https://mooseframework.inl.gov
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
GeochemistryReactorBase Class Referenceabstract

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

#include <GeochemistryReactorBase.h>

Inheritance diagram for GeochemistryReactorBase:
[legend]

Public Types

enum  TEST_TYPE
 
typedef DataFileName DataFileParameterType
 

Public Member Functions

 GeochemistryReactorBase (const InputParameters &parameters)
 
virtual void initialize () override
 
virtual void threadJoin (const UserObject &) override
 
virtual void finalize () override
 
virtual void execute () override
 
virtual const GeochemicalSystem & getGeochemicalSystem (dof_id_type node_id) const =0
 
virtual const std::stringstream & getSolverOutput (dof_id_type node_id) const =0
 
virtual unsigned getSolverIterations (dof_id_type node_id) const =0
 
virtual Real getSolverResidual (dof_id_type node_id) const =0
 
virtual const DenseVector< Real > & getMoleAdditions (dof_id_type node_id) const =0
 
virtual Real getMolesDumped (dof_id_type node_id, const std::string &species) const =0
 
const PertinentGeochemicalSystem & getPertinentGeochemicalSystem () const
 returns a reference to the PertinentGeochemicalSystem used to creat the ModelGeochemicalDatabase More...
 
virtual void subdomainSetup () override
 
bool isUniqueNodeExecute ()
 
SubProblem & getSubProblem () const
 
bool shouldDuplicateInitialExecution () const
 
virtual Real spatialValue (const Point &) const
 
virtual const std::vector< Point > spatialPoints () const
 
void gatherSum (T &value)
 
void gatherMax (T &value)
 
void gatherMin (T &value)
 
void gatherProxyValueMax (T1 &proxy, T2 &value)
 
void gatherProxyValueMin (T1 &proxy, T2 &value)
 
void setPrimaryThreadCopy (UserObject *primary)
 
UserObject * primaryThreadCopy ()
 
std::set< UserObjectName > getDependObjects () const
 
virtual bool needThreadedCopy () const
 
const std::set< std::string > & getRequestedItems () override
 
const std::set< std::string > & getSuppliedItems () override
 
unsigned int systemNumber () const
 
virtual bool enabled () const
 
std::shared_ptr< MooseObject > getSharedPtr ()
 
std::shared_ptr< const MooseObject > getSharedPtr () const
 
MooseApp & getMooseApp () const
 
const std::string & type () const
 
const std::string & name () const
 
std::string typeAndName () const
 
MooseObjectParameterName uniqueParameterName (const std::string &parameter_name) const
 
MooseObjectName uniqueName () const
 
const InputParameters & parameters () const
 
const hit::Node * getHitNode () const
 
bool hasBase () const
 
const std::string & getBase () 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 &name) const
 
void connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) 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
 
std::string messagePrefix (const bool hit_prefix=true) const
 
std::string errorPrefix (const std::string &) const
 
void mooseError (Args &&... args) const
 
void mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const
 
void mooseErrorNonPrefixed (Args &&... args) const
 
void mooseWarning (Args &&... args) const
 
void mooseWarningNonPrefixed (Args &&... args) const
 
void mooseDeprecated (Args &&... args) const
 
void mooseInfo (Args &&... args) const
 
void callMooseError (std::string msg, const bool with_prefix, const hit::Node *node=nullptr) const
 
std::string getDataFileName (const std::string &param) const
 
std::string getDataFileNameByName (const std::string &relative_path) const
 
std::string getDataFilePath (const std::string &relative_path) const
 
virtual void initialSetup ()
 
virtual void timestepSetup ()
 
virtual void jacobianSetup ()
 
virtual void residualSetup ()
 
virtual void customSetup (const ExecFlagType &)
 
const ExecFlagEnum & getExecuteOnEnum () const
 
UserObjectName getUserObjectName (const std::string &param_name) const
 
const T & getUserObject (const std::string &param_name, bool is_dependency=true) const
 
const T & getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const
 
const UserObject & getUserObjectBase (const std::string &param_name, bool is_dependency=true) const
 
const UserObject & getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const
 
const std::vector< SubdomainName > & blocks () const
 
unsigned int numBlocks () const
 
virtual const std::set< SubdomainID > & blockIDs () const
 
unsigned int blocksMaxDimension () const
 
bool hasBlocks (const SubdomainName &name) const
 
bool hasBlocks (const std::vector< SubdomainName > &names) const
 
bool hasBlocks (const std::set< SubdomainName > &names) const
 
bool hasBlocks (SubdomainID id) const
 
bool hasBlocks (const std::vector< SubdomainID > &ids) const
 
bool hasBlocks (const std::set< SubdomainID > &ids) const
 
bool isBlockSubset (const std::set< SubdomainID > &ids) const
 
bool isBlockSubset (const std::vector< SubdomainID > &ids) const
 
bool hasBlockMaterialProperty (const std::string &prop_name)
 
const std::set< SubdomainID > & meshBlockIDs () const
 
virtual bool blockRestricted () const
 
virtual void checkVariable (const MooseVariableFieldBase &variable) const
 
virtual const std::set< BoundaryID > & boundaryIDs () const
 
const std::vector< BoundaryName > & boundaryNames () const
 
unsigned int numBoundaryIDs () const
 
bool hasBoundary (const BoundaryName &name) const
 
bool hasBoundary (const std::vector< BoundaryName > &names) const
 
bool hasBoundary (const BoundaryID &id) const
 
bool hasBoundary (const std::vector< BoundaryID > &ids, TEST_TYPE type=ALL) const
 
bool hasBoundary (const std::set< BoundaryID > &ids, TEST_TYPE type=ALL) const
 
bool isBoundarySubset (const std::set< BoundaryID > &ids) const
 
bool isBoundarySubset (const std::vector< BoundaryID > &ids) const
 
bool hasBoundaryMaterialProperty (const std::string &prop_name) const
 
virtual bool boundaryRestricted () const
 
const std::set< BoundaryID > & meshBoundaryIDs () const
 
virtual bool checkVariableBoundaryIntegrity () const
 
virtual const VariableValue & coupledValueByName (const std::string &var_name)
 
virtual const ArrayVariableValue & coupledArrayValueByName (const std::string &var_name)
 
const std::unordered_map< std::string, std::vector< MooseVariableFieldBase *> > & getCoupledVars () const
 
const std::vector< MooseVariableFieldBase *> & getCoupledMooseVars () const
 
const std::vector< MooseVariable *> & getCoupledStandardMooseVars () const
 
const std::vector< VectorMooseVariable *> & getCoupledVectorMooseVars () const
 
const std::vector< ArrayMooseVariable *> & getCoupledArrayMooseVars () const
 
void addFEVariableCoupleableVectorTag (TagID tag)
 
void addFEVariableCoupleableMatrixTag (TagID tag)
 
std::set< TagID > & getFEVariableCoupleableVectorTags ()
 
const std::set< TagID > & getFEVariableCoupleableVectorTags () const
 
std::set< TagID > & getFEVariableCoupleableMatrixTags ()
 
const std::set< TagID > & getFEVariableCoupleableMatrixTags () const
 
auto & getWritableCoupledVariables () const
 
bool hasWritableCoupledVariables () const
 
const ADVariableValue * getADDefaultValue (const std::string &var_name) const
 
const ADVectorVariableValue * getADDefaultVectorValue (const std::string &var_name) const
 
const ADVariableGradient & getADDefaultGradient () const
 
const ADVectorVariableGradient & getADDefaultVectorGradient () const
 
const ADVariableSecond & getADDefaultSecond () const
 
const ADVectorVariableCurl & getADDefaultCurl () const
 
const std::vector< MooseVariableScalar *> & getCoupledMooseScalarVars ()
 
const std::set< TagID > & getScalarVariableCoupleableVectorTags () const
 
const std::set< TagID > & getScalarVariableCoupleableMatrixTags () const
 
const std::set< MooseVariableFieldBase *> & getMooseVariableDependencies () const
 
std::set< MooseVariableFieldBase *> checkAllVariables (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_omit={})
 
std::set< MooseVariableFieldBase *> checkVariables (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_check)
 
void addMooseVariableDependency (MooseVariableFieldBase *var)
 
void addMooseVariableDependency (const std::vector< MooseVariableFieldBase * > &vars)
 
bool isImplicit ()
 
Moose::StateArg determineState () const
 
void setRandomResetFrequency (ExecFlagType exec_flag)
 
unsigned long getRandomLong () const
 
Real getRandomReal () const
 
unsigned int getSeed (std::size_t id)
 
unsigned int getMasterSeed () const
 
bool isNodal () const
 
ExecFlagType getResetOnTime () const
 
void setRandomDataPointer (RandomData *random_data)
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
const Function & getFunction (const std::string &name) const
 
const Function & getFunctionByName (const FunctionName &name) const
 
bool hasFunction (const std::string &param_name) const
 
bool hasFunctionByName (const FunctionName &name) const
 
bool isDefaultPostprocessorValue (const std::string &param_name, const unsigned int index=0) const
 
bool hasPostprocessor (const std::string &param_name, const unsigned int index=0) const
 
bool hasPostprocessorByName (const PostprocessorName &name) const
 
std::size_t coupledPostprocessors (const std::string &param_name) const
 
const PostprocessorName & getPostprocessorName (const std::string &param_name, const unsigned int index=0) const
 
const VectorPostprocessorValue & getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const
 
const VectorPostprocessorValue & getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const VectorPostprocessorValue & getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const
 
const ScatterVectorPostprocessorValue & getScatterVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValue & getScatterVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValue & getScatterVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const
 
const ScatterVectorPostprocessorValue & getScatterVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
bool hasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const
 
bool hasVectorPostprocessor (const std::string &param_name) const
 
bool hasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const
 
bool hasVectorPostprocessorByName (const VectorPostprocessorName &name) const
 
const VectorPostprocessorName & getVectorPostprocessorName (const std::string &param_name) const
 
T & getSampler (const std::string &name)
 
Sampler & getSampler (const std::string &name)
 
T & getSamplerByName (const SamplerName &name)
 
Sampler & getSamplerByName (const SamplerName &name)
 
virtual void meshChanged ()
 
virtual void meshDisplaced ()
 
PerfGraph & perfGraph ()
 
const PostprocessorValue & getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValue & getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValue & getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValue & getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValue & getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const
 
const PostprocessorValue & getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const
 
virtual const PostprocessorValue & getPostprocessorValueByName (const PostprocessorName &name) const
 
virtual const PostprocessorValue & getPostprocessorValueByName (const PostprocessorName &name) const
 
const PostprocessorValue & getPostprocessorValueOldByName (const PostprocessorName &name) const
 
const PostprocessorValue & getPostprocessorValueOldByName (const PostprocessorName &name) const
 
const PostprocessorValue & getPostprocessorValueOlderByName (const PostprocessorName &name) const
 
const PostprocessorValue & getPostprocessorValueOlderByName (const PostprocessorName &name) const
 
bool isVectorPostprocessorDistributed (const std::string &param_name) const
 
bool isVectorPostprocessorDistributed (const std::string &param_name) const
 
bool isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const
 
bool isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const
 
const Distribution & getDistribution (const std::string &name) const
 
const T & getDistribution (const std::string &name) const
 
const Distribution & getDistribution (const std::string &name) const
 
const T & getDistribution (const std::string &name) const
 
const Distribution & getDistributionByName (const DistributionName &name) const
 
const T & getDistributionByName (const std::string &name) const
 
const Distribution & getDistributionByName (const DistributionName &name) const
 
const T & getDistributionByName (const std::string &name) const
 
const Parallel::Communicator & comm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static InputParameters sharedParams ()
 contains params that are shared with AddGeochemistrySolverAction and its children More...
 
static InputParameters validParams ()
 
static void callMooseError (MooseApp *const app, const InputParameters &params, std::string msg, const bool with_prefix, const hit::Node *node)
 
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 const std::string type_param
 
static const std::string name_param
 
static const std::string unique_name_param
 
static const std::string app_param
 
static const std::string moose_base_param
 
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 ReporterContextBase & getReporterContextBaseByName (const ReporterName &reporter_name) const
 
const ReporterName & getReporterName (const std::string &param_name) const
 
T & declareRestartableData (const std::string &data_name, Args &&... args)
 
ManagedValue< T > declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)
 
const T & getRestartableData (const std::string &data_name) const
 
T & declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)
 
T & declareRecoverableData (const std::string &data_name, Args &&... args)
 
T & declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)
 
T & declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)
 
std::string restartableName (const std::string &data_name) const
 
const T & getMeshProperty (const std::string &data_name, const std::string &prefix)
 
const T & getMeshProperty (const std::string &data_name)
 
bool hasMeshProperty (const std::string &data_name, const std::string &prefix) const
 
bool hasMeshProperty (const std::string &data_name, const std::string &prefix) const
 
bool hasMeshProperty (const std::string &data_name) const
 
bool hasMeshProperty (const std::string &data_name) const
 
std::string meshPropertyName (const std::string &data_name) const
 
PerfID registerTimedSection (const std::string &section_name, const unsigned int level) const
 
PerfID registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const
 
std::string timedSectionName (const std::string &section_name) const
 
virtual bool hasBlockMaterialPropertyHelper (const std::string &prop_name)
 
void initializeBlockRestrictable (const MooseObject *moose_object)
 
Moose::CoordinateSystemType getBlockCoordSystem ()
 
bool hasBoundaryMaterialPropertyHelper (const std::string &prop_name) const
 
virtual void coupledCallback (const std::string &, bool) const
 
virtual bool isCoupled (const std::string &var_name, unsigned int i=0) const
 
virtual bool isCoupledConstant (const std::string &var_name) const
 
unsigned int coupledComponents (const std::string &var_name) const
 
VariableName coupledName (const std::string &var_name, unsigned int comp=0) const
 
std::vector< VariableName > coupledNames (const std::string &var_name) const
 
virtual unsigned int coupled (const std::string &var_name, unsigned int comp=0) const
 
std::vector< unsigned int > coupledIndices (const std::string &var_name) const
 
virtual const VariableValue & coupledValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledValues (const std::string &var_name) const
 
std::vector< const VectorVariableValue *> coupledVectorValues (const std::string &var_name) const
 
const GenericVariableValue< is_ad > & coupledGenericValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericValue (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericValue (const std::string &var_name, unsigned int comp) const
 
const GenericVectorVariableValue< is_ad > & coupledGenericVectorValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVectorVariableValue< false > & coupledGenericVectorValue (const std::string &var_name, unsigned int comp) const
 
const GenericVectorVariableValue< true > & coupledGenericVectorValue (const std::string &var_name, unsigned int comp) const
 
std::vector< const GenericVariableValue< is_ad > *> coupledGenericValues (const std::string &var_name) const
 
std::vector< const GenericVariableValue< false > *> coupledGenericValues (const std::string &var_name) const
 
std::vector< const GenericVariableValue< true > *> coupledGenericValues (const std::string &var_name) const
 
const GenericVariableValue< is_ad > & coupledGenericDofValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericDofValue (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericDofValue (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< is_ad > & coupledGenericDot (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericDot (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericDot (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< is_ad > & coupledGenericDotDot (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericDotDot (const std::string &var_name, unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericDotDot (const std::string &var_name, unsigned int comp) const
 
virtual const VariableValue & coupledValueLower (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVariableValue *> adCoupledValues (const std::string &var_name) const
 
const ADVariableValue & adCoupledLowerValue (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableValue & adCoupledVectorValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVectorVariableValue *> adCoupledVectorValues (const std::string &var_name) const
 
virtual const VariableValue & coupledVectorTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableValue & coupledVectorTagValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
std::vector< const VariableValue *> coupledVectorTagValues (const std::string &var_names, TagID tag) const
 
std::vector< const VariableValue *> coupledVectorTagValues (const std::string &var_names, const std::string &tag_name) const
 
virtual const ArrayVariableValue & coupledVectorTagArrayValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const ArrayVariableValue & coupledVectorTagArrayValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
std::vector< const ArrayVariableValue *> coupledVectorTagArrayValues (const std::string &var_names, TagID tag) const
 
std::vector< const ArrayVariableValue *> coupledVectorTagArrayValues (const std::string &var_names, const std::string &tag_name) const
 
virtual const VariableGradient & coupledVectorTagGradient (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableGradient & coupledVectorTagGradient (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
std::vector< const VariableGradient *> coupledVectorTagGradients (const std::string &var_names, TagID tag) const
 
std::vector< const VariableGradient *> coupledVectorTagGradients (const std::string &var_names, const std::string &tag_name) const
 
virtual const ArrayVariableGradient & coupledVectorTagArrayGradient (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const ArrayVariableGradient & coupledVectorTagArrayGradient (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
std::vector< const ArrayVariableGradient *> coupledVectorTagArrayGradients (const std::string &var_names, TagID tag) const
 
std::vector< const ArrayVariableGradient *> coupledVectorTagArrayGradients (const std::string &var_names, const std::string &tag_name) const
 
virtual const VariableValue & coupledVectorTagDofValue (const std::string &var_name, TagID tag, unsigned int index=0) const
 
virtual const VariableValue & coupledVectorTagDofValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
const ArrayVariableValue & coupledVectorTagArrayDofValue (const std::string &var_name, const std::string &tag_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledVectorTagDofValues (const std::string &var_names, TagID tag) const
 
std::vector< const VariableValue *> coupledVectorTagDofValues (const std::string &var_names, const std::string &tag_name) const
 
virtual const VariableValue & coupledMatrixTagValue (const std::string &var_names, TagID tag, unsigned int index=0) const
 
virtual const VariableValue & coupledMatrixTagValue (const std::string &var_names, const std::string &tag_name, unsigned int index=0) const
 
std::vector< const VariableValue *> coupledMatrixTagValues (const std::string &var_names, TagID tag) const
 
std::vector< const VariableValue *> coupledMatrixTagValues (const std::string &var_names, const std::string &tag_name) const
 
virtual const VectorVariableValue & coupledVectorValue (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayValue (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ArrayVariableValue *> coupledArrayValues (const std::string &var_name) const
 
MooseWritableVariable & writableVariable (const std::string &var_name, unsigned int comp=0)
 
virtual VariableValue & writableCoupledValue (const std::string &var_name, unsigned int comp=0)
 
void checkWritableVar (MooseWritableVariable *var)
 
virtual const VariableValue & coupledValueOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledValuesOld (const std::string &var_name) const
 
std::vector< const VectorVariableValue *> coupledVectorValuesOld (const std::string &var_name) const
 
virtual const VariableValue & coupledValueOlder (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledValuesOlder (const std::string &var_name) const
 
virtual const VariableValue & coupledValuePreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorValueOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorValueOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayValueOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayValueOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradient & coupledGradient (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableGradient *> coupledGradients (const std::string &var_name) const
 
const ADVariableGradient & adCoupledGradient (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableGradient & adCoupledGradientDot (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVariableGradient *> adCoupledGradients (const std::string &var_name) const
 
const GenericVariableGradient< is_ad > & coupledGenericGradient (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableGradient< false > & coupledGenericGradient (const std::string &var_name, unsigned int comp) const
 
const GenericVariableGradient< true > & coupledGenericGradient (const std::string &var_name, unsigned int comp) const
 
std::vector< const GenericVariableGradient< is_ad > *> coupledGenericGradients (const std::string &var_name) const
 
std::vector< const GenericVariableGradient< false > *> coupledGenericGradients (const std::string &var_name) const
 
std::vector< const GenericVariableGradient< true > *> coupledGenericGradients (const std::string &var_name) const
 
const ADVectorVariableGradient & adCoupledVectorGradient (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableSecond & adCoupledSecond (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableSecond & adCoupledVectorSecond (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradient & coupledGradientOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableGradient *> coupledGradientsOld (const std::string &var_name) const
 
virtual const VariableGradient & coupledGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradient & coupledGradientPreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradient & coupledGradientDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableGradient & coupledGradientDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradient & coupledVectorGradient (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradient & coupledVectorGradientOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableGradient & coupledVectorGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradient & coupledArrayGradient (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradient & coupledArrayGradientOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradient & coupledArrayGradientOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableGradient & coupledArrayGradientDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurl & coupledCurl (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurl & coupledCurlOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableCurl & coupledCurlOlder (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableCurl & adCoupledCurl (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergence & coupledDiv (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergence & coupledDivOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableDivergence & coupledDivOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecond & coupledSecond (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecond & coupledSecondOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecond & coupledSecondOlder (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableSecond & coupledSecondPreviousNL (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDot (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledDots (const std::string &var_name) const
 
virtual const VariableValue & coupledDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledDot (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const ADVariableValue *> adCoupledDots (const std::string &var_name) const
 
const ADVariableValue & adCoupledDotDot (const std::string &var_name, unsigned int comp=0) const
 
const ADVectorVariableValue & adCoupledVectorDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VectorVariableValue & coupledVectorDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledVectorDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledVectorDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const ArrayVariableValue & coupledArrayDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDotDu (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledArrayDotDu (const std::string &var_name, unsigned int comp=0) const
 
const T & coupledNodalValue (const std::string &var_name, unsigned int comp=0) const
 
const Moose::ADType< T >::type & adCoupledNodalValue (const std::string &var_name, unsigned int comp=0) const
 
const T & coupledNodalValueOld (const std::string &var_name, unsigned int comp=0) const
 
const T & coupledNodalValueOlder (const std::string &var_name, unsigned int comp=0) const
 
const T & coupledNodalValuePreviousNL (const std::string &var_name, unsigned int comp=0) const
 
const T & coupledNodalDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledNodalDotDot (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledNodalDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledNodalDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
virtual const VariableValue & coupledDofValues (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValues (const std::string &var_name) const
 
virtual const VariableValue & coupledDofValuesOld (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValuesOld (const std::string &var_name) const
 
virtual const VariableValue & coupledDofValuesOlder (const std::string &var_name, unsigned int comp=0) const
 
std::vector< const VariableValue *> coupledAllDofValuesOlder (const std::string &var_name) const
 
virtual const ArrayVariableValue & coupledArrayDofValues (const std::string &var_name, unsigned int comp=0) const
 
virtual const ADVariableValue & adCoupledDofValues (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adZeroValue () const
 
const ADVariableGradient & adZeroGradient () const
 
const ADVariableSecond & adZeroSecond () const
 
const GenericVariableValue< is_ad > & genericZeroValue ()
 
const GenericVariableValue< false > & genericZeroValue ()
 
const GenericVariableValue< true > & genericZeroValue ()
 
const GenericVariableGradient< is_ad > & genericZeroGradient ()
 
const GenericVariableGradient< false > & genericZeroGradient ()
 
const GenericVariableGradient< true > & genericZeroGradient ()
 
const GenericVariableSecond< is_ad > & genericZeroSecond ()
 
const GenericVariableSecond< false > & genericZeroSecond ()
 
const GenericVariableSecond< true > & genericZeroSecond ()
 
bool checkVar (const std::string &var_name, unsigned int comp=0, unsigned int comp_bound=0) const
 
const MooseVariableFieldBase * getFEVar (const std::string &var_name, unsigned int comp) const
 
const MooseVariableFieldBase * getFieldVar (const std::string &var_name, unsigned int comp) const
 
MooseVariableFieldBase * getFieldVar (const std::string &var_name, unsigned int comp)
 
const T * getVarHelper (const std::string &var_name, unsigned int comp) const
 
T * getVarHelper (const std::string &var_name, unsigned int comp)
 
MooseVariable * getVar (const std::string &var_name, unsigned int comp)
 
const MooseVariable * getVar (const std::string &var_name, unsigned int comp) const
 
VectorMooseVariable * getVectorVar (const std::string &var_name, unsigned int comp)
 
const VectorMooseVariable * getVectorVar (const std::string &var_name, unsigned int comp) const
 
ArrayMooseVariable * getArrayVar (const std::string &var_name, unsigned int comp)
 
const ArrayMooseVariable * getArrayVar (const std::string &var_name, unsigned int comp) const
 
void validateExecutionerType (const std::string &name, const std::string &fn_name) const
 
std::vector< T > coupledVectorHelper (const std::string &var_name, const Func &func) const
 
bool isCoupledScalar (const std::string &var_name, unsigned int i=0) const
 
unsigned int coupledScalarComponents (const std::string &var_name) const
 
unsigned int coupledScalar (const std::string &var_name, unsigned int comp=0) const
 
libMesh::Order coupledScalarOrder (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< is_ad > & coupledGenericScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const
 
const VariableValue & coupledVectorTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValue & coupledMatrixTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValue & coupledScalarValueOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarValueOlder (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDu (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
const MooseVariableScalar * getScalarVar (const std::string &var_name, unsigned int comp) const
 
const T & getReporterValue (const std::string &param_name, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, const std::size_t time_index=0)
 
const T & getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)
 
const T & getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValue (const std::string &param_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 
bool hasReporterValueByName (const ReporterName &reporter_name) const
 

Static Protected Member Functions

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

Protected Attributes

const unsigned _num_my_nodes
 Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is handled) More...
 
ModelGeochemicalDatabase _mgd
 my copy of the underlying ModelGeochemicalDatabase More...
 
const PertinentGeochemicalSystem & _pgs
 Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase. More...
 
const unsigned _num_basis
 number of basis species More...
 
const unsigned _num_eqm
 number of equilibrium species More...
 
const Real _initial_max_ionic_str
 Initial value of maximum ionic strength. More...
 
GeochemistryIonicStrength _is
 The ionic strength calculator. More...
 
GeochemistryActivityCoefficientsDebyeHuckel _gac
 The activity calculator. More...
 
const unsigned _max_swaps_allowed
 Maximum number of swaps allowed during a single solve. More...
 
GeochemistrySpeciesSwapper _swapper
 The species swapper. More...
 
const Real _small_molality
 A small value of molality. More...
 
std::vector< std::stringstream > _solver_output
 The solver output at each node. More...
 
std::vector< unsigned > _tot_iter
 Number of iterations used by the solver at each node. More...
 
std::vector< Real > _abs_residual
 L1norm of the solver residual at each node. More...
 
MooseMesh & _mesh
 
const unsigned int _qp
 
const Node *const & _current_node
 
const bool & _unique_node_execute
 
SubProblem & _subproblem
 
FEProblemBase & _fe_problem
 
SystemBase & _sys
 
const THREAD_ID _tid
 
Assembly & _assembly
 
const Moose::CoordinateSystemType & _coord_sys
 
const bool _duplicate_initial_execution
 
std::set< std::string > _depend_uo
 
const bool & _enabled
 
MooseApp & _app
 
Factory & _factory
 
ActionFactory & _action_factory
 
const std::string & _type
 
const std::string & _name
 
const InputParameters & _pars
 
const ExecFlagEnum & _execute_enum
 
const ExecFlagType & _current_execute_flag
 
MooseApp & _restartable_app
 
const std::string _restartable_system_name
 
const THREAD_ID _restartable_tid
 
const bool _restartable_read_only
 
FEProblemBase & _mci_feproblem
 
FEProblemBase & _mdi_feproblem
 
MooseApp & _pg_moose_app
 
const std::string _prefix
 
const MaterialData * _blk_material_data
 
const InputParameters & _c_parameters
 
const std::string & _c_name
 
const std::string & _c_type
 
FEProblemBase & _c_fe_problem
 
const SystemBase *const _c_sys
 
std::unordered_map< std::string, std::vector< MooseVariableFieldBase *> > _coupled_vars
 
std::vector< MooseVariableFieldBase *> _coupled_moose_vars
 
std::vector< MooseVariable *> _coupled_standard_moose_vars
 
std::vector< VectorMooseVariable *> _coupled_vector_moose_vars
 
std::vector< ArrayMooseVariable *> _coupled_array_moose_vars
 
std::vector< MooseVariableField< Real > *> _coupled_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.

174  : NodalUserObject(parameters),
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()),
179  _num_basis(_mgd.basis_species_name.size()),
180  _num_eqm(_mgd.eqm_species_name.size()),
181  _initial_max_ionic_str(getParam<Real>("max_ionic_strength") /
182  (1.0 + getParam<unsigned>("ramp_max_ionic_strength_initial"))),
183  _is(_initial_max_ionic_str,
184  _initial_max_ionic_str,
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")),
192  _solver_output(_num_my_nodes),
193  _tot_iter(_num_my_nodes, 0),
194  _abs_residual(_num_my_nodes, 0.0)
195 {
196 }
GeochemistryReactorBase::_num_basis
const unsigned _num_basis
number of basis species
Definition: GeochemistryReactorBase.h:83
SubProblem::mesh
virtual MooseMesh & mesh()=0
GeochemistryReactorBase::_max_swaps_allowed
const unsigned _max_swaps_allowed
Maximum number of swaps allowed during a single solve.
Definition: GeochemistryReactorBase.h:93
GeochemistryReactorBase::_tot_iter
std::vector< unsigned > _tot_iter
Number of iterations used by the solver at each node.
Definition: GeochemistryReactorBase.h:101
GeochemistryReactorBase::_num_eqm
const unsigned _num_eqm
number of equilibrium species
Definition: GeochemistryReactorBase.h:85
GeochemistryReactorBase::_mgd
ModelGeochemicalDatabase _mgd
my copy of the underlying ModelGeochemicalDatabase
Definition: GeochemistryReactorBase.h:79
NodalUserObject::NodalUserObject
NodalUserObject(const InputParameters &parameters)
NodalUserObject::parameters
const InputParameters & parameters() const
GeochemistryReactorBase::_pgs
const PertinentGeochemicalSystem & _pgs
Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.
Definition: GeochemistryReactorBase.h:81
GeochemistryReactorBase::_initial_max_ionic_str
const Real _initial_max_ionic_str
Initial value of maximum ionic strength.
Definition: GeochemistryReactorBase.h:87
NodalUserObject::_subproblem
SubProblem & _subproblem
GeochemistryReactorBase::_num_my_nodes
const unsigned _num_my_nodes
Number of nodes handled by this processor (will need to be made un-const when mesh adaptivity is hand...
Definition: GeochemistryReactorBase.h:73
MooseMesh::getMesh
MeshBase & getMesh()
GeochemistryReactorBase::_solver_output
std::vector< std::stringstream > _solver_output
The solver output at each node.
Definition: GeochemistryReactorBase.h:99
GeochemistryReactorBase::_is
GeochemistryIonicStrength _is
The ionic strength calculator.
Definition: GeochemistryReactorBase.h:89
GeochemistryReactorBase::_abs_residual
std::vector< Real > _abs_residual
L1norm of the solver residual at each node.
Definition: GeochemistryReactorBase.h:103
GeochemistryReactorBase::_swapper
GeochemistrySpeciesSwapper _swapper
The species swapper.
Definition: GeochemistryReactorBase.h:95
GeochemistryReactorBase::_small_molality
const Real _small_molality
A small value of molality.
Definition: GeochemistryReactorBase.h:97
ModelGeochemicalDatabase::eqm_species_name
std::vector< std::string > eqm_species_name
eqm_species_name[i] = name of the i^th eqm species
Definition: PertinentGeochemicalSystem.h:193
GeochemistryReactorBase::_gac
GeochemistryActivityCoefficientsDebyeHuckel _gac
The activity calculator.
Definition: GeochemistryReactorBase.h:91
ModelGeochemicalDatabase::basis_species_name
std::vector< std::string > basis_species_name
basis_species_name[j] = name of the j^th basis species
Definition: PertinentGeochemicalSystem.h:161

Member Function Documentation

◆ execute()

virtual void GeochemistryReactorBase::execute ( )
inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 30 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeIndependentReactor::execute().

30 {}

◆ finalize()

virtual void GeochemistryReactorBase::finalize ( )
inlineoverridevirtual

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 29 of file GeochemistryReactorBase.h.

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

29 {}

◆ getGeochemicalSystem()

virtual const GeochemicalSystem& GeochemistryReactorBase::getGeochemicalSystem ( dof_id_type  node_id) const
pure virtual
Returns
a reference to the equilibrium geochemical system at the given node
Parameters
node_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; };
GeochemistryReactorBase::_pgs
const PertinentGeochemicalSystem & _pgs
Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.
Definition: GeochemistryReactorBase.h:81

◆ getSolverIterations()

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

Implements NodalUserObject.

Reimplemented in GeochemistrySpatialReactor, GeochemistryTimeDependentReactor, and GeochemistryTimeIndependentReactor.

Definition at line 27 of file GeochemistryReactorBase.h.

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

27 {}

◆ sharedParams()

InputParameters GeochemistryReactorBase::sharedParams ( )
static

contains params that are shared with AddGeochemistrySolverAction and its children

Definition at line 13 of file GeochemistryReactorBase.C.

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

14 {
15  InputParameters params = emptyInputParameters();
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");
33  params.addRequiredParam<MultiMooseEnum>(
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");
55  params.addRequiredParam<MultiMooseEnum>(
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 }
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)
emptyInputParameters
InputParameters emptyInputParameters()
Real
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
InputParameters::addRangeCheckedParam
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 {
156  InputParameters params = NodalUserObject::validParams();
157  params += GeochemistryReactorBase::sharedParams();
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 }
NodalUserObject::validParams
static InputParameters validParams()
GeochemistryReactorBase::sharedParams
static InputParameters sharedParams()
contains params that are shared with AddGeochemistrySolverAction and its children ...
Definition: GeochemistryReactorBase.C:13
InputParameters::addRequiredParam
void addRequiredParam(const std::string &name, const std::string &doc_string)
Real
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
InputParameters::addClassDescription
void addClassDescription(const std::string &doc_string)
InputParameters::addRangeCheckedParam
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

L1norm of the solver residual at each node.

Definition at line 103 of file GeochemistryReactorBase.h.

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

◆ _gac

GeochemistryActivityCoefficientsDebyeHuckel GeochemistryReactorBase::_gac
protected

The activity calculator.

Definition at line 91 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _initial_max_ionic_str

const Real GeochemistryReactorBase::_initial_max_ionic_str
protected

Initial value of maximum ionic strength.

Definition at line 87 of file GeochemistryReactorBase.h.

◆ _is

GeochemistryIonicStrength GeochemistryReactorBase::_is
protected

The ionic strength calculator.

Definition at line 89 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _max_swaps_allowed

const unsigned GeochemistryReactorBase::_max_swaps_allowed
protected

Maximum number of swaps allowed during a single solve.

Definition at line 93 of file GeochemistryReactorBase.h.

◆ _mgd

ModelGeochemicalDatabase GeochemistryReactorBase::_mgd
protected

my copy of the underlying ModelGeochemicalDatabase

Definition at line 79 of file GeochemistryReactorBase.h.

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

◆ _num_basis

const unsigned GeochemistryReactorBase::_num_basis
protected

number of basis species

Definition at line 83 of file GeochemistryReactorBase.h.

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

◆ _num_eqm

const unsigned GeochemistryReactorBase::_num_eqm
protected

number of equilibrium species

Definition at line 85 of file GeochemistryReactorBase.h.

◆ _num_my_nodes

const unsigned GeochemistryReactorBase::_num_my_nodes
protected

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

Definition at line 73 of file GeochemistryReactorBase.h.

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

◆ _pgs

const PertinentGeochemicalSystem& GeochemistryReactorBase::_pgs
protected

Reference to the original PertinentGeochemicalSystem used to create the ModelGeochemicalDatabase.

Definition at line 81 of file GeochemistryReactorBase.h.

Referenced by getPertinentGeochemicalSystem().

◆ _small_molality

const Real GeochemistryReactorBase::_small_molality
protected

A small value of molality.

Definition at line 97 of file GeochemistryReactorBase.h.

Referenced by GeochemistryTimeDependentReactor::postSolveFlowThrough().

◆ _solver_output

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

The solver output at each node.

Definition at line 99 of file GeochemistryReactorBase.h.

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

◆ _swapper

GeochemistrySpeciesSwapper GeochemistryReactorBase::_swapper
protected

The species swapper.

Definition at line 95 of file GeochemistryReactorBase.h.

Referenced by GeochemistrySpatialReactor::GeochemistrySpatialReactor().

◆ _tot_iter

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

Number of iterations used by the solver at each node.

Definition at line 101 of file GeochemistryReactorBase.h.

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

The documentation for this class was generated from the following files:
Generated on Fri Aug 29 2025 20:22:23 for https://mooseframework.inl.gov by   doxygen 1.8.14