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

#include <gmpIphreeqcReaction.h>

Inheritance diagram for GmpIphreeqcReaction:

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Collaboration diagram for GmpIphreeqcReaction:

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

virtual	~GmpIphreeqcReaction ()
	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.

bool	checksNodalAccessors ()

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

bool	createIPhreeqcInput (IPhreeqc &R, const char *dump, int node)

bool	runIPhreeqc (IPhreeqc &R)

bool	evaluateInitialConditions (QString &input)

virtual bool	setsInitialConditions (IPhreeqc &R, int node)

bool	getSelectedPhreeqcOutputs (IPhreeqc &phreeqc, GmVector &data, int node)

bool	saveIPhreeqcValuesToNode (IPhreeqc &R, int node)

bool	updatesSolution (IPhreeqc &R, GmValueAccessor *ionAcc, int node)
	Updates solution ions of each especies for the next Phreeqc simulation.

bool	updatesKinetics (IPhreeqc &R, GmValueAccessor *ionAcc, int node)
	Updates kinetic reaction of each mineral for the next Phreeqc simulation.

bool	updatesEquilibrium (IPhreeqc &R, GmValueAccessor *ionAcc, int node)
	Updates equilibrium reaction of each mineral for the next Phreeqc simulation.

bool	loadsChemicalParameters (QString &inputPhreeqc)

bool	loadsOutputData (const QString &line, QString &Keyword, QList< QPair< QString, int > > &data, int offset=1)

QString	extractSegment (const QString &input, const QString &startWord, const QString &endWord)

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

bool	runIphreeqcNodes ()

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

void	getMineralValues (const GmElement *e, GmVector &Rg, GmVector &Re, 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

Protected Types
enum	iPhreeqcReactionPhysicsAttributeIds { IPHREEQC_DATABASE_ID = GmpChemicalFemPhysics::NUM_ATTRIBUTE_IDS , INPUT_A_ID , POROS_A_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 , EqM_NA_ID , KiM_NA_ID , poroM_NA_ID , poroMOld_NA_ID , NUM_NA_IDS }
	IDs for physics node attributes. More...

enum	GaussAttributeIds { MASS_GA_ID = GmpChemicalFemPhysics::NUM_GA_IDS , NUM_GA_IDS }

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	checkAndLoadPrivateData (LuaTable &table)

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.

bool	fillElementalMass ()

Protected Member Functions inherited from GmpChemicalFemPhysics

Private Attributes
bool	_isKinetics

bool	_isEquilibrium

bool	_isSaturation

int	_nOut

IPhreeqc	_iphreeqc

QByteArray	_dumpData

QList< QPair< QString, int > >	_solution

QList< QPair< QString, int > >	_kiMineral

QList< QPair< QString, int > >	_eqMineral

QList< QPair< QString, int > >	_siMineral

QString	_selectedOutput

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

◆ GaussAttributeIds

enum GmpIphreeqcReaction::GaussAttributeIds

protected

Enumerator
NUM_GA_IDS	The number of gauss attributes.

◆ iPhreeqcReactionPhysicsAttributeIds

enum GmpIphreeqcReaction::iPhreeqcReactionPhysicsAttributeIds

protected

Additional IDs for physics attributes.

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

◆ NodeAttributeIds

enum GmpIphreeqcReaction::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.
EqM_NA_ID	Base Id for Reaction in equillibrium.
KiM_NA_ID	Base Id for mineral for reaction.
poroM_NA_ID	Base Id for porosity variation.
NUM_NA_IDS	The number of node attribute ids above.

Member Function Documentation

◆ calcDerivedResults()

bool GmpIphreeqcReaction::calcDerivedResults ( bool nonLinearSolver )

virtual

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

Reimplemented from GmpChemicalFemPhysics.

◆ checkLoadedData()

bool GmpIphreeqcReaction::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 * GmpIphreeqcReaction::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 GmpIphreeqcReaction::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/gmpIphreeqcReaction.h
src/gmpIphreeqcReaction.cpp

Public Member Functions

Protected Types

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ GaussAttributeIds

◆ iPhreeqcReactionPhysicsAttributeIds

◆ NodeAttributeIds

Member Function Documentation

◆ calcDerivedResults()

◆ checkLoadedData()

◆ physicsMetaDataMap()

◆ reactionRate()