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GeochemistryQuantityAux Class Reference

AuxKernel to extract information from a Geochemistry*Reactor to record into an AuxVariable. More...

#include <GeochemistryQuantityAux.h>

Inheritance diagram for GeochemistryQuantityAux:
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Public Types

enum  TEST_TYPE
 
typedef DataFileName DataFileParameterType
 

Public Member Functions

 GeochemistryQuantityAux (const InputParameters &parameters)
 
virtual void compute ()
 
void compute ()
 
void compute ()
 
bool isNodal () const
 
bool isMortar ()
 
MooseVariableField< Real > & variable ()
 
const std::set< UserObjectName > & getDependObjects () const
 
void coupledCallback (const std::string &var_name, bool is_old) const override
 
virtual const std::set< std::string > & getRequestedItems () override
 
virtual const std::set< std::string > & getSuppliedItems () override
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyOld (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOld (const std::string &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOlder (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOlder (const std::string &name, MaterialData &material_data)
 
void insert ()
 
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
 
MooseVariableBase * mooseVariableBase () const
 
MooseVariableField< Real > & mooseVariableField ()
 
MooseVariableFE< Real > * mooseVariable () const
 
MooseVariableFV< Real > * mooseVariableFV () const
 
MooseLinearVariableFV< Real > * mooseLinearVariableFV () 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 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 void initialSetup ()
 
virtual void timestepSetup ()
 
virtual void jacobianSetup ()
 
virtual void residualSetup ()
 
virtual void subdomainSetup ()
 
virtual void customSetup (const ExecFlagType &)
 
const ExecFlagEnum & getExecuteOnEnum () 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)
 
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
 
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
 
bool isImplicit ()
 
Moose::StateArg determineState () const
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name, MaterialData &material_data)
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name)
 
std::pair< const MaterialProperty< T > *, std::set< SubdomainID > > getBlockMaterialProperty (const MaterialPropertyName &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialProperty ()
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialPropertyByName (const std::string &prop_name)
 
const MaterialProperty< T > & getZeroMaterialProperty (Ts... args)
 
std::set< SubdomainID > getMaterialPropertyBlocks (const std::string &name)
 
std::vector< SubdomainName > getMaterialPropertyBlockNames (const std::string &name)
 
std::set< BoundaryID > getMaterialPropertyBoundaryIDs (const std::string &name)
 
std::vector< BoundaryName > getMaterialPropertyBoundaryNames (const std::string &name)
 
void checkBlockAndBoundaryCompatibility (std::shared_ptr< MaterialBase > discrete)
 
std::unordered_map< SubdomainID, std::vector< MaterialBase *> > buildRequiredMaterials (bool allow_stateful=true)
 
void statefulPropertiesAllowed (bool)
 
bool getMaterialPropertyCalled () const
 
virtual const std::unordered_set< unsigned int > & getMatPropDependencies () const
 
virtual void resolveOptionalProperties ()
 
const GenericMaterialProperty< T, is_ad > & getPossiblyConstantGenericMaterialPropertyByName (const MaterialPropertyName &prop_name, MaterialData &material_data, const unsigned int state)
 
bool 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
 
void setRandomResetFrequency (ExecFlagType exec_flag)
 
unsigned long getRandomLong () const
 
Real getRandomReal () const
 
unsigned int getSeed (std::size_t id)
 
unsigned int getMasterSeed () const
 
ExecFlagType getResetOnTime () const
 
void setRandomDataPointer (RandomData *random_data)
 
PenetrationLocator & getPenetrationLocator (const BoundaryName &primary, const BoundaryName &secondary, Order order)
 
PenetrationLocator & getQuadraturePenetrationLocator (const BoundaryName &primary, const BoundaryName &secondary, Order order)
 
NearestNodeLocator & getNearestNodeLocator (const BoundaryName &primary, const BoundaryName &secondary)
 
NearestNodeLocator & getQuadratureNearestNodeLocator (const BoundaryName &primary, const BoundaryName &secondary)
 
bool requiresGeometricSearch () const
 
virtual void meshChanged ()
 
virtual unsigned int getElementIDIndex (const std::string &id_parameter_name, unsigned int comp=0) const
 
virtual unsigned int getElementIDIndexByName (const std::string &id_name) const
 
virtual const dof_id_type & getElementID (const std::string &id_parameter_name, unsigned int comp=0) const
 
dof_id_type getElementID (const Elem *elem, unsigned int elem_id_index) const
 
virtual const dof_id_type & getElementIDNeighbor (const std::string &id_parameter_name, unsigned int comp=0) const
 
virtual const dof_id_type & getElementIDByName (const std::string &id_name) const
 
virtual const dof_id_type & getElementIDNeighborByName (const std::string &id_name) const
 
bool hasElementID (const std::string &id_name) const
 
dof_id_type maxElementID (unsigned int elem_id_index) const
 
dof_id_type minElementID (unsigned int elem_id_index) const
 
bool areElemIDsIdentical (const std::string &id_name1, const std::string &id_name2) const
 
std::unordered_map< dof_id_type, std::set< dof_id_type > > getElemIDMapping (const std::string &id_name1, const std::string &id_name2) const
 
std::set< dof_id_type > getAllElemIDs (unsigned int elem_id_index) const
 
std::set< dof_id_type > getElemIDsOnBlocks (unsigned int elem_id_index, const std::set< SubdomainID > &blks) 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 hasUserObject (const std::string &param_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
const GenericOptionalMaterialProperty< T, is_ad > & getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const GenericOptionalMaterialProperty< T, is_ad > & getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalMaterialProperty< T > & getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalMaterialProperty< T > & getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalADMaterialProperty< T > & getOptionalADMaterialProperty (const std::string &name)
 
const OptionalADMaterialProperty< T > & getOptionalADMaterialProperty (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOld (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOld (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOlder (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOlder (const std::string &name)
 
MaterialBase & getMaterial (const std::string &name)
 
MaterialBase & getMaterial (const std::string &name)
 
MaterialBase & getMaterialByName (const std::string &name, bool no_warn=false)
 
MaterialBase & getMaterialByName (const std::string &name, bool no_warn=false)
 
bool hasMaterialProperty (const std::string &name)
 
bool hasMaterialProperty (const std::string &name)
 
bool hasMaterialPropertyByName (const std::string &name)
 
bool hasMaterialPropertyByName (const std::string &name)
 
bool hasADMaterialProperty (const std::string &name)
 
bool hasADMaterialProperty (const std::string &name)
 
bool hasADMaterialPropertyByName (const std::string &name)
 
bool hasADMaterialPropertyByName (const std::string &name)
 
bool hasGenericMaterialProperty (const std::string &name)
 
bool hasGenericMaterialProperty (const std::string &name)
 
bool hasGenericMaterialPropertyByName (const std::string &name)
 
bool hasGenericMaterialPropertyByName (const std::string &name)
 
const 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
 
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
 
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 Parallel::Communicator & comm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static InputParameters validParams ()
 
static bool restricted (const std::set< BoundaryID > &ids)
 
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 std::string deduceFunctorName (const std::string &name, const InputParameters &params)
 

Public Attributes

 ALL
 
 ANY
 
const ConsoleStream _console
 

Static Public Attributes

static constexpr PropertyValue::id_type default_property_id
 
static constexpr PropertyValue::id_type zero_property_id
 

Protected Types

enum  QuantityChoiceEnum {
  QuantityChoiceEnum::MOLAL, QuantityChoiceEnum::MG_PER_KG, QuantityChoiceEnum::FREE_MG, QuantityChoiceEnum::FREE_CM3,
  QuantityChoiceEnum::NEGLOG10A, QuantityChoiceEnum::ACTIVITY, QuantityChoiceEnum::BULK_MOLES, QuantityChoiceEnum::SURFACE_CHARGE,
  QuantityChoiceEnum::SURFACE_POTENTIAL, QuantityChoiceEnum::TEMPERATURE, QuantityChoiceEnum::KINETIC_MOLES, QuantityChoiceEnum::KINETIC_ADDITIONS,
  QuantityChoiceEnum::MOLES_DUMPED, QuantityChoiceEnum::TRANSPORTED_MOLES_IN_ORIGINAL_BASIS
}
 
typedef Moose::DOFType< Real >::type OutputData
 

Protected Member Functions

virtual Real computeValue () override
 
virtual const VariableValue & coupledDot (const std::string &var_name, unsigned int comp=0) const override
 
virtual const VariableValue & coupledDotDu (const std::string &var_name, unsigned int comp=0) const override
 
virtual void precalculateValue ()
 
const OutputTools< Real >::VariableValue & uOld () const
 
const OutputTools< Real >::VariableValue & uOlder () const
 
virtual const OutputTools< Real >::VariableValue & value ()
 
virtual const OutputTools< Real >::VariableValue & valueOld ()
 
virtual const OutputTools< Real >::VariableValue & valueOlder ()
 
virtual const OutputTools< Real >::VariableValue & dot ()
 
virtual const OutputTools< Real >::VariableValue & dotDot ()
 
virtual const OutputTools< Real >::VariableValue & dotOld ()
 
virtual const OutputTools< Real >::VariableValue & dotDotOld ()
 
virtual const VariableValue & dotDu ()
 
virtual const VariableValue & dotDotDu ()
 
virtual const OutputTools< Real >::VariableGradient & gradient ()
 
virtual const OutputTools< Real >::VariableGradient & gradientOld ()
 
virtual const OutputTools< Real >::VariableGradient & gradientOlder ()
 
virtual const OutputTools< Real >::VariableSecond & second ()
 
virtual const OutputTools< Real >::VariableSecond & secondOld ()
 
virtual const OutputTools< Real >::VariableSecond & secondOlder ()
 
virtual const OutputTools< Real >::VariableTestSecond & secondTest ()
 
virtual const OutputTools< Real >::VariableTestSecond & secondTestFace ()
 
virtual const OutputTools< Real >::VariablePhiSecond & secondPhi ()
 
virtual const OutputTools< Real >::VariablePhiSecond & secondPhiFace ()
 
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 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
 
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 & 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
 
virtual void checkMaterialProperty (const std::string &name, const unsigned int state)
 
void markMatPropRequested (const std::string &)
 
MaterialPropertyName getMaterialPropertyName (const std::string &name) const
 
void checkExecutionStage ()
 
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
 
std::string deduceFunctorName (const std::string &name) const
 
const Moose::Functor< T > & getFunctor (const std::string &name)
 
const Moose::Functor< T > & getFunctor (const std::string &name, THREAD_ID tid)
 
const Moose::Functor< T > & getFunctor (const std::string &name, SubProblem &subproblem)
 
const Moose::Functor< T > & getFunctor (const std::string &name, SubProblem &subproblem, THREAD_ID tid)
 
bool isFunctor (const std::string &name) const
 
bool isFunctor (const std::string &name, const SubProblem &subproblem) const
 
Moose::ElemArg makeElemArg (const Elem *elem, bool correct_skewnewss=false) const
 
void checkFunctorSupportsSideIntegration (const std::string &name, bool qp_integration)
 
const GenericMaterialProperty< T, is_ad > * defaultGenericMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > * defaultGenericMaterialProperty (const std::string &name)
 
const MaterialProperty< T > * defaultMaterialProperty (const std::string &name)
 
const MaterialProperty< T > * defaultMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > * defaultADMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > * defaultADMaterialProperty (const std::string &name)
 

Protected Attributes

const std::string & _species
 The species of interest. More...
 
const GeochemistryReactorBase & _reactor
 
enum GeochemistryQuantityAux::QuantityChoiceEnum _quantity_choice
 
unsigned _surface_sorption_mineral_index
 index into mgd.surface_sorption_name corresponding to the species: this is used if quantity is surface_charge or surface_potential More...
 
const bool & _check_boundary_restricted
 
SubProblem & _subproblem
 
SystemBase & _sys
 
SystemBase & _nl_sys
 
AuxiliarySystem & _aux_sys
 
THREAD_ID _tid
 
MooseVariableField< Real > & _var
 
bool _nodal
 
const OutputTools< Real >::VariableValue & _u
 
Assembly & _assembly
 
bool _bnd
 
MooseMesh & _mesh
 
const OutputTools< Real >::VariableTestValue & _test
 
const MooseArray< Point > & _q_point
 
const QBase *const & _qrule
 
const MooseArray< Real > & _JxW
 
const MooseArray< Real > & _coord
 
const Elem *const & _current_elem
 
const unsigned int & _current_side
 
const Real & _current_elem_volume
 
const Real & _current_side_volume
 
const Node *const & _current_node
 
const BoundaryID & _current_boundary_id
 
NumericVector< Number > & _solution
 
const Elem *const & _current_lower_d_elem
 
const bool _coincident_lower_d_calc
 
unsigned int _qp
 
unsigned int _n_local_dofs
 
DenseVector< OutputData > _local_re
 
DenseVector< OutputData > _local_sol
 
DenseMatrix< Number > _local_ke
 
const bool & _enabled
 
MooseApp & _app
 
const std::string _type
 
const std::string _name
 
const InputParameters & _pars
 
Factory & _factory
 
ActionFactory & _action_factory
 
MooseVariableFE< Real > * _variable
 
MooseVariableFV< Real > * _fv_variable
 
MooseLinearVariableFV< Real > * _linear_fv_variable
 
MooseVariableField< Real > * _field_variable
 
Assembly * _mvi_assembly
 
const MaterialData * _blk_material_data
 
const ExecFlagEnum & _execute_enum
 
const ExecFlagType & _current_execute_flag
 
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 InputParameters & _mi_params
 
const std::string _mi_name
 
const MooseObjectName _mi_moose_object_name
 
FEProblemBase & _mi_feproblem
 
SubProblem & _mi_subproblem
 
const THREAD_ID _mi_tid
 
const Moose::MaterialDataType _material_data_type
 
MaterialData & _material_data
 
bool _stateful_allowed
 
bool _get_material_property_called
 
std::vector< std::unique_ptr< PropertyValue > > _default_properties
 
std::unordered_set< unsigned int > _material_property_dependencies
 
const MaterialPropertyName _get_suffix
 
const bool _use_interpolated_state
 
GeometricSearchData & _geometric_search_data
 
bool _requires_geometric_search
 
MooseApp & _restartable_app
 
const std::string _restartable_system_name
 
const THREAD_ID _restartable_tid
 
const bool _restartable_read_only
 
FEProblemBase & _mci_feproblem
 
const Parallel::Communicator & _communicator
 

Static Protected Attributes

static const std::string _interpolated_old
 
static const std::string _interpolated_older
 

Detailed Description

AuxKernel to extract information from a Geochemistry*Reactor to record into an AuxVariable.

Definition at line 18 of file GeochemistryQuantityAux.h.

Member Enumeration Documentation

◆ QuantityChoiceEnum

enum GeochemistryQuantityAux::QuantityChoiceEnum
strongprotected
Enumerator
MOLAL 
MG_PER_KG 
FREE_MG 
FREE_CM3 
NEGLOG10A 
ACTIVITY 
BULK_MOLES 
SURFACE_CHARGE 
SURFACE_POTENTIAL 
TEMPERATURE 
KINETIC_MOLES 
KINETIC_ADDITIONS 
MOLES_DUMPED 
TRANSPORTED_MOLES_IN_ORIGINAL_BASIS 

Definition at line 33 of file GeochemistryQuantityAux.h.

33  {
34  MOLAL,
35  MG_PER_KG,
36  FREE_MG,
37  FREE_CM3,
38  NEGLOG10A,
39  ACTIVITY,
40  BULK_MOLES,
41  SURFACE_CHARGE,
42  SURFACE_POTENTIAL,
43  TEMPERATURE,
44  KINETIC_MOLES,
45  KINETIC_ADDITIONS,
46  MOLES_DUMPED,
47  TRANSPORTED_MOLES_IN_ORIGINAL_BASIS
48  } _quantity_choice;
GeochemistryQuantityAux::_quantity_choice
enum GeochemistryQuantityAux::QuantityChoiceEnum _quantity_choice

Constructor & Destructor Documentation

◆ GeochemistryQuantityAux()

GeochemistryQuantityAux::GeochemistryQuantityAux ( const InputParameters &  parameters)

Definition at line 49 of file GeochemistryQuantityAux.C.

50  : AuxKernel(parameters),
51  _species(getParam<std::string>("species")),
52  _reactor(getUserObject<GeochemistryReactorBase>("reactor")),
53  _quantity_choice(getParam<MooseEnum>("quantity").getEnum<QuantityChoiceEnum>()),
54  _surface_sorption_mineral_index(0)
55 {
56  const ModelGeochemicalDatabase & mgd =
57  _reactor.getPertinentGeochemicalSystem().modelGeochemicalDatabase();
58  if (!(mgd.basis_species_index.count(_species) == 1 ||
59  mgd.eqm_species_index.count(_species) == 1 || mgd.kin_species_index.count(_species) == 1))
60  paramError(
61  "species",
62  _species,
63  " does not appear in the model's geochemical system either as a basis or equilibrium "
64  "or kinetic species, but you requested an Aux involving it");
65 
66  bool is_mineral = false;
67  if (mgd.basis_species_index.count(_species) == 1)
68  is_mineral = mgd.basis_species_mineral[mgd.basis_species_index.at(_species)];
69  else if (mgd.eqm_species_index.count(_species) == 1)
70  is_mineral = mgd.eqm_species_mineral[mgd.eqm_species_index.at(_species)];
71  else
72  is_mineral = mgd.kin_species_mineral[mgd.kin_species_index.at(_species)];
73  bool is_kinetic = (mgd.kin_species_index.count(_species) == 1);
74 
75  if (!is_mineral && (_quantity_choice == QuantityChoiceEnum::FREE_CM3 ||
76  _quantity_choice == QuantityChoiceEnum::FREE_MG ||
77  _quantity_choice == QuantityChoiceEnum::SURFACE_CHARGE ||
78  _quantity_choice == QuantityChoiceEnum::SURFACE_POTENTIAL ||
79  _quantity_choice == QuantityChoiceEnum::MOLES_DUMPED))
80  paramError(
81  "quantity",
82  "the free_mg, free_cm3, moles_dumped and surface-related quantities are only available for "
83  "mineral species");
84  if ((is_mineral || is_kinetic) && (_quantity_choice == QuantityChoiceEnum::MOLAL ||
85  _quantity_choice == QuantityChoiceEnum::MG_PER_KG))
86  paramError("quantity",
87  "the molal and mg_per_kg quantities are only available for "
88  "non-kinetic, non-mineral species");
89  if (_quantity_choice == QuantityChoiceEnum::SURFACE_CHARGE ||
90  _quantity_choice == QuantityChoiceEnum::SURFACE_POTENTIAL)
91  {
92  _surface_sorption_mineral_index = std::distance(
93  mgd.surface_sorption_name.begin(),
94  std::find(mgd.surface_sorption_name.begin(), mgd.surface_sorption_name.end(), _species));
95  if (_surface_sorption_mineral_index >= mgd.surface_sorption_name.size())
96  paramError("species",
97  "cannot record surface charge or surface potential for a species that is not "
98  "involved in surface sorption");
99  }
100  if (!is_kinetic && (_quantity_choice == QuantityChoiceEnum::KINETIC_MOLES ||
101  _quantity_choice == QuantityChoiceEnum::KINETIC_ADDITIONS))
102  paramError("quantity",
103  "the kinetic_moles and kinetic_additions quantities are only available for kinetic "
104  "species");
105  if (is_kinetic && (_quantity_choice == QuantityChoiceEnum::NEGLOG10A ||
106  _quantity_choice == QuantityChoiceEnum::ACTIVITY ||
107  _quantity_choice == QuantityChoiceEnum::BULK_MOLES))
108  paramError("species", "cannot record activity, neglog10a or bulk_moles for a kinetic species");
109  if (_quantity_choice == QuantityChoiceEnum::TRANSPORTED_MOLES_IN_ORIGINAL_BASIS)
110  _reactor.getPertinentGeochemicalSystem().getIndexOfOriginalBasisSpecies(
111  _species); // will throw error if species not in original basis
112 }
ModelGeochemicalDatabase::kin_species_mineral
std::vector< bool > kin_species_mineral
kin_species_mineral[j] = true iff the j^th kinetic species is a mineral
Definition: PertinentGeochemicalSystem.h:306
PertinentGeochemicalSystem::getIndexOfOriginalBasisSpecies
unsigned getIndexOfOriginalBasisSpecies(const std::string &name) const
Definition: PertinentGeochemicalSystem.C:69
ModelGeochemicalDatabase::surface_sorption_name
std::vector< std::string > surface_sorption_name
surface_sorption_name[k] = name of the mineral involved in surface sorption.
Definition: PertinentGeochemicalSystem.h:232
GeochemistryQuantityAux::_species
const std::string & _species
The species of interest.
Definition: GeochemistryQuantityAux.h:29
ModelGeochemicalDatabase::basis_species_index
std::unordered_map< std::string, unsigned > basis_species_index
basis_species_index[name] = index of the basis species, within all ModelGeochemicalDatabase internal ...
Definition: PertinentGeochemicalSystem.h:158
mgd
const ModelGeochemicalDatabase mgd
Definition: GeochemistryActivityCoefficientsDebyeHuckelTest.C:28
GeochemistryQuantityAux::_reactor
const GeochemistryReactorBase & _reactor
Definition: GeochemistryQuantityAux.h:31
ModelGeochemicalDatabase::eqm_species_index
std::unordered_map< std::string, unsigned > eqm_species_index
eqm_species_index[name] = index of the equilibrium species (secondary aqueous species, redox couples in equilibrium with the aqueous solution, minerals in equilibrium with the aqueous solution, gases in equilibrium with the aqueous solution) within all ModelGeochemicalDatabase internal datastrcutres, with given name
Definition: PertinentGeochemicalSystem.h:190
ModelGeochemicalDatabase::kin_species_index
std::unordered_map< std::string, unsigned > kin_species_index
kin_species_index[name] = index of the kinetic species, within all ModelGeochemicalDatabase internal ...
Definition: PertinentGeochemicalSystem.h:300
PertinentGeochemicalSystem::modelGeochemicalDatabase
const ModelGeochemicalDatabase & modelGeochemicalDatabase() const
Return a reference to the ModelGeochemicalDatabase structure.
Definition: PertinentGeochemicalSystem.C:850
AuxKernelTempl< Real >::paramError
void paramError(const std::string &param, Args... args) const
GeochemistryQuantityAux::_surface_sorption_mineral_index
unsigned _surface_sorption_mineral_index
index into mgd.surface_sorption_name corresponding to the species: this is used if quantity is surfac...
Definition: GeochemistryQuantityAux.h:54
GeochemistryQuantityAux::_quantity_choice
enum GeochemistryQuantityAux::QuantityChoiceEnum _quantity_choice
ModelGeochemicalDatabase::basis_species_mineral
std::vector< bool > basis_species_mineral
basis_species_mineral[j] = true iff the j^th basis species is a mineral
Definition: PertinentGeochemicalSystem.h:164
AuxKernelTempl< Real >::parameters
const InputParameters & parameters() const
ModelGeochemicalDatabase
Data structure to hold all relevant information from the database file.
Definition: PertinentGeochemicalSystem.h:99
ModelGeochemicalDatabase::eqm_species_mineral
std::vector< bool > eqm_species_mineral
eqm_species_mineral[i] = true iff the i^th equilibrium species is a mineral
Definition: PertinentGeochemicalSystem.h:196
GeochemistryReactorBase::getPertinentGeochemicalSystem
const PertinentGeochemicalSystem & getPertinentGeochemicalSystem() const
returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase ...
Definition: GeochemistryReactorBase.h:73

Member Function Documentation

◆ computeValue()

Real GeochemistryQuantityAux::computeValue ( )
overrideprotectedvirtual

Implements AuxKernelTempl< Real >.

Definition at line 115 of file GeochemistryQuantityAux.C.

116 {
117  Real ret = 0.0;
118  const GeochemicalSystem & egs = _reactor.getGeochemicalSystem(_current_node->id());
119  const ModelGeochemicalDatabase & mgd = egs.getModelGeochemicalDatabase();
120  const PertinentGeochemicalSystem & pgs = _reactor.getPertinentGeochemicalSystem();
121  if (_quantity_choice == QuantityChoiceEnum::SURFACE_CHARGE)
122  ret = egs.getSurfaceCharge(_surface_sorption_mineral_index);
123  else if (_quantity_choice == QuantityChoiceEnum::SURFACE_POTENTIAL)
124  ret = egs.getSurfacePotential(_surface_sorption_mineral_index);
125  else if (_quantity_choice == QuantityChoiceEnum::TEMPERATURE)
126  ret = egs.getTemperature();
127  else if (_quantity_choice == QuantityChoiceEnum::MOLES_DUMPED)
128  ret = _reactor.getMolesDumped(_current_node->id(), _species);
129  else if (_quantity_choice == QuantityChoiceEnum::TRANSPORTED_MOLES_IN_ORIGINAL_BASIS)
130  ret = egs.getTransportedBulkInOriginalBasis()(pgs.getIndexOfOriginalBasisSpecies(_species));
131  else
132  {
133  if (mgd.basis_species_index.count(_species) == 1)
134  {
135  const unsigned basis_ind = mgd.basis_species_index.at(_species);
136  switch (_quantity_choice)
137  {
138  case QuantityChoiceEnum::MG_PER_KG:
139  ret = egs.getSolventMassAndFreeMolalityAndMineralMoles()[basis_ind] *
140  mgd.basis_species_molecular_weight[basis_ind] * 1000.0;
141  break;
142  case QuantityChoiceEnum::FREE_MG:
143  ret = egs.getSolventMassAndFreeMolalityAndMineralMoles()[basis_ind] *
144  mgd.basis_species_molecular_weight[basis_ind] * 1000.0;
145  break;
146  case QuantityChoiceEnum::FREE_CM3:
147  ret = egs.getSolventMassAndFreeMolalityAndMineralMoles()[basis_ind] *
148  mgd.basis_species_molecular_volume[basis_ind];
149  break;
150  case QuantityChoiceEnum::NEGLOG10A:
151  ret = -std::log10(egs.getBasisActivity(basis_ind));
152  break;
153  case QuantityChoiceEnum::ACTIVITY:
154  ret = egs.getBasisActivity(basis_ind);
155  break;
156  case QuantityChoiceEnum::BULK_MOLES:
157  ret = egs.getBulkMolesOld()[basis_ind];
158  break;
159  default:
160  ret = egs.getSolventMassAndFreeMolalityAndMineralMoles()[basis_ind];
161  }
162  }
163  else if (mgd.eqm_species_index.count(_species) == 1)
164  {
165  const unsigned eqm_ind = mgd.eqm_species_index.at(_species);
166  switch (_quantity_choice)
167  {
168  case QuantityChoiceEnum::MG_PER_KG:
169  ret = egs.getEquilibriumMolality(eqm_ind) * mgd.eqm_species_molecular_weight[eqm_ind] *
170  1000.0;
171  break;
172  case QuantityChoiceEnum::FREE_CM3:
173  ret = egs.getEquilibriumMolality(eqm_ind) * mgd.eqm_species_molecular_volume[eqm_ind];
174  break;
175  case QuantityChoiceEnum::FREE_MG:
176  ret = egs.getEquilibriumMolality(eqm_ind) * mgd.eqm_species_molecular_weight[eqm_ind] *
177  1000.0;
178  break;
179  case QuantityChoiceEnum::NEGLOG10A:
180  ret = -std::log10(egs.getEquilibriumActivity(eqm_ind));
181  break;
182  case QuantityChoiceEnum::ACTIVITY:
183  ret = egs.getEquilibriumActivity(eqm_ind);
184  break;
185  case QuantityChoiceEnum::BULK_MOLES:
186  ret = 0.0;
187  break;
188  default:
189  ret = egs.getEquilibriumMolality(eqm_ind);
190  }
191  }
192  else
193  {
194  const unsigned kin_ind = mgd.kin_species_index.at(_species);
195  switch (_quantity_choice)
196  {
197  case QuantityChoiceEnum::FREE_CM3:
198  ret = egs.getKineticMoles(kin_ind) * mgd.kin_species_molecular_volume[kin_ind];
199  break;
200  case QuantityChoiceEnum::FREE_MG:
201  ret = egs.getKineticMoles(kin_ind) * mgd.kin_species_molecular_weight[kin_ind] * 1000.0;
202  break;
203  case QuantityChoiceEnum::KINETIC_ADDITIONS:
204  ret = _reactor.getMoleAdditions(_current_node->id())(kin_ind + egs.getNumInBasis());
205  break;
206  default:
207  ret = egs.getKineticMoles(kin_ind);
208  }
209  }
210  }
211  return ret;
212 }
ModelGeochemicalDatabase::eqm_species_molecular_weight
std::vector< Real > eqm_species_molecular_weight
all quantities have a molecular weight (g)
Definition: PertinentGeochemicalSystem.h:211
GeochemicalSystem::getTemperature
Real getTemperature() const
Definition: GeochemicalSystem.C:1864
PertinentGeochemicalSystem::getIndexOfOriginalBasisSpecies
unsigned getIndexOfOriginalBasisSpecies(const std::string &name) const
Definition: PertinentGeochemicalSystem.C:69
GeochemicalSystem::getBulkMolesOld
const std::vector< Real > & getBulkMolesOld() const
Definition: GeochemicalSystem.C:803
GeochemistryQuantityAux::_species
const std::string & _species
The species of interest.
Definition: GeochemistryQuantityAux.h:29
ModelGeochemicalDatabase::basis_species_index
std::unordered_map< std::string, unsigned > basis_species_index
basis_species_index[name] = index of the basis species, within all ModelGeochemicalDatabase internal ...
Definition: PertinentGeochemicalSystem.h:158
AuxKernelTempl< Real >::_current_node
const Node *const & _current_node
mgd
const ModelGeochemicalDatabase mgd
Definition: GeochemistryActivityCoefficientsDebyeHuckelTest.C:28
ModelGeochemicalDatabase::kin_species_molecular_weight
std::vector< Real > kin_species_molecular_weight
all quantities have a molecular weight (g/mol)
Definition: PertinentGeochemicalSystem.h:315
ModelGeochemicalDatabase::kin_species_molecular_volume
std::vector< Real > kin_species_molecular_volume
all quantities have a molecular volume (cm^3/mol) (only nonzero for minerals, however) ...
Definition: PertinentGeochemicalSystem.h:318
GeochemistryQuantityAux::_reactor
const GeochemistryReactorBase & _reactor
Definition: GeochemistryQuantityAux.h:31
ModelGeochemicalDatabase::eqm_species_index
std::unordered_map< std::string, unsigned > eqm_species_index
eqm_species_index[name] = index of the equilibrium species (secondary aqueous species, redox couples in equilibrium with the aqueous solution, minerals in equilibrium with the aqueous solution, gases in equilibrium with the aqueous solution) within all ModelGeochemicalDatabase internal datastrcutres, with given name
Definition: PertinentGeochemicalSystem.h:190
GeochemicalSystem::getNumInBasis
unsigned getNumInBasis() const
returns the number of species in the basis
Definition: GeochemicalSystem.C:1693
ModelGeochemicalDatabase::kin_species_index
std::unordered_map< std::string, unsigned > kin_species_index
kin_species_index[name] = index of the kinetic species, within all ModelGeochemicalDatabase internal ...
Definition: PertinentGeochemicalSystem.h:300
GeochemicalSystem::getBasisActivity
Real getBasisActivity(unsigned i) const
Definition: GeochemicalSystem.C:870
GeochemicalSystem::getEquilibriumActivity
Real getEquilibriumActivity(unsigned eqm_ind) const
Returns the value of activity for the equilibrium species with index eqm_index.
Definition: GeochemicalSystem.C:2319
GeochemistryReactorBase::getGeochemicalSystem
virtual const GeochemicalSystem & getGeochemicalSystem(dof_id_type node_id) const =0
GeochemicalSystem::getKineticMoles
Real getKineticMoles(unsigned kin) const
Definition: GeochemicalSystem.C:906
GeochemistryReactorBase::getMolesDumped
virtual Real getMolesDumped(dof_id_type node_id, const std::string &species) const =0
PertinentGeochemicalSystem
Constructs and stores a minimal amount of information that is pertinent to the user-defined geochemic...
Definition: PertinentGeochemicalSystem.h:382
GeochemicalSystem::getModelGeochemicalDatabase
const ModelGeochemicalDatabase & getModelGeochemicalDatabase() const
Definition: GeochemicalSystem.C:1571
GeochemistryReactorBase::getMoleAdditions
virtual const DenseVector< Real > & getMoleAdditions(dof_id_type node_id) const =0
GeochemistryQuantityAux::_surface_sorption_mineral_index
unsigned _surface_sorption_mineral_index
index into mgd.surface_sorption_name corresponding to the species: this is used if quantity is surfac...
Definition: GeochemistryQuantityAux.h:54
ModelGeochemicalDatabase::basis_species_molecular_weight
std::vector< Real > basis_species_molecular_weight
all quantities have a molecular weight (g)
Definition: PertinentGeochemicalSystem.h:179
GeochemistryQuantityAux::_quantity_choice
enum GeochemistryQuantityAux::QuantityChoiceEnum _quantity_choice
Real
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
GeochemicalSystem::getSurfacePotential
Real getSurfacePotential(unsigned sp) const
Definition: GeochemicalSystem.C:1813
ModelGeochemicalDatabase::eqm_species_molecular_volume
std::vector< Real > eqm_species_molecular_volume
all quantities have a molecular volume (cm^3) (only nonzero for minerals, however) ...
Definition: PertinentGeochemicalSystem.h:214
GeochemicalSystem::getEquilibriumMolality
Real getEquilibriumMolality(unsigned j) const
Definition: GeochemicalSystem.C:888
GeochemicalSystem
This class holds information about bulk composition, molalities, activities, activity coefficients...
Definition: GeochemicalSystem.h:39
ModelGeochemicalDatabase
Data structure to hold all relevant information from the database file.
Definition: PertinentGeochemicalSystem.h:99
ModelGeochemicalDatabase::basis_species_molecular_volume
std::vector< Real > basis_species_molecular_volume
all quantities have a molecular volume (cm^3) (only nonzero for minerals, however) ...
Definition: PertinentGeochemicalSystem.h:182
GeochemicalSystem::getSolventMassAndFreeMolalityAndMineralMoles
const std::vector< Real > & getSolventMassAndFreeMolalityAndMineralMoles() const
Definition: GeochemicalSystem.C:831
GeochemicalSystem::getTransportedBulkInOriginalBasis
DenseVector< Real > getTransportedBulkInOriginalBasis() const
Definition: GeochemicalSystem.C:819
GeochemicalSystem::getSurfaceCharge
Real getSurfaceCharge(unsigned sp) const
Definition: GeochemicalSystem.C:1827
GeochemistryReactorBase::getPertinentGeochemicalSystem
const PertinentGeochemicalSystem & getPertinentGeochemicalSystem() const
returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase ...
Definition: GeochemistryReactorBase.h:73

◆ validParams()

InputParameters GeochemistryQuantityAux::validParams ( )
static

Definition at line 15 of file GeochemistryQuantityAux.C.

16 {
17  InputParameters params = AuxKernel::validParams();
18  params.addClassDescription(
19  "Extracts information from the Reactor and records it in the AuxVariable");
20  params.addRequiredParam<std::string>("species", "Species name");
21  MooseEnum quantity_choice("molal mg_per_kg free_mg free_cm3 neglog10a activity bulk_moles "
22  "surface_charge surface_potential temperature kinetic_moles "
23  "kinetic_additions moles_dumped transported_moles_in_original_basis",
24  "molal");
25  params.addParam<MooseEnum>(
26  "quantity",
27  quantity_choice,
28  "Type of quantity to output. These are available for non-kinetic species: activity (which "
29  "equals "
30  "fugacity for gases); bulk moles (this will be zero if the species is not in the basis); "
31  "neglog10a = -log10(activity); transported_moles_in_original_basis (will throw an error if "
32  "species is not in original basis). These are available only for non-kinetic non-minerals: "
33  "molal = "
34  "mol(species)/kg(solvent_water); mg_per_kg = mg(species)/kg(solvent_water). These are "
35  "available only for minerals: "
36  "free_mg = free mg; free_cm3 = free cubic-centimeters; moles_dumped = moles dumped when "
37  "special dump and flow-through modes are active. These are available for minerals "
38  "that host sorbing sites: surface_charge (C/m^2); surface_potential (V). These are "
39  "available for kinetic species: kinetic_moles; kinetic_additions (-dt * rate = mole "
40  "increment in kinetic species for this timestep). If "
41  "quantity=temperature, then the 'species' is ignored and the AuxVariable will record the "
42  "aqueous solution temperature in degC");
43  params.addRequiredParam<UserObjectName>("reactor",
44  "The name of the Geochemistry*Reactor user object.");
45  params.declareControllable("species");
46  return params;
47 }
InputParameters::addParam
void addParam(const std::string &name, const std::initializer_list< typename T::value_type > &value, const std::string &doc_string)
InputParameters::addRequiredParam
void addRequiredParam(const std::string &name, const std::string &doc_string)
InputParameters::addClassDescription
void addClassDescription(const std::string &doc_string)
AuxKernelTempl< Real >::validParams
static InputParameters validParams()
InputParameters::declareControllable
void declareControllable(const std::string &name, std::set< ExecFlagType > execute_flags={})

Member Data Documentation

◆ _quantity_choice

enum GeochemistryQuantityAux::QuantityChoiceEnum GeochemistryQuantityAux::_quantity_choice
protected

Referenced by computeValue(), and GeochemistryQuantityAux().

◆ _reactor

const GeochemistryReactorBase& GeochemistryQuantityAux::_reactor
protected

Definition at line 31 of file GeochemistryQuantityAux.h.

Referenced by computeValue(), and GeochemistryQuantityAux().

◆ _species

const std::string& GeochemistryQuantityAux::_species
protected

The species of interest.

Definition at line 29 of file GeochemistryQuantityAux.h.

Referenced by computeValue(), and GeochemistryQuantityAux().

◆ _surface_sorption_mineral_index

unsigned GeochemistryQuantityAux::_surface_sorption_mineral_index
protected

index into mgd.surface_sorption_name corresponding to the species: this is used if quantity is surface_charge or surface_potential

Definition at line 54 of file GeochemistryQuantityAux.h.

Referenced by computeValue(), and GeochemistryQuantityAux().

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