Extends the basic chemical physics transport equation by providing reaction rates based on the Iphreeqc package. More...

#include <gmpChemicalReaction.h>

Inheritance diagram for GmpChemicalReaction:

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Collaboration diagram for GmpChemicalReaction:

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Public Member Functions
	GmpChemicalReaction (GmSimulationData *simulation, QString id, QString description, const GmLogCategory &logger)

virtual	~GmpChemicalReaction ()
	Destructor.

virtual const char *	pluginType () const

virtual const QVariantMap *	physicsMetaDataMap ()
	Returns a pointer to the basic chemical physics attribute map, built when the function is called for the first time. Will be extended by sub-classes providing the reactive term.

virtual bool	checkLoadedData ()
	Checks the existance of the velocity accessor, and also sizes for the dispersion and retardation coefficients, as well as sizes for the prescribed concentration and prescribed flux boundary conditions.

virtual bool	beforeElementStiffnessLoop (const GmpFemMatrixSet &elemMatrices, const GmpFemVectorSet &elemVectors)

virtual void	createIPhreeqcIC (IPhreeqc &R, int node)

virtual bool	runIPhreeqcIC (IPhreeqc &R)

virtual bool	saveIPhreeqcValuestoMeshIC (IPhreeqc &R, int node)

virtual bool	createIPhreeqcBC (IPhreeqc &R)

virtual bool	runIPhreeqcBC (IPhreeqc &R)

virtual bool	saveIPhreeqcValuestoBCNode (IPhreeqc &R)

virtual bool	createIPhreeqcInput (IPhreeqc &R, int node)

virtual bool	runIPhreeqc (IPhreeqc &R)

virtual bool	saveIPhreeqcValuestoNode (IPhreeqc &R, int node)

char *	concatenateChar (std::string name, long double val)

char *	concatenateChar (std::string name, GmVector val)

char *	concatenateChar (std::string name, long double val1, std::string name2, long double val2)

char *	concatenateChar (std::string name, long double val1, std::string name2)

char *	concatenateChar (std::string name, std::string name2, int val1, std::string name3)

virtual GmVector	fillSolutionParameters (GmCellAccessor ac, const GmElement e, const GmVector *coord, int ip) const

virtual GmMatrix	fillEquilibriumParameters (GmCellAccessor ac, const GmElement e, const GmVector *coord, int ip) const

virtual bool	calcDerivedResults (bool nonLinearSolver)
	Calc velocity and flow on nodes and/or Gauss points.

virtual bool	runIphreeqcNodes ()

virtual bool	runInitIphreeqcNodes ()

virtual bool	runBCIPhreeqc ()

virtual void	getReactionValues (const GmElement *e, const GmVector &Rg, GmVector &Re, int pos) const

virtual void	FillElementalReaction (const GmElement *e, GmVector &elemFe, const GmVector &Fr, int pos) const

Public Member Functions inherited from GmpChemicalFemPhysics
	GmpChemicalFemPhysics (GmSimulationData *simulation, QString id, QString description, const GmLogCategory &logger)
	Constructor. Will be called by the plugin loading code.

virtual	~GmpChemicalFemPhysics ()
	Destructor.

virtual const char *	pluginName () const

virtual FemResultType	fillElementData (const GmElement *e, GmpFemMatrixSet &elemMatrices, GmpFemVectorSet &elemVectors)
	Fills the element stiffness matrix for element 'e' with diffusive and convective terms. Calls the virtual function reactionRate() for filling the external forces().

virtual FemResultType	fillElementDataForBc (const GmElement e, const GmBoundaryCondition bc, int bcIndex, int bcListIndex, int border, GmpFemMatrixSet &elemMatrices, GmpFemVectorSet &elemVectors)
	Fills the element force vector elemF for element 'e', taking into account fixed flux boundary conditions.

virtual bool	fixedNodalDofsBc (QVector< int > &nodes, QVector< int > &dof, QVector< double > &values, bool *constantValues) const
	See comments on base class. Fills vectors with prescribed node concentrations

virtual bool	fillFixedNodalDofsBCAlkalinity (QVector< int > &nodes, QVector< int > &dof, QVector< double > &values, bool *constantValues) const
	See comments on base class. Fills vectors with prescribed node concentrations.

virtual bool	fillFixedNodalDofsBCbasalt (QVector< int > &nodes, QVector< int > &dof, QVector< double > &values, bool *constantValues) const

Public Attributes
char	buffer [200]

Protected Types
enum	iPhreeqcReactionPhysicsAttributeIds { IPHREEQC_DATABASE_ID = GmpChemicalFemPhysics::NUM_ATTRIBUTE_IDS , REACTION_TYPE_ID , TEMP_A_ID , PE_A_ID , DW_A_ID , MW_A_ID , ALK_A_ID , PH_A_ID , Ca_A_ID , Cl_A_ID , Mg_A_ID , C_A_ID , Fe_A_ID , Na_A_ID , NEc_A_ID , NEd_A_ID , SIc_A_ID , SId_A_ID , nKc_A_ID , nKd_A_ID , SRc_A_ID , SRd_A_ID , POROS_A_ID , TEMP_Abc_ID , PE_Abc_ID , DW_Abc_ID , MW_Abc_ID , ALK_Abc_ID , PH_Abc_ID , Ca_Abc_ID , Cl_Abc_ID , Mg_Abc_ID , C_Abc_ID , Fe_Abc_ID , Na_Abc_ID , NUM_ATTRIBUTE_IDS }
	Additional IDs for physics attributes. More...

enum	NodeAttributeIds { IonSol_NA_ID = GmpChemicalFemPhysics::NUM_NA_IDS , IonSolOld_NA_ID , SIndex_NA_ID , SIndexOld_NA_ID , PH_NA_ID , PHOld_NA_ID , EqRxn_NA_ID , EqRxnOld_NA_ID , Mineral_NA_ID , MineralOld_NA_ID , poroM_NA_ID , poroMOld_NA_ID , KinCtr_NA_ID , KinCtrOld_NA_ID , NUM_NA_IDS }
	IDs for physics node attributes. More...

enum	iPHreeqcReactionElemPropertyIds { TemSol_ID = GmpChemicalFemPhysics::NUM_PROPERTY_IDS , BonCon_D , Fip_D , NUM_PROPERTY_IDS }
	Additional IDs for physics element properties. More...

Protected Types inherited from GmpChemicalFemPhysics
enum	PhysicsAttributeIds { ISOPARAMETRIC_ID , MULTI_DISPERSION_ID , MULTI_RETARDATION_ID , ALKALINITY_ID , BASALTRXN_ID , NUM_ATTRIBUTE_IDS }
	IDs for physics attributes. More...

enum	StateVarIds { C_ID }
	IDs fo physics state vars. More...

enum	NodeAttributeIds { NUM_NA_IDS }
	IDs for physics node attributes. More...

enum	GaussAttributeIds { V_GA_ID , NUM_GA_IDS }
	IDs for physics Gauss attributes. More...

enum	ElementPropertyIds { D_ID , K_ID , V_ID , PHI_ID , THICKNESS_ID , NUM_PROPERTY_IDS }
	IDs for physics element properties. More...

enum	BoundaryConditionIds { PRESCRIBED_C_BC_ID , PRESCRIBED_FLUX_BC_ID , PRESCRIBED_MIXED_BC_ID , PRESCRIBED_CN_BC_ID , NUM_BC_IDS }
	IDs for accepted boundary condition types. More...

enum	BoundaryConditionValueIds { BC_C_ID , BC_CN_ID , BC_Q_ID , BC_QDIR_ID , BC_MX_ID , NUM_BCV_IDS }
	IDs for property values from accepted boundary condition types. More...

Protected Member Functions
virtual bool	reactionRate (const GmElement e, const GmVector ip, int ipIndex, const GmVector &N, const GmVector &C, double wtJ, GmVector &elemFe, GmMatrix &elemK, bool needsFe, bool needsK)
	Virtual function called by fillElementData() for each integration point so that derived classes can add specific reaction rate terms to the convection-diffusion equation.

Protected Member Functions inherited from GmpChemicalFemPhysics

Private Attributes
IPhreeqc	_IPhreeqcReaction

Additional Inherited Members
Protected Attributes inherited from GmpChemicalFemPhysics
GmVector	_data
	Save alkalinity data for boundary condition.

GmVector	_Cglobal

Detailed Description

Extends the basic chemical physics transport equation by providing reaction rates based on the Iphreeqc package.

Member Enumeration Documentation

◆ iPHreeqcReactionElemPropertyIds

enum GmpChemicalReaction::iPHreeqcReactionElemPropertyIds

protected

Additional IDs for physics element properties.

Enumerator
TemSol_ID	Id for retrieving the solution parameters accessor.
NUM_PROPERTY_IDS	The number of property ids above.

◆ iPhreeqcReactionPhysicsAttributeIds

enum GmpChemicalReaction::iPhreeqcReactionPhysicsAttributeIds

protected

Additional IDs for physics attributes.

Enumerator
IPHREEQC_DATABASE_ID	Id for retrieving the reaction matrix physics attribute.
REACTION_TYPE_ID	Id for retrieving the reaction type physics attribute.
NUM_ATTRIBUTE_IDS	The number of attribute ids above.

◆ NodeAttributeIds

enum GmpChemicalReaction::NodeAttributeIds

protected

IDs for physics node attributes.

Enumerator
IonSol_NA_ID	Base Id for Ion transport node attribute(s)
IonSolOld_NA_ID	Base Id for history of Ion transport node attribute(s)
SIndex_NA_ID	Base Id for Saturation index.
PH_NA_ID	Base Id for pH solution.
EqRxn_NA_ID	Base Id for Reaction in equillibrium.
Mineral_NA_ID	Base Id for mineral for reaction.
poroM_NA_ID	Base Id for porosity variation.
KinCtr_NA_ID	Base Id for Kinetics reaction Control.
NUM_NA_IDS	The number of node attribute ids above.

Member Function Documentation

◆ calcDerivedResults()

bool GmpChemicalReaction::calcDerivedResults ( bool nonLinearSolver )

virtual

Calc velocity and flow on nodes and/or Gauss points.

Reimplemented from GmpChemicalFemPhysics.

◆ checkLoadedData()

bool GmpChemicalReaction::checkLoadedData ( )

virtual

Checks the existance of the velocity accessor, and also sizes for the dispersion and retardation coefficients, as well as sizes for the prescribed concentration and prescribed flux boundary conditions.

Reimplemented from GmpChemicalFemPhysics.

◆ physicsMetaDataMap()

const QVariantMap * GmpChemicalReaction::physicsMetaDataMap ( )

virtual

Returns a pointer to the basic chemical physics attribute map, built when the function is called for the first time. Will be extended by sub-classes providing the reactive term.

Reimplemented from GmpChemicalFemPhysics.

◆ reactionRate()

bool GmpChemicalReaction::reactionRate	(	const GmElement *	e,
		const GmVector *	ip,
		int	ipIndex,
		const GmVector &	N,
		const GmVector &	C,
		double	wtJ,
		GmVector &	elemFe,
		GmMatrix &	elemK,
		bool	needsFe,
		bool	needsK )

protectedvirtual

Virtual function called by fillElementData() for each integration point so that derived classes can add specific reaction rate terms to the convection-diffusion equation.

It receives as parameters the current element, integration point coordinate and index being processed, along with the shape function vector calculated over this point, a concentration vector for the element nodes and a constant 'wtJ' storing the product of the current integration point weight, the element thickness for 2D scenarions and the element Jacobian determinant.

The function should add its contributions to the elemFe and elemK vector / matrix according to the request given by needsFe and needsK.

Implements GmpChemicalFemPhysics.

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

inc/gmpChemicalReaction.h
src/gmpChemicalReaction.cpp

Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ iPHreeqcReactionElemPropertyIds

◆ iPhreeqcReactionPhysicsAttributeIds

◆ NodeAttributeIds

Member Function Documentation

◆ calcDerivedResults()

◆ checkLoadedData()

◆ physicsMetaDataMap()

◆ reactionRate()