GeochemistrySpatialReactor.h.

Referenced by execute(), initialize(), and threadJoin().

◆ _gac

GeochemistryActivityCoefficientsDebyeHuckel GeochemistryReactorBase::_gac

protectedinherited

The activity calculator.

Definition at line 91 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor().

◆ _initial_max_ionic_str

const Real GeochemistryReactorBase::_initial_max_ionic_str

protectedinherited

Initial value of maximum ionic strength.

Definition at line 87 of file GeochemistryReactorBase.h.

◆ _initial_temperature

const Real GeochemistrySpatialReactor::_initial_temperature

protected

Initial equilibration temperature.

Definition at line 45 of file GeochemistrySpatialReactor.h.

Referenced by GeochemistrySpatialReactor().

◆ _is

GeochemistryIonicStrength GeochemistryReactorBase::_is

protectedinherited

The ionic strength calculator.

Definition at line 89 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor().

◆ _max_swaps_allowed

const unsigned GeochemistryReactorBase::_max_swaps_allowed

protectedinherited

Maximum number of swaps allowed during a single solve.

Definition at line 93 of file GeochemistryReactorBase.h.

◆ _mgd

ModelGeochemicalDatabase GeochemistryReactorBase::_mgd

protectedinherited

my copy of the underlying ModelGeochemicalDatabase

Definition at line 79 of file GeochemistryReactorBase.h.

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

◆ _mgd_at_node

std::vector<ModelGeochemicalDatabase> GeochemistrySpatialReactor::_mgd_at_node

protected

ModelGeochemicalDatabase at each node.

Definition at line 51 of file GeochemistrySpatialReactor.h.

Referenced by GeochemistrySpatialReactor().

◆ _mole_additions

std::vector<DenseVector<Real> > GeochemistrySpatialReactor::_mole_additions

protected

Moles of each basis species added at each node at the current timestep, along with kinetic rates.

Definition at line 85 of file GeochemistrySpatialReactor.h.

Referenced by execute(), getMoleAdditions(), initialSetup(), and threadJoin().

◆ _mole_rates

DenseVector<Real> GeochemistrySpatialReactor::_mole_rates

protected

Rate of mole additions.

Definition at line 83 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _my_node_number

std::unordered_map<dof_id_type, unsigned> GeochemistrySpatialReactor::_my_node_number

protected

_my_node_number[_current_node->id()] = node number used in this object that corresponds to _current_node->id()

Definition at line 91 of file GeochemistrySpatialReactor.h.

Referenced by buildMyNodeNumber(), execute(), getGeochemicalSystem(), getMoleAdditions(), getSolverIterations(), getSolverOutput(), and getSolverResidual().

◆ _nthreads

unsigned GeochemistrySpatialReactor::_nthreads

protected

number of threads used to execute this UserObject

Definition at line 103 of file GeochemistrySpatialReactor.h.

Referenced by finalize(), initialize(), and threadJoin().

◆ _num_basis

const unsigned GeochemistryReactorBase::_num_basis

protectedinherited

number of basis species

Definition at line 83 of file GeochemistryReactorBase.h.

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

◆ _num_controlled_activity

const unsigned GeochemistrySpatialReactor::_num_controlled_activity

protected

Number of species with controlled activity or fugacity.

Definition at line 79 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _num_eqm

const unsigned GeochemistryReactorBase::_num_eqm

protectedinherited

number of equilibrium species

Definition at line 85 of file GeochemistryReactorBase.h.

◆ _num_kin

const unsigned GeochemistrySpatialReactor::_num_kin

protected

Number of kinetic species.

Definition at line 49 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _num_my_nodes

const unsigned GeochemistryReactorBase::_num_my_nodes

protectedinherited

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

◆ _num_removed_fixed

const unsigned GeochemistrySpatialReactor::_num_removed_fixed

protected

Number of elements in the vector _remove_fixed_activity_name;.

Definition at line 73 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _num_source_species

const unsigned GeochemistrySpatialReactor::_num_source_species

protected

Number of source species.

Definition at line 65 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _pgs

const PertinentGeochemicalSystem& GeochemistryReactorBase::_pgs

protectedinherited

Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

Definition at line 81 of file GeochemistryReactorBase.h.

Referenced by GeochemistryReactorBase::getPertinentGeochemicalSystem().

◆ _ramp_subsequent

const unsigned GeochemistrySpatialReactor::_ramp_subsequent

protected

the ramp_max_ionic_strength to use during time-stepping

Definition at line 89 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _remove_fixed_activity_name

const std::vector<std::string> GeochemistrySpatialReactor::_remove_fixed_activity_name

protected

Names of species to remove the fixed activity or fugacity constraint from.

Definition at line 69 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _remove_fixed_activity_time

const std::vector<Real> GeochemistrySpatialReactor::_remove_fixed_activity_time

protected

Times at which to remove the fixed activity or fugacity from the species in _remove_fixed_activity_name.

Definition at line 71 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _removed_fixed_activity

std::vector<std::vector<bool> > GeochemistrySpatialReactor::_removed_fixed_activity

protected

Whether the activity or activity constraint has been removed at each node.

Definition at line 75 of file GeochemistrySpatialReactor.h.

Referenced by execute(), finalize(), and threadJoin().

◆ _small_molality

const Real GeochemistryReactorBase::_small_molality

protectedinherited

A small value of molality.

Definition at line 97 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::postSolveFlowThrough().

◆ _solver

GeochemicalSolver GeochemistrySpatialReactor::_solver

protected

The solver.

Definition at line 57 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and initialSetup().

◆ _solver_output

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

protectedinherited

The solver output at each node.

Definition at line 99 of file GeochemistryReactorBase.h.

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

◆ _source_species_names

const std::vector<std::string> GeochemistrySpatialReactor::_source_species_names

protected

Names of the source species.

Definition at line 63 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _source_species_rates

std::vector<const VariableValue *> GeochemistrySpatialReactor::_source_species_rates

protected

Rates of the source species.

Definition at line 67 of file GeochemistrySpatialReactor.h.

Referenced by execute(), and GeochemistrySpatialReactor().

◆ _swapper

GeochemistrySpeciesSwapper GeochemistryReactorBase::_swapper

protectedinherited

The species swapper.

Definition at line 95 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor().

◆ _temperature

const VariableValue& GeochemistrySpatialReactor::_temperature

protected

Temperature specified by user.

Definition at line 47 of file GeochemistrySpatialReactor.h.

Referenced by execute().

◆ _tot_iter

std::vector<unsigned> GeochemistryReactorBase::_tot_iter

protectedinherited

Number of iterations used by the solver at each node.

Definition at line 101 of file GeochemistryReactorBase.h.

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

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

geochemistry/include/userobjects/GeochemistrySpatialReactor.h
geochemistry/src/userobjects/GeochemistrySpatialReactor.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

◆ GeochemistrySpatialReactor()

Member Function Documentation

◆ buildMyNodeNumber()

◆ execute()

◆ finalize()

◆ getGeochemicalSystem()

◆ getMoleAdditions()

◆ getMolesDumped()

◆ getPertinentGeochemicalSystem()

◆ getSolverIterations()

◆ getSolverOutput()

◆ getSolverResidual()

◆ initialize()

◆ initialSetup()

◆ meshChanged()

◆ sharedParams()

◆ threadJoin()

◆ validParams()

Member Data Documentation

◆ _abs_residual

◆ _adaptive_timestepping

◆ _close_system_at_time

◆ _closed_system

◆ _controlled_activity_species_names

◆ _controlled_activity_species_values

◆ _dmole_additions

◆ _dt_dec

◆ _dt_inc

◆ _dt_min

◆ _egs_at_node

◆ _egs_copy

◆ _execute_done

◆ _gac

◆ _initial_max_ionic_str

◆ _initial_temperature

◆ _is

◆ _max_swaps_allowed

◆ _mgd

◆ _mgd_at_node

◆ _mole_additions

◆ _mole_rates

◆ _my_node_number

◆ _nthreads

◆ _num_basis

◆ _num_controlled_activity

◆ _num_eqm

◆ _num_kin

◆ _num_my_nodes

◆ _num_removed_fixed

◆ _num_source_species

◆ _pgs

◆ _ramp_subsequent

◆ _remove_fixed_activity_name

◆ _remove_fixed_activity_time

◆ _removed_fixed_activity

◆ _small_molality

◆ _solver

◆ _solver_output

◆ _source_species_names

◆ _source_species_rates

◆ _swapper

◆ _temperature

◆ _tot_iter