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GeochemistryKineticRate Class Reference

User object that defines a kinetic rate. More...

#include <GeochemistryKineticRate.h>

Inheritance diagram for GeochemistryKineticRate:
[legend]

Public Types

typedef DataFileName DataFileParameterType
 

Public Member Functions

 GeochemistryKineticRate (const InputParameters &parameters)
 
virtual void initialize () override final
 
virtual void execute () override final
 
virtual void finalize () override final
 
const KineticRateUserDescription & getRateDescription () const
 provides a reference to the rate description held by this object More...
 
SubProblem & getSubProblem () const
 
bool shouldDuplicateInitialExecution () const
 
virtual Real spatialValue (const Point &) const
 
virtual const std::vector< Point > spatialPoints () const
 
void gatherSum (T &value)
 
void gatherMax (T &value)
 
void gatherMin (T &value)
 
void gatherProxyValueMax (T1 &proxy, T2 &value)
 
void gatherProxyValueMin (T1 &proxy, T2 &value)
 
void setPrimaryThreadCopy (UserObject *primary)
 
UserObject * primaryThreadCopy ()
 
std::set< UserObjectName > getDependObjects () const
 
virtual bool needThreadedCopy () const
 
const std::set< std::string > & getRequestedItems () override
 
const std::set< std::string > & getSuppliedItems () override
 
unsigned int systemNumber () const
 
virtual bool enabled () const
 
std::shared_ptr< MooseObject > getSharedPtr ()
 
std::shared_ptr< const MooseObject > getSharedPtr () const
 
MooseApp & getMooseApp () const
 
const std::string & type () const
 
virtual const std::string & name () const
 
std::string typeAndName () const
 
std::string errorPrefix (const std::string &error_type) const
 
void callMooseError (std::string msg, const bool with_prefix) const
 
MooseObjectParameterName uniqueParameterName (const std::string &parameter_name) const
 
const InputParameters & parameters () const
 
MooseObjectName uniqueName () const
 
const T & getParam (const std::string &name) const
 
std::vector< std::pair< T1, T2 > > getParam (const std::string &param1, const std::string &param2) const
 
const T * queryParam (const std::string &name) const
 
const T & getRenamedParam (const std::string &old_name, const std::string &new_name) const
 
T getCheckedPointerParam (const std::string &name, const std::string &error_string="") const
 
bool isParamValid (const std::string &name) const
 
bool isParamSetByUser (const std::string &nm) const
 
void paramError (const std::string &param, Args... args) const
 
void paramWarning (const std::string &param, Args... args) const
 
void paramInfo (const std::string &param, Args... args) const
 
void connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const
 
void mooseError (Args &&... args) const
 
void mooseErrorNonPrefixed (Args &&... args) const
 
void mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const
 
void mooseWarning (Args &&... args) const
 
void mooseWarningNonPrefixed (Args &&... args) const
 
void mooseDeprecated (Args &&... args) const
 
void mooseInfo (Args &&... args) const
 
std::string getDataFileName (const std::string &param) const
 
std::string getDataFileNameByName (const std::string &relative_path) const
 
std::string getDataFilePath (const std::string &relative_path) const
 
virtual void initialSetup ()
 
virtual void timestepSetup ()
 
virtual void jacobianSetup ()
 
virtual void residualSetup ()
 
virtual void customSetup (const ExecFlagType &)
 
const ExecFlagEnum & getExecuteOnEnum () const
 
UserObjectName getUserObjectName (const std::string &param_name) const
 
const T & getUserObject (const std::string &param_name, bool is_dependency=true) const
 
const T & getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const
 
const UserObject & getUserObjectBase (const std::string &param_name, bool is_dependency=true) const
 
const UserObject & getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const
 
const std::vector< MooseVariableScalar *> & getCoupledMooseScalarVars ()
 
const std::set< TagID > & getScalarVariableCoupleableVectorTags () const
 
const std::set< TagID > & getScalarVariableCoupleableMatrixTags () const
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialProperty (const std::string &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialProperty (const std::string &name, const unsigned int state=0)
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name, MaterialData &material_data)
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > & getADMaterialProperty (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOld (const std::string &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOld (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOld (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOlder (const std::string &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOlder (const std::string &name)
 
const MaterialProperty< T > & getMaterialPropertyOlder (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const GenericMaterialProperty< T, is_ad > & getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const MaterialProperty< T > & getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name)
 
const ADMaterialProperty< T > & getADMaterialPropertyByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOldByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name, MaterialData &material_data)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name)
 
const MaterialProperty< T > & getMaterialPropertyOlderByName (const MaterialPropertyName &name)
 
std::pair< const MaterialProperty< T > *, std::set< SubdomainID > > getBlockMaterialProperty (const MaterialPropertyName &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialProperty ()
 
const GenericMaterialProperty< T, is_ad > & getGenericZeroMaterialPropertyByName (const std::string &prop_name)
 
const MaterialProperty< T > & getZeroMaterialProperty (Ts... args)
 
std::set< SubdomainID > getMaterialPropertyBlocks (const std::string &name)
 
std::vector< SubdomainName > getMaterialPropertyBlockNames (const std::string &name)
 
std::set< BoundaryID > getMaterialPropertyBoundaryIDs (const std::string &name)
 
std::vector< BoundaryName > getMaterialPropertyBoundaryNames (const std::string &name)
 
void checkBlockAndBoundaryCompatibility (std::shared_ptr< MaterialBase > discrete)
 
std::unordered_map< SubdomainID, std::vector< MaterialBase *> > buildRequiredMaterials (bool allow_stateful=true)
 
void statefulPropertiesAllowed (bool)
 
bool getMaterialPropertyCalled () const
 
virtual const std::unordered_set< unsigned int > & getMatPropDependencies () const
 
virtual void resolveOptionalProperties ()
 
const GenericMaterialProperty< T, is_ad > & getPossiblyConstantGenericMaterialPropertyByName (const MaterialPropertyName &prop_name, MaterialData &material_data, const unsigned int state)
 
bool isImplicit ()
 
Moose::StateArg determineState () const
 
virtual void threadJoin (const UserObject &) override
 
virtual void threadJoin (const UserObject &) override
 
virtual void subdomainSetup () override
 
virtual void subdomainSetup () override
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObject (const std::string &param_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
bool hasUserObjectByName (const UserObjectName &object_name) const
 
const GenericOptionalMaterialProperty< T, is_ad > & getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const GenericOptionalMaterialProperty< T, is_ad > & getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalMaterialProperty< T > & getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalMaterialProperty< T > & getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)
 
const OptionalADMaterialProperty< T > & getOptionalADMaterialProperty (const std::string &name)
 
const OptionalADMaterialProperty< T > & getOptionalADMaterialProperty (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOld (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOld (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOlder (const std::string &name)
 
const OptionalMaterialProperty< T > & getOptionalMaterialPropertyOlder (const std::string &name)
 
MaterialBase & getMaterial (const std::string &name)
 
MaterialBase & getMaterial (const std::string &name)
 
MaterialBase & getMaterialByName (const std::string &name, bool no_warn=false)
 
MaterialBase & getMaterialByName (const std::string &name, bool no_warn=false)
 
bool hasMaterialProperty (const std::string &name)
 
bool hasMaterialProperty (const std::string &name)
 
bool hasMaterialPropertyByName (const std::string &name)
 
bool hasMaterialPropertyByName (const std::string &name)
 
bool hasADMaterialProperty (const std::string &name)
 
bool hasADMaterialProperty (const std::string &name)
 
bool hasADMaterialPropertyByName (const std::string &name)
 
bool hasADMaterialPropertyByName (const std::string &name)
 
bool hasGenericMaterialProperty (const std::string &name)
 
bool hasGenericMaterialProperty (const std::string &name)
 
bool hasGenericMaterialPropertyByName (const std::string &name)
 
bool hasGenericMaterialPropertyByName (const std::string &name)
 
const 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 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)
 

Public Attributes

const ConsoleStream _console
 

Static Public Attributes

static constexpr PropertyValue::id_type default_property_id
 
static constexpr PropertyValue::id_type zero_property_id
 
static constexpr auto SYSTEM
 
static constexpr auto NAME
 

Protected Member Functions

virtual void addPostprocessorDependencyHelper (const PostprocessorName &name) const override
 
virtual void addVectorPostprocessorDependencyHelper (const VectorPostprocessorName &name) const override
 
virtual void addUserObjectDependencyHelper (const UserObject &uo) const override
 
void addReporterDependencyHelper (const ReporterName &reporter_name) override
 
const ReporterName & getReporterName (const std::string &param_name) const
 
T & declareRestartableData (const std::string &data_name, Args &&... args)
 
ManagedValue< T > declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)
 
const T & getRestartableData (const std::string &data_name) const
 
T & declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)
 
T & declareRecoverableData (const std::string &data_name, Args &&... args)
 
T & declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)
 
T & declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)
 
std::string restartableName (const std::string &data_name) const
 
const T & getMeshProperty (const std::string &data_name, const std::string &prefix)
 
const T & getMeshProperty (const std::string &data_name)
 
bool hasMeshProperty (const std::string &data_name, const std::string &prefix) const
 
bool hasMeshProperty (const std::string &data_name, const std::string &prefix) const
 
bool hasMeshProperty (const std::string &data_name) const
 
bool hasMeshProperty (const std::string &data_name) const
 
std::string meshPropertyName (const std::string &data_name) const
 
PerfID registerTimedSection (const std::string &section_name, const unsigned int level) const
 
PerfID registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const
 
std::string timedSectionName (const std::string &section_name) const
 
bool isCoupledScalar (const std::string &var_name, unsigned int i=0) const
 
unsigned int coupledScalarComponents (const std::string &var_name) const
 
unsigned int coupledScalar (const std::string &var_name, unsigned int comp=0) const
 
libMesh::Order coupledScalarOrder (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< is_ad > & coupledGenericScalarValue (const std::string &var_name, unsigned int comp=0) const
 
const GenericVariableValue< false > & coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const
 
const GenericVariableValue< true > & coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const
 
const VariableValue & coupledVectorTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValue & coupledMatrixTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const
 
const VariableValue & coupledScalarValueOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarValueOlder (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const ADVariableValue & adCoupledScalarDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDot (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDotOld (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDu (const std::string &var_name, unsigned int comp=0) const
 
const VariableValue & coupledScalarDotDotDu (const std::string &var_name, unsigned int comp=0) const
 
const MooseVariableScalar * getScalarVar (const std::string &var_name, unsigned int comp) const
 
virtual void checkMaterialProperty (const std::string &name, const unsigned int state)
 
void markMatPropRequested (const std::string &)
 
MaterialPropertyName getMaterialPropertyName (const std::string &name) const
 
void checkExecutionStage ()
 
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
 
const GenericMaterialProperty< T, is_ad > * defaultGenericMaterialProperty (const std::string &name)
 
const GenericMaterialProperty< T, is_ad > * defaultGenericMaterialProperty (const std::string &name)
 
const MaterialProperty< T > * defaultMaterialProperty (const std::string &name)
 
const MaterialProperty< T > * defaultMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > * defaultADMaterialProperty (const std::string &name)
 
const ADMaterialProperty< T > * defaultADMaterialProperty (const std::string &name)
 

Static Protected Member Functions

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

Protected Attributes

SubProblem & _subproblem
 
FEProblemBase & _fe_problem
 
SystemBase & _sys
 
const THREAD_ID _tid
 
Assembly & _assembly
 
const Moose::CoordinateSystemType & _coord_sys
 
const bool _duplicate_initial_execution
 
std::set< std::string > _depend_uo
 
const bool & _enabled
 
MooseApp & _app
 
const std::string _type
 
const std::string _name
 
const InputParameters & _pars
 
Factory & _factory
 
ActionFactory & _action_factory
 
const ExecFlagEnum & _execute_enum
 
const ExecFlagType & _current_execute_flag
 
MooseApp & _restartable_app
 
const std::string _restartable_system_name
 
const THREAD_ID _restartable_tid
 
const bool _restartable_read_only
 
FEProblemBase & _mci_feproblem
 
FEProblemBase & _mdi_feproblem
 
MooseApp & _pg_moose_app
 
const std::string _prefix
 
FEProblemBase & _sc_fe_problem
 
const THREAD_ID _sc_tid
 
const Real & _real_zero
 
const VariableValue & _scalar_zero
 
const Point & _point_zero
 
const InputParameters & _mi_params
 
const std::string _mi_name
 
const MooseObjectName _mi_moose_object_name
 
FEProblemBase & _mi_feproblem
 
SubProblem & _mi_subproblem
 
const THREAD_ID _mi_tid
 
const Moose::MaterialDataType _material_data_type
 
MaterialData & _material_data
 
bool _stateful_allowed
 
bool _get_material_property_called
 
std::vector< std::unique_ptr< PropertyValue > > _default_properties
 
std::unordered_set< unsigned int > _material_property_dependencies
 
const MaterialPropertyName _get_suffix
 
const bool _use_interpolated_state
 
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
 

Static Protected Attributes

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

Private Attributes

const std::vector< std::string > _promoting_names
 
const std::vector< Real > _monod_ind
 
const std::vector< Real > _half_sat
 
const KineticRateUserDescription _rate_description
 

Detailed Description

User object that defines a kinetic rate.

Definition at line 18 of file GeochemistryKineticRate.h.

Constructor & Destructor Documentation

◆ GeochemistryKineticRate()

GeochemistryKineticRate::GeochemistryKineticRate ( const InputParameters &  parameters)

Definition at line 130 of file GeochemistryKineticRate.C.

131  : GeneralUserObject(parameters),
132  _promoting_names(getParam<std::vector<std::string>>("promoting_species_names")),
133  _monod_ind(isParamValid("promoting_monod_indices")
134  ? getParam<std::vector<Real>>("promoting_monod_indices")
135  : std::vector<Real>(_promoting_names.size(), 0.0)),
136  _half_sat(isParamValid("promoting_half_saturation")
137  ? getParam<std::vector<Real>>("promoting_half_saturation")
138  : std::vector<Real>(_promoting_names.size(), 0.0)),
139  _rate_description(getParam<std::string>("kinetic_species_name"),
140  getParam<Real>("intrinsic_rate_constant"),
141  getParam<Real>("area_quantity"),
142  getParam<bool>("multiply_by_mass"),
143  getParam<Real>("kinetic_molal_index"),
144  getParam<Real>("kinetic_monod_index"),
145  getParam<Real>("kinetic_half_saturation"),
146  _promoting_names,
147  getParam<std::vector<Real>>("promoting_indices"),
148  _monod_ind,
149  _half_sat,
150  getParam<Real>("theta"),
151  getParam<Real>("eta"),
152  getParam<Real>("activation_energy"),
153  getParam<Real>("one_over_T0"),
154  getParam<MooseEnum>("direction").getEnum<DirectionChoiceEnum>(),
155  getParam<std::string>("non_kinetic_biological_catalyst"),
156  getParam<Real>("non_kinetic_biological_efficiency"),
157  getParam<Real>("kinetic_biological_efficiency"),
158  getParam<Real>("energy_captured"))
159 {
160 }
GeochemistryKineticRate::_rate_description
const KineticRateUserDescription _rate_description
Definition: GeochemistryKineticRate.h:36
GeochemistryKineticRate::_half_sat
const std::vector< Real > _half_sat
Definition: GeochemistryKineticRate.h:35
GeneralUserObject::isParamValid
bool isParamValid(const std::string &name) const
GeneralUserObject::getParam
const T & getParam(const std::string &name) const
GeochemistryKineticRate::_promoting_names
const std::vector< std::string > _promoting_names
Definition: GeochemistryKineticRate.h:33
GeneralUserObject::GeneralUserObject
GeneralUserObject(const InputParameters &parameters)
GeneralUserObject::parameters
const InputParameters & parameters() const
GeochemistryKineticRate::_monod_ind
const std::vector< Real > _monod_ind
Definition: GeochemistryKineticRate.h:34
DirectionChoiceEnum
DirectionChoiceEnum
This controls the direction of a kinetic rate BOTH: both dissolution and precipitation are allowed PR...
Definition: GeochemistryKineticRateCalculator.h:28

Member Function Documentation

◆ execute()

void GeochemistryKineticRate::execute ( )
finaloverridevirtual

Implements GeneralUserObject.

Definition at line 168 of file GeochemistryKineticRate.C.

169 {
170 }

◆ finalize()

void GeochemistryKineticRate::finalize ( )
finaloverridevirtual

Implements GeneralUserObject.

Definition at line 173 of file GeochemistryKineticRate.C.

174 {
175 }

◆ getRateDescription()

const KineticRateUserDescription & GeochemistryKineticRate::getRateDescription ( ) const

provides a reference to the rate description held by this object

Definition at line 178 of file GeochemistryKineticRate.C.

179 {
180  return _rate_description;
181 }
GeochemistryKineticRate::_rate_description
const KineticRateUserDescription _rate_description
Definition: GeochemistryKineticRate.h:36

◆ initialize()

void GeochemistryKineticRate::initialize ( )
finaloverridevirtual

Implements GeneralUserObject.

Definition at line 163 of file GeochemistryKineticRate.C.

164 {
165 }

◆ validParams()

InputParameters GeochemistryKineticRate::validParams ( )
static

Definition at line 15 of file GeochemistryKineticRate.C.

16 {
17  InputParameters params = GeneralUserObject::validParams();
18  params.addRequiredParam<std::string>(
19  "kinetic_species_name",
20  "The name of the kinetic species that will be controlled by this rate");
21  params.addRequiredRangeCheckedParam<Real>("intrinsic_rate_constant",
22  "intrinsic_rate_constant >= 0.0",
23  "The intrinsic rate constant for the reaction");
24  params.addRangeCheckedParam<Real>(
25  "area_quantity",
26  1.0,
27  "area_quantity > 0.0",
28  "The surface area of the kinetic species in m^2 (if multiply_by_mass = false) or the "
29  "specific surface area of the kinetic species in m^2/g (if multiply_by_mass = true)");
30  params.addParam<bool>(
31  "multiply_by_mass",
32  false,
33  "Whether the rate should be multiplied by the kinetic_species mass (in grams)");
34  params.addParam<Real>("kinetic_molal_index",
35  0.0,
36  "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
37  "(kinetic_species_molality^kinetic_molal_index + "
38  "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
39  params.addParam<Real>("kinetic_monod_index",
40  0.0,
41  "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
42  "(kinetic_species_molality^kinetic_molal_index + "
43  "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
44  params.addParam<Real>("kinetic_half_saturation",
45  0.0,
46  "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
47  "(kinetic_species_molality^kinetic_molal_index + "
48  "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
49  params.addParam<std::vector<std::string>>(
50  "promoting_species_names", {}, "Names of any promoting species");
51  params.addParam<std::vector<Real>>("promoting_indices", {}, "Indices of the promoting species");
52  params.addParam<std::vector<Real>>(
53  "promoting_monod_indices",
54  "Indices of the monod denominators of the promoting species. If not given, then the default "
55  "is 0 for each promoting species, meaning that there is no monod form");
56  params.addParam<std::vector<Real>>("promoting_half_saturation",
57  "Half-saturation constants for the monod expression. If not "
58  "given, then the default is 0 for each promoting species");
59  params.addParam<Real>("theta", 1.0, "Theta parameter, which appears in |1 - (Q/K)^theta|^eta");
60  params.addParam<Real>("eta", 1.0, "Eta parameter, which appears in |1 - (Q/K)^theta|^eta");
61  params.addRangeCheckedParam<Real>(
62  "activation_energy",
63  0.0,
64  "activation_energy >= 0.0",
65  "Activation energy, in J.mol^-1, which appears in exp(activation_energy / R * (1/T0 - 1/T))");
66  params.addParam<Real>(
67  "one_over_T0",
68  0.0,
69  "1/T0, in 1/Kelvin, which appears in exp(activation_energy / R * (1/T0 - 1/T))");
70  MooseEnum direction("both dissolution precipitation raw death", "both");
71  params.addParam<MooseEnum>(
72  "direction",
73  direction,
74  "Direction of reaction. Let Q = the activity product of the kinetic reaction, and K = the "
75  "equilibrium constant of the reaction. Then direction means the following. both = "
76  "dissolution and precipitation are allowed. (Specifically, if Q < K then dissolution will "
77  "occur, that is, the kinetic species mass will decrease with time. If Q > K then "
78  "precipitation will occur, that is, the kinetic species mass will increase with time.) "
79  "dissolution = if Q < K then dissolution will occur, and when Q > K then the rate will be "
80  "set to zero so that precipitation will be prevented. precipitation = if Q > K then "
81  "precipitation will occur, and when Q < K then the rate will be set to zero so that "
82  "dissolution will be prevented. raw = the rate will not depend on sgn(1 - (Q/K)), which "
83  "means dissolution will occur if intrinsic_rate_constant > 0, and precipitation will occur "
84  "when intrinsic_rate_constant < 0. death = the rate will not depend on sgn(1 - (Q/K)), "
85  "which means dissolution will occur if intrinsic_rate_constant > 0, and precipitation will "
86  "occur when intrinsic_rate_constant < 0, and, in addition, no reactants will be produced or "
87  "consumed by this kinetic reaction (only the kinetic species mass will change).");
88  params.addParam<std::string>(
89  "non_kinetic_biological_catalyst",
90  "H2O",
91  "Name of the primary or equilibrium species that acts as a biological catalyst.");
92  params.addParam<Real>(
93  "non_kinetic_biological_efficiency",
94  0.0,
95  "When one mole of the kinetic species dissolves, non_kinetic_biological_efficiency moles of "
96  "the non_kinetic_biological_catalyst is created");
97  params.addParam<Real>(
98  "kinetic_biological_efficiency",
99  -1,
100  "This is used when modelling biologically-catalysed reactions, when the biomass is treated "
101  "as a kinetic species, and the reactants and reactant-products are in equilibrium in the "
102  "aqueous solution. When one mole of reaction is catalysed, the biomass increases by "
103  "kinetic_biological_efficiency moles");
104  params.addParam<Real>(
105  "energy_captured",
106  0.0,
107  "In biologically-catalysed kinetic reactions, this is the energy captured by the cell, per "
108  "mol of reaction turnover. Specifically, for each mole of kinetic reaction, the microbe "
109  "will produce m moles of ATP via a reaction such as ADP + PO4--- -> ATP + H2O, with "
110  "free-energy change G (usually around 45 kJ/mol). Then, energy_captured = m * G. For "
111  "non-biologically-catalysed reactions, this should be zero. The impact of energy_captured "
112  "is that the reaction's equilibrium constant is K_database * exp(-energy_captured / R / "
113  "T_in_Kelvin)");
114  params.addClassDescription(
115  "User object that defines a kinetic rate. Note that more than one rate can be prescribed to "
116  "a single kinetic_species: the sum the individual rates defines the overall rate. "
117  "GeochemistryKineticRate simply specifies the algebraic form for a kinetic rate: to actually "
118  "use it in a calculation, you must use it in the GeochemicalModelDefinition. The rate is "
119  "intrinsic_rate_constant * area_quantity * (optionally, mass of kinetic_species in "
120  "grams) * kinetic_molality^kinetic_molal_index / (kinetic_molality^kinetic_molal_index + "
121  "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index * "
122  "(product_over_promoting_species m^promoting_index / (m^promoting_index + "
123  "promoting_half_saturation^promiting_index)^promoting_monod_index) * |1 - (Q/K)^theta|^eta * "
124  "exp(activation_energy / R * (1/T0 - 1/T)) * Direction(1 - (Q/K)). Please see the markdown "
125  "documentation for examples");
126 
127  return params;
128 }
InputParameters::addRequiredRangeCheckedParam
void addRequiredRangeCheckedParam(const std::string &name, const std::string &parsed_function, const std::string &doc_string)
GeneralUserObject::validParams
static InputParameters validParams()
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)
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

◆ _half_sat

const std::vector<Real> GeochemistryKineticRate::_half_sat
private

Definition at line 35 of file GeochemistryKineticRate.h.

◆ _monod_ind

const std::vector<Real> GeochemistryKineticRate::_monod_ind
private

Definition at line 34 of file GeochemistryKineticRate.h.

◆ _promoting_names

const std::vector<std::string> GeochemistryKineticRate::_promoting_names
private

Definition at line 33 of file GeochemistryKineticRate.h.

◆ _rate_description

const KineticRateUserDescription GeochemistryKineticRate::_rate_description
private

Definition at line 36 of file GeochemistryKineticRate.h.

Referenced by getRateDescription().

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