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GeochemistryReactorBase Class Referenceabstract

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

#include <GeochemistryReactorBase.h>

Inheritance diagram for GeochemistryReactorBase:
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Public Types

enum  TEST_TYPE
 
typedef DataFileName DataFileParameterType
 

Public Member Functions

 GeochemistryReactorBase (const InputParameters &parameters)
 
virtual void initialize () override
 
virtual void threadJoin (const UserObject &) override
 
virtual void finalize () override
 
virtual void execute () override
 
virtual const GeochemicalSystemgetGeochemicalSystem (dof_id_type node_id) const =0
 
virtual const std::stringstream & getSolverOutput (dof_id_type node_id) const =0
 
virtual unsigned getSolverIterations (dof_id_type node_id) const =0
 
virtual Real getSolverResidual (dof_id_type node_id) const =0
 
virtual const DenseVector< Real > & getMoleAdditions (dof_id_type node_id) const =0
 
virtual Real getMolesDumped (dof_id_type node_id, const std::string &species) const =0
 
const PertinentGeochemicalSystemgetPertinentGeochemicalSystem () const
 returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase More...
 
virtual void subdomainSetup () override
 
bool isUniqueNodeExecute ()
 
SubProblemgetSubProblem () 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)
 
UserObjectprimaryThreadCopy ()
 
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< MooseObjectgetSharedPtr ()
 
std::shared_ptr< const MooseObjectgetSharedPtr () const
 
MooseAppgetMooseApp () 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 InputParametersparameters () 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 & getRenamedParam (const std::string &old_name, const std::string &new_name) const
 
getCheckedPointerParam (const std::string &name, const std::string &error_string="") const
 
bool isParamValid (const std::string &name) const
 
bool isParamSetByUser (const std::string &nm) const
 
void paramError (const std::string &param, Args... args) const
 
void paramWarning (const std::string &param, Args... args) const
 
void paramInfo (const std::string &param, Args... args) const
 
void connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const
 
void mooseError (Args &&... args) const
 
void mooseErrorNonPrefixed (Args &&... args) const
 
void mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const
 
void mooseWarning (Args &&... args) const
 
void mooseWarningNonPrefixed (Args &&... args) const
 
void mooseDeprecated (Args &&... args) const
 
void mooseInfo (Args &&... args) const
 
std::string getDataFileName (const std::string &param) const
 
std::string getDataFileNameByName (const std::string &relative_path) const
 
std::string getDataFilePath (const std::string &relative_path) const
 
virtual void initialSetup ()
 
virtual void timestepSetup ()
 
virtual void jacobianSetup ()
 
virtual void residualSetup ()
 
virtual void customSetup (const ExecFlagType &)
 
const ExecFlagEnumgetExecuteOnEnum () 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 UserObjectgetUserObjectBase (const std::string &param_name, bool is_dependency=true) const
 
const UserObjectgetUserObjectBaseByName (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 (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 VariableValuecoupledValueByName (const std::string &var_name)
 
virtual const ArrayVariableValuecoupledArrayValueByName (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 ADVariableValuegetADDefaultValue (const std::string &var_name) const
 
const ADVectorVariableValuegetADDefaultVectorValue (const std::string &var_name) const
 
const ADVariableGradientgetADDefaultGradient () const
 
const ADVectorVariableGradientgetADDefaultVectorGradient () const
 
const ADVariableSecondgetADDefaultSecond () const
 
const ADVectorVariableCurlgetADDefaultCurl () 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)
 
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 FunctiongetFunction (const std::string &name) const
 
const FunctiongetFunctionByName (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 VectorPostprocessorValuegetVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const
 
const VectorPostprocessorValuegetVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const VectorPostprocessorValuegetVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const
 
const ScatterVectorPostprocessorValuegetScatterVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValuegetScatterVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValuegetScatterVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValuegetScatterVectorPostprocessorValueOldByName (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)
 
SamplergetSampler (const std::string &name)
 
T & getSamplerByName (const SamplerName &name)
 
SamplergetSamplerByName (const SamplerName &name)
 
virtual void meshChanged ()
 
PerfGraphperfGraph ()
 
const PostprocessorValuegetPostprocessorValue (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValuegetPostprocessorValue (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValuegetPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValuegetPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValuegetPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValuegetPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const
 
virtual const PostprocessorValuegetPostprocessorValueByName (const PostprocessorName &name) const
 
virtual const PostprocessorValuegetPostprocessorValueByName (const PostprocessorName &name) const
 
const PostprocessorValuegetPostprocessorValueOldByName (const PostprocessorName &name) const
 
const PostprocessorValuegetPostprocessorValueOldByName (const PostprocessorName &name) const
 
const PostprocessorValuegetPostprocessorValueOlderByName (const PostprocessorName &name) const
 
const PostprocessorValuegetPostprocessorValueOlderByName (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 DistributiongetDistribution (const std::string &name) const
 
const T & getDistribution (const std::string &name) const
 
const DistributiongetDistribution (const std::string &name) const
 
const T & getDistribution (const std::string &name) const
 
const DistributiongetDistributionByName (const DistributionName &name) const
 
const T & getDistributionByName (const std::string &name) const
 
const DistributiongetDistributionByName (const DistributionName &name) const
 
const T & getDistributionByName (const std::string &name) const
 
const Parallel::Communicator & comm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static InputParameters sharedParams ()
 contains params that are shared with AddGeochemistrySolverAction and its children More...
 
static InputParameters validParams ()
 
static void sort (typename std::vector< T > &vector)
 
static void sortDFS (typename std::vector< T > &vector)
 
static void cyclicDependencyError (CyclicDependencyException< T2 > &e, const std::string &header)
 
static bool restricted (const std::set< BoundaryID > &ids)
 

Public Attributes

 ALL
 
 ANY
 
const ConsoleStream _console
 

Static Public Attributes

static constexpr auto SYSTEM
 
static constexpr auto NAME
 

Protected Member Functions

virtual void addPostprocessorDependencyHelper (const PostprocessorName &name) const override
 
virtual void addVectorPostprocessorDependencyHelper (const VectorPostprocessorName &name) const override
 
virtual void addUserObjectDependencyHelper (const UserObject &uo) const override
 
void addReporterDependencyHelper (const ReporterName &reporter_name) override
 
const ReporterNamegetReporterName (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 intcoupledIndices (const std::string &var_name) const
 
virtual const VariableValuecoupledValue (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
 
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 VariableValuecoupledValueLower (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValueadCoupledValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVariableValue *> adCoupledValues (const std::string &var_name) const
 
const ADVariableValueadCoupledLowerValue (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableValueadCoupledVectorValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVectorVariableValue *> adCoupledVectorValues (const std::string &var_name) const
 
virtual const VariableValuecoupledVectorTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableValuecoupledVectorTagValue (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 ArrayVariableValuecoupledVectorTagArrayValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const ArrayVariableValuecoupledVectorTagArrayValue (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 VariableGradientcoupledVectorTagGradient (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableGradientcoupledVectorTagGradient (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 ArrayVariableGradientcoupledVectorTagArrayGradient (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const ArrayVariableGradientcoupledVectorTagArrayGradient (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 VariableValuecoupledVectorTagDofValue (const std::string &var_name, TagID tag, unsigned int index=0) const
 
virtual const VariableValuecoupledVectorTagDofValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
const ArrayVariableValuecoupledVectorTagArrayDofValue (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 VariableValuecoupledMatrixTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableValuecoupledMatrixTagValue (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 VectorVariableValuecoupledVectorValue (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ArrayVariableValue *> coupledArrayValues (const std::string &var_name) const
 
MooseWritableVariablewritableVariable (const std::string &var_name, unsigned int comp=0)
 
virtual VariableValuewritableCoupledValue (const std::string &var_name, unsigned int comp=0)
 
void checkWritableVar (MooseWritableVariable *var)
 
virtual const VariableValuecoupledValueOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledValuesOld (const std::string &var_name) const
 
virtual const VariableValuecoupledValueOlder (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledValuesOlder (const std::string &var_name) const
 
virtual const VariableValuecoupledValuePreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorValueOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorValueOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayValueOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayValueOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradientcoupledGradient (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableGradient *> coupledGradients (const std::string &var_name) const
 
const ADVariableGradientadCoupledGradient (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableGradientadCoupledGradientDot (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 ADVectorVariableGradientadCoupledVectorGradient (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableSecondadCoupledSecond (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableSecondadCoupledVectorSecond (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradientcoupledGradientOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableGradient *> coupledGradientsOld (const std::string &var_name) const
 
virtual const VariableGradientcoupledGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradientcoupledGradientPreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradientcoupledGradientDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradientcoupledGradientDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradientcoupledVectorGradient (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradientcoupledVectorGradientOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradientcoupledVectorGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradientcoupledArrayGradient (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradientcoupledArrayGradientOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradientcoupledArrayGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradientcoupledArrayGradientDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurlcoupledCurl (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurlcoupledCurlOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurlcoupledCurlOlder (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableCurladCoupledCurl (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergencecoupledDiv (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergencecoupledDivOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergencecoupledDivOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecondcoupledSecond (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecondcoupledSecondOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecondcoupledSecondOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecondcoupledSecondPreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDot (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledDots (const std::string &var_name) const
 
virtual const VariableValuecoupledDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValueadCoupledDot (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVariableValue *> adCoupledDots (const std::string &var_name) const
 
const ADVariableValueadCoupledDotDot (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableValueadCoupledVectorDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValuecoupledVectorDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledVectorDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledVectorDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValuecoupledArrayDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledArrayDotDu (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 >::typeadCoupledNodalValue (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 VariableValuecoupledNodalDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledNodalDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledNodalDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValuecoupledDofValues (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValues (const std::string &var_name) const
 
virtual const VariableValuecoupledDofValuesOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValuesOld (const std::string &var_name) const
 
virtual const VariableValuecoupledDofValuesOlder (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValuesOlder (const std::string &var_name) const
 
virtual const ArrayVariableValuecoupledArrayDofValues (const std::string &var_name, unsigned int comp=0) const
 
virtual const ADVariableValueadCoupledDofValues (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValueadZeroValue () const
 
const ADVariableGradientadZeroGradient () const
 
const ADVariableSecondadZeroSecond () 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 MooseVariableFieldBasegetFEVar (const std::string &var_name, unsigned int comp) const
 
const MooseVariableFieldBasegetFieldVar (const std::string &var_name, unsigned int comp) const
 
MooseVariableFieldBasegetFieldVar (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)
 
MooseVariablegetVar (const std::string &var_name, unsigned int comp)
 
const MooseVariablegetVar (const std::string &var_name, unsigned int comp) const
 
VectorMooseVariablegetVectorVar (const std::string &var_name, unsigned int comp)
 
const VectorMooseVariablegetVectorVar (const std::string &var_name, unsigned int comp) const
 
ArrayMooseVariablegetArrayVar (const std::string &var_name, unsigned int comp)
 
const ArrayMooseVariablegetArrayVar (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 VariableValuecoupledScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValueadCoupledScalarValue (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 VariableValuecoupledVectorTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValuecoupledMatrixTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValuecoupledScalarValueOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarValueOlder (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValueadCoupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDotDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDotDu (const std::string &var_name, unsigned int comp=0) const
 
const VariableValuecoupledScalarDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
const MooseVariableScalargetScalarVar (const std::string &var_name, unsigned int comp) const
 
void addMooseVariableDependency (MooseVariableFieldBase *var)
 
void addMooseVariableDependency (const std::vector< MooseVariableFieldBase * > &vars)
 
const T & getReporterValue (const std::string &param_name, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 

Static Protected Member Functions

static std::string meshPropertyName (const std::string &data_name, const std::string &prefix)
 

Protected Attributes

const unsigned _num_my_nodes
 Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is handled) More...
 
ModelGeochemicalDatabase _mgd
 my copy of the underlying ModelGeochemicalDatabase More...
 
const PertinentGeochemicalSystem_pgs
 Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase. More...
 
const unsigned _num_basis
 number of basis species More...
 
const unsigned _num_eqm
 number of equilibrium species More...
 
const Real _initial_max_ionic_str
 Initial value of maximum ionic strength. More...
 
GeochemistryIonicStrength _is
 The ionic strength calculator. More...
 
GeochemistryActivityCoefficientsDebyeHuckel _gac
 The activity calculator. More...
 
const unsigned _max_swaps_allowed
 Maximum number of swaps allowed during a single solve. More...
 
GeochemistrySpeciesSwapper _swapper
 The species swapper. More...
 
const Real _small_molality
 A small value of molality. More...
 
std::vector< std::stringstream > _solver_output
 The solver output at each node. More...
 
std::vector< unsigned > _tot_iter
 Number of iterations used by the solver at each node. More...
 
std::vector< Real_abs_residual
 L1norm of the solver residual at each node. More...
 
MooseMesh_mesh
 
const unsigned int _qp
 
const Node *const & _current_node
 
const bool & _unique_node_execute
 
SubProblem_subproblem
 
FEProblemBase_fe_problem
 
SystemBase_sys
 
const THREAD_ID _tid
 
Assembly_assembly
 
const Moose::CoordinateSystemType_coord_sys
 
const bool _duplicate_initial_execution
 
std::set< std::string > _depend_uo
 
const bool & _enabled
 
MooseApp_app
 
const std::string _type
 
const std::string _name
 
const InputParameters_pars
 
Factory_factory
 
ActionFactory_action_factory
 
const ExecFlagEnum_execute_enum
 
const ExecFlagType_current_execute_flag
 
MooseApp_restartable_app
 
const std::string _restartable_system_name
 
const THREAD_ID _restartable_tid
 
const bool _restartable_read_only
 
FEProblemBase_mci_feproblem
 
MooseApp_pg_moose_app
 
const std::string _prefix
 
const MaterialData_blk_material_data
 
const InputParameters_c_parameters
 
const std::string & _c_name
 
const std::string & _c_type
 
FEProblemBase_c_fe_problem
 
const SystemBase *const _c_sys
 
std::unordered_map< std::string, std::vector< MooseVariableFieldBase *> > _coupled_vars
 
std::vector< MooseVariableFieldBase *> _coupled_moose_vars
 
std::vector< MooseVariable *> _coupled_standard_moose_vars
 
std::vector< VectorMooseVariable *> _coupled_vector_moose_vars
 
std::vector< ArrayMooseVariable *> _coupled_array_moose_vars
 
std::vector< MooseVariableFV< Real > *> _coupled_standard_fv_moose_vars
 
std::vector< MooseLinearVariableFV< Real > *> _coupled_standard_linear_fv_moose_vars
 
const std::unordered_map< std::string, std::string > & _new_to_deprecated_coupled_vars
 
bool _c_nodal
 
bool _c_is_implicit
 
const bool _c_allow_element_to_nodal_coupling
 
THREAD_ID _c_tid
 
std::unordered_map< std::string, std::vector< std::unique_ptr< VariableValue > > > _default_value
 
std::unordered_map< std::string, std::unique_ptr< MooseArray< ADReal > > > _ad_default_value
 
std::unordered_map< std::string, std::unique_ptr< VectorVariableValue > > _default_vector_value
 
std::unordered_map< std::string, std::unique_ptr< ArrayVariableValue > > _default_array_value
 
std::unordered_map< std::string, std::unique_ptr< MooseArray< ADRealVectorValue > > > _ad_default_vector_value
 
VariableValue _default_value_zero
 
VariableGradient _default_gradient
 
MooseArray< ADRealVectorValue_ad_default_gradient
 
MooseArray< ADRealTensorValue_ad_default_vector_gradient
 
VariableSecond _default_second
 
MooseArray< ADRealTensorValue_ad_default_second
 
MooseArray< ADRealVectorValue_ad_default_curl
 
const VariableValue_zero
 
const VariablePhiValue_phi_zero
 
const MooseArray< ADReal > & _ad_zero
 
const VariableGradient_grad_zero
 
const MooseArray< ADRealVectorValue > & _ad_grad_zero
 
const VariablePhiGradient_grad_phi_zero
 
const VariableSecond_second_zero
 
const MooseArray< ADRealTensorValue > & _ad_second_zero
 
const VariablePhiSecond_second_phi_zero
 
const VectorVariableValue_vector_zero
 
const VectorVariableCurl_vector_curl_zero
 
VectorVariableValue _default_vector_value_zero
 
VectorVariableGradient _default_vector_gradient
 
VectorVariableCurl _default_vector_curl
 
VectorVariableDivergence _default_div
 
ArrayVariableValue _default_array_value_zero
 
ArrayVariableGradient _default_array_gradient
 
bool _coupleable_neighbor
 
FEProblemBase_sc_fe_problem
 
const THREAD_ID _sc_tid
 
const Real_real_zero
 
const VariableValue_scalar_zero
 
const Point & _point_zero
 
const InputParameters_ti_params
 
FEProblemBase_ti_feproblem
 
bool _is_implicit
 
Real_t
 
const Real_t_old
 
int_t_step
 
Real_dt
 
Real_dt_old
 
bool _is_transient
 
const Parallel::Communicator & _communicator
 

Detailed Description

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

Definition at line 19 of file GeochemistryReactorBase.h.

Constructor & Destructor Documentation

◆ GeochemistryReactorBase()

GeochemistryReactorBase::GeochemistryReactorBase ( const InputParameters parameters)

Definition at line 173 of file GeochemistryReactorBase.C.

175  _num_my_nodes(_subproblem.mesh().getMesh().n_local_nodes()),
176  _mgd(getUserObject<GeochemicalModelDefinition>("model_definition").getDatabase()),
177  _pgs(getUserObject<GeochemicalModelDefinition>("model_definition")
178  .getPertinentGeochemicalSystem()),
181  _initial_max_ionic_str(getParam<Real>("max_ionic_strength") /
182  (1.0 + getParam<unsigned>("ramp_max_ionic_strength_initial"))),
185  getParam<bool>("ionic_str_using_basis_only"),
186  getParam<bool>("stoichiometric_ionic_str_using_Cl_only")),
187  _gac(_is,
188  getUserObject<GeochemicalModelDefinition>("model_definition").getOriginalFullDatabase()),
189  _max_swaps_allowed(getParam<unsigned>("max_swaps_allowed")),
190  _swapper(_num_basis, getParam<Real>("stoichiometry_tolerance")),
191  _small_molality(getParam<Real>("swap_threshold") * getParam<Real>("abs_tol")),
195 {
196 }
const unsigned _num_basis
number of basis species
virtual MooseMesh & mesh()=0
const unsigned _max_swaps_allowed
Maximum number of swaps allowed during a single solve.
std::vector< unsigned > _tot_iter
Number of iterations used by the solver at each node.
const unsigned _num_eqm
number of equilibrium species
ModelGeochemicalDatabase _mgd
my copy of the underlying ModelGeochemicalDatabase
NodalUserObject(const InputParameters &parameters)
const PertinentGeochemicalSystem & _pgs
Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.
const Real _initial_max_ionic_str
Initial value of maximum ionic strength.
SubProblem & _subproblem
const unsigned _num_my_nodes
Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is hand...
MeshBase & getMesh()
std::vector< std::stringstream > _solver_output
The solver output at each node.
GeochemistryIonicStrength _is
The ionic strength calculator.
std::vector< Real > _abs_residual
L1norm of the solver residual at each node.
GeochemistrySpeciesSwapper _swapper
The species swapper.
const InputParameters & parameters() const
const Real _small_molality
A small value of molality.
std::vector< std::string > eqm_species_name
eqm_species_name[i] = name of the i^th eqm species
GeochemistryActivityCoefficientsDebyeHuckel _gac
The activity calculator.
std::vector< std::string > basis_species_name
basis_species_name[j] = name of the j^th basis species

Member Function Documentation

◆ execute()

virtual void GeochemistryReactorBase::execute ( )
inlineoverridevirtual

◆ finalize()

virtual void GeochemistryReactorBase::finalize ( )
inlineoverridevirtual

◆ getGeochemicalSystem()

virtual const GeochemicalSystem& GeochemistryReactorBase::getGeochemicalSystem ( dof_id_type  node_id) const
pure virtual
Returns
a reference to the equilibrium geochemical system at the given node
Parameters
node_idthe ID of the node

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

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

◆ getMoleAdditions()

virtual const DenseVector<Real>& GeochemistryReactorBase::getMoleAdditions ( dof_id_type  node_id) const
pure virtual
Returns
the mole additions (the first num_basis of these are additions to the bulk composition of the equilibrium system, the last num_kin of these are -dt*kinetic_reaction_rate, ie dt*dissolution_rate) at the specified node_id
Parameters
node_idthe node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

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

◆ getMolesDumped()

virtual Real GeochemistryReactorBase::getMolesDumped ( dof_id_type  node_id,
const std::string &  species 
) const
pure virtual
Returns
the moles dumped of the given species at the specified node_id
Parameters
speciesthe name of the species
node_idthe node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryQuantityAux::computeValue().

◆ getPertinentGeochemicalSystem()

const PertinentGeochemicalSystem& GeochemistryReactorBase::getPertinentGeochemicalSystem ( ) const
inline

returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase

Definition at line 73 of file GeochemistryReactorBase.h.

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

73 { return _pgs; };
const PertinentGeochemicalSystem & _pgs
Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

◆ getSolverIterations()

virtual unsigned GeochemistryReactorBase::getSolverIterations ( dof_id_type  node_id) const
pure virtual
Returns
the total number of iterations used by the most recent solve at the specified node_id
Parameters
node_idthe node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ getSolverOutput()

virtual const std::stringstream& GeochemistryReactorBase::getSolverOutput ( dof_id_type  node_id) const
pure virtual
Returns
a reference to the most recent solver output (containing iteration info, swap info, residuals, etc) at the specified node_id
Parameters
node_idthe node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ getSolverResidual()

virtual Real GeochemistryReactorBase::getSolverResidual ( dof_id_type  node_id) const
pure virtual
Returns
the L1norm of the residual at the end of the most recent solve at the specified node_id
Parameters
node_idthe node ID

Implemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Referenced by GeochemistryConsoleOutput::output().

◆ initialize()

virtual void GeochemistryReactorBase::initialize ( )
inlineoverridevirtual

◆ sharedParams()

InputParameters GeochemistryReactorBase::sharedParams ( )
static

contains params that are shared with AddGeochemistrySolverAction and its children

Definition at line 13 of file GeochemistryReactorBase.C.

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

14 {
16  params.addParam<std::vector<std::string>>(
17  "swap_out_of_basis",
18  {},
19  "Species that should be removed from the model_definition's basis and be replaced with the "
20  "swap_into_basis species");
21  params.addParam<std::vector<std::string>>(
22  "swap_into_basis",
23  {},
24  "Species that should be removed from the model_definition's equilibrium species list and "
25  "added to the basis. There must be the same number of species in swap_out_of_basis and "
26  "swap_into_basis. These swaps are performed before any other computations during the "
27  "initial problem setup. If this list contains more than one species, the swapping is "
28  "performed one-by-one, starting with the first pair (swap_out_of_basis[0] and "
29  "swap_into_basis[0]), then the next pair, etc");
30  MultiMooseEnum constraint_user_meaning(
31  "kg_solvent_water bulk_composition bulk_composition_with_kinetic free_concentration "
32  "free_mineral activity log10activity fugacity log10fugacity");
34  "constraint_meaning",
35  constraint_user_meaning,
36  "Meanings of the numerical values given in constraint_value. kg_solvent_water: can only be "
37  "applied to H2O and units must be kg. bulk_composition: can be applied to all non-gas "
38  "species, and represents the total amount of the basis species contained as free species as "
39  "well as the amount found in secondary species but not in kinetic species, and units must be "
40  "moles or mass (kg, g, etc). bulk_composition_with_kinetic: can be applied to all non-gas "
41  "species, and represents the total amount of the basis species contained as free species as "
42  "well as the amount found in secondary species and in kinetic species, and units must be "
43  "moles or mass (kg, g, etc). free_concentration: can be applied to all basis species that "
44  "are not gas and not H2O and not mineral, and represents the total amount of the basis "
45  "species existing freely (not as secondary species) within the solution, and units must be "
46  "molal or mass_per_kg_solvent. free_mineral: can be applied to all mineral basis species, "
47  "and represents the total amount of the mineral existing freely (precipitated) within the "
48  "solution, and units must be moles, mass or cm3. activity and log10activity: can be applied "
49  "to basis species that are not gas and not mineral and not sorbing sites, and represents the "
50  "activity of the basis species (recall pH = -log10activity), and units must be "
51  "dimensionless. fugacity and log10fugacity: can be applied to gases, and units must be "
52  "dimensionless");
53  MultiMooseEnum constraint_unit("dimensionless moles molal kg g mg ug kg_per_kg_solvent "
54  "g_per_kg_solvent mg_per_kg_solvent ug_per_kg_solvent cm3");
56  "constraint_unit",
57  constraint_unit,
58  "Units of the numerical values given in constraint_value. Dimensionless: should only be "
59  "used for activity or fugacity constraints. Moles: mole number. Molal: moles per kg "
60  "solvent water. kg: kilograms. g: grams. mg: milligrams. ug: micrograms. "
61  "kg_per_kg_solvent: kilograms per kg solvent water. g_per_kg_solvent: grams per kg solvent "
62  "water. mg_per_kg_solvent: milligrams per kg solvent water. ug_per_kg_solvent: micrograms "
63  "per kg solvent water. cm3: cubic centimeters");
64  params.addRequiredParam<std::vector<std::string>>(
65  "constraint_species",
66  "Names of the species that have their values fixed to constraint_value with meaning "
67  "constraint_meaning. All basis species (after swap_into_basis and swap_out_of_basis) must "
68  "be provided with exactly one constraint. These constraints are used to compute the "
69  "configuration during the initial problem setup, and in time-dependent simulations they may "
70  "be modified as time progresses.");
71  params.addRequiredParam<std::vector<Real>>(
72  "constraint_value", "Numerical value of the containts on constraint_species");
73  params.addRangeCheckedParam<Real>(
74  "max_ionic_strength", 3.0, "max_ionic_strength >= 0.0", "Maximum value of ionic strength");
75  params.addParam<unsigned>(
76  "extra_iterations_to_make_consistent",
77  0,
78  "Extra iterations to make the molalities, activities, etc, consistent "
79  "before commencing the Newton process to find the aqueous configuration");
80  params.addRequiredParam<std::string>(
81  "charge_balance_species",
82  "Charge balance will be enforced on this basis species. This means that its bulk mole "
83  "number may be changed from the initial value you provide in order to ensure charge "
84  "neutrality. After the initial swaps have been performed, this must be in the basis, and it "
85  "must be provided with a bulk_composition constraint_meaning.");
86  params.addParam<std::vector<std::string>>(
87  "prevent_precipitation",
88  {},
89  "Mineral species in this list will be prevented from precipitating, irrespective of their "
90  "saturation index (unless they are initially in the basis)");
91  params.addParam<Real>(
92  "abs_tol",
93  1E-10,
94  "If the residual of the algebraic system (measured in mol) is lower than this value, the "
95  "Newton process (that finds the aqueous configuration) is deemed to have converged");
96  params.addParam<Real>("rel_tol",
97  1E-200,
98  "If the residual of the algebraic system (measured in mol) is lower than "
99  "this value times the initial residual, the Newton process (that finds the "
100  "aqueous configuration) is deemed to have converged");
101  params.addRangeCheckedParam<Real>("min_initial_molality",
102  1E-20,
103  "min_initial_molality > 0.0",
104  "Minimum value of the initial-guess molality used in the "
105  "Newton process to find the aqueous configuration");
106  params.addParam<unsigned>(
107  "max_iter",
108  100,
109  "Maximum number of Newton iterations allowed when finding the aqueous configuration");
110  params.addParam<Real>(
111  "max_initial_residual",
112  1E3,
113  "Attempt to alter the initial-guess molalities so that the initial residual for the Newton "
114  "process (that finds the aqueous configuration) is less than this number of moles");
115  params.addRangeCheckedParam<Real>(
116  "swap_threshold",
117  0.1,
118  "swap_threshold >= 0.0",
119  "If the molality of a basis species in the algebraic system falls below swap_threshold * "
120  "abs_tol then it is swapped out of the basis. The dimensions of swap_threshold are "
121  "1/kg(solvent water)");
122  params.addParam<unsigned>(
123  "max_swaps_allowed",
124  20,
125  "Maximum number of swaps allowed during a single attempt at finding the aqueous "
126  "configuration. Usually only a handful of swaps are used: this parameter prevents endless "
127  "cyclic swapping that prevents the algorithm from progressing");
128  params.addParam<unsigned>(
129  "ramp_max_ionic_strength_initial",
130  20,
131  "The number of iterations over which to progressively increase the maximum ionic strength "
132  "(from zero to max_ionic_strength) during the initial equilibration. Increasing this can "
133  "help in convergence of the Newton process, at the cost of spending more time finding the "
134  "aqueous configuration.");
135  params.addParam<bool>(
136  "ionic_str_using_basis_only",
137  false,
138  "If set to true, ionic strength and stoichiometric ionic strength will be computed using "
139  "only the basis molalities, ignoring molalities of equilibrium species. Since basis "
140  "molality is usually greater than equilibrium molality, and the whole Debye-Huckel concept "
141  "of activity coefficients depending on ionic strength is only approximate in practice, "
142  "setting this parameter true often results in a reasonable approximation. It can aid in "
143  "convergence since it eliminates problems associated with unphysical huge equilibrium "
144  "molalities that can occur during Newton iteration to the solution");
145  params.addParam<bool>("stoichiometric_ionic_str_using_Cl_only",
146  false,
147  "If set to true, the stoichiometric ionic strength will be set equal to "
148  "Cl- molality (or max_ionic_strength if the Cl- molality is too "
149  "big). This flag overrides ionic_str_using_basis_molality_only");
150  return params;
151 }
void addParam(const std::string &name, const std::initializer_list< typename T::value_type > &value, const std::string &doc_string)
void addRequiredParam(const std::string &name, const std::string &doc_string)
InputParameters emptyInputParameters()
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void addRangeCheckedParam(const std::string &name, const T &value, const std::string &parsed_function, const std::string &doc_string)

◆ threadJoin()

virtual void GeochemistryReactorBase::threadJoin ( const UserObject )
inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor.

Definition at line 28 of file GeochemistryReactorBase.h.

28 {}

◆ validParams()

InputParameters GeochemistryReactorBase::validParams ( )
static

Definition at line 154 of file GeochemistryReactorBase.C.

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

155 {
158 
159  params.addRequiredParam<UserObjectName>(
160  "model_definition", "The name of the GeochemicalModelDefinition user object.");
161  params.addRangeCheckedParam<Real>(
162  "stoichiometry_tolerance",
163  1E-6,
164  "stoichiometry_tolerance >= 0.0",
165  "Swapping involves inverting matrices via a singular value decomposition. During this "
166  "process: (1) if abs(singular value) < stoi_tol * L1norm(singular values), then the "
167  "matrix is deemed singular (so the basis swap is deemed invalid); (2) if abs(any "
168  "stoichiometric coefficient) < stoi_tol then it is set to zero.");
169  params.addClassDescription("Base class for UserObject to solve geochemistry reactions");
170  return params;
171 }
static InputParameters validParams()
static InputParameters sharedParams()
contains params that are shared with AddGeochemistrySolverAction and its children ...
void addRequiredParam(const std::string &name, const std::string &doc_string)
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void addClassDescription(const std::string &doc_string)
void addRangeCheckedParam(const std::string &name, const T &value, const std::string &parsed_function, const std::string &doc_string)

Member Data Documentation

◆ _abs_residual

std::vector<Real> GeochemistryReactorBase::_abs_residual
protected

◆ _gac

GeochemistryActivityCoefficientsDebyeHuckel GeochemistryReactorBase::_gac
protected

The activity calculator.

Definition at line 91 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _initial_max_ionic_str

const Real GeochemistryReactorBase::_initial_max_ionic_str
protected

Initial value of maximum ionic strength.

Definition at line 87 of file GeochemistryReactorBase.h.

◆ _is

GeochemistryIonicStrength GeochemistryReactorBase::_is
protected

The ionic strength calculator.

Definition at line 89 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _max_swaps_allowed

const unsigned GeochemistryReactorBase::_max_swaps_allowed
protected

Maximum number of swaps allowed during a single solve.

Definition at line 93 of file GeochemistryReactorBase.h.

◆ _mgd

ModelGeochemicalDatabase GeochemistryReactorBase::_mgd
protected

◆ _num_basis

const unsigned GeochemistryReactorBase::_num_basis
protected

◆ _num_eqm

const unsigned GeochemistryReactorBase::_num_eqm
protected

number of equilibrium species

Definition at line 85 of file GeochemistryReactorBase.h.

◆ _num_my_nodes

const unsigned GeochemistryReactorBase::_num_my_nodes
protected

◆ _pgs

const PertinentGeochemicalSystem& GeochemistryReactorBase::_pgs
protected

Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

Definition at line 81 of file GeochemistryReactorBase.h.

Referenced by getPertinentGeochemicalSystem().

◆ _small_molality

const Real GeochemistryReactorBase::_small_molality
protected

A small value of molality.

Definition at line 97 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::postSolveFlowThrough().

◆ _solver_output

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

◆ _swapper

GeochemistrySpeciesSwapper GeochemistryReactorBase::_swapper
protected

The species swapper.

Definition at line 95 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _tot_iter

std::vector<unsigned> GeochemistryReactorBase::_tot_iter
protected

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