#include <HeartBidomainSolver.hpp>

Collaboration diagram for HeartBidomainSolver< Mesh, SolverType >:

Protected Member Functions
void	solveSystem (matrixPtr_Type matrFull, vector_Type &rhsFull)
	Solves PDE system. More...

void	applyBoundaryConditions (matrix_Type &matrix, vector_Type &rhs, bchandlerRaw_Type &BCh)
	Apply BC. More...

Real	computeMean (vector_Type &x)
	compute mean of vector x More...

void	removeValue (vector_Type &x, Real &value)
	removes a scalar from each entry of vector x More...

Protected Attributes
const data_type &	M_data
	Data. More...

FESpace< Mesh, MapEpetra > &	M_pFESpace
	u FE space More...

FESpace< Mesh, MapEpetra > &	M_uFESpace

const std::shared_ptr< Epetra_Comm >	M_comm
	MPI communicator. More...

Int	M_me

BCHandler *	M_BCh_electric
	Bidomain BC. More...

bool	M_setBC

MapEpetra	M_localMap
	Map. More...

MapEpetra	M_localMap_u

MapEpetra	M_localMapVec

matrixPtr_Type	M_matrMass
	mass matrix More...

matrixPtr_Type	M_matrStiff
	Stiff matrix: D*stiff. More...

matrixPtr_Type	M_matrNoBC

vector_Type	M_rhsNoBC
	Right hand side for the PDE. More...

vector_Type	M_solutionIntraExtraPotential
	Global solution _u. More...

vector_Type	M_solutionTransmembranePotential

vector_Type	M_solutionExtraPotential

vector_Type	M_solutionIntraExtraPotentialExtrapolated

vector_Type	M_solutionTransmembranePotentialExtrapolated

vector_Type	M_fiberVector
	Local fibers vector. More...

vector_Type	M_residual
	residual More...

SolverType	M_linearSolver
	Solver. More...

prec_Type	M_prec

Real	M_diagonalize

bool	M_verbose
	Boolean that indicates if output is sent to cout. More...

bool	M_updated
	Boolean that indicates if the matrix is updated for the current iteration. More...

bool	M_reusePrec
	Boolean that indicates if the precond has to be recomputed. More...

bool	M_resetPreconditioner

Int	M_maxIterSolver
	Integer storing the max number of solver iteration with prec recomputing. More...

bool	M_recomputeMatrix
	Boolean that indicates if the matrix has to be recomputed. More...

TimeAdvanceBDF< vector_Type >	M_BDFIntraExtraPotential

Private Member Functions
UInt	potentialFESpaceDimension () const

Private Attributes
MatrixElemental	M_elmatStiff
	Elementary matrices. More...

MatrixElemental	M_elmatMass

Real	massCoeff

Type definitions
typedef HeartBidomainData	data_type

typedef Real(*	Function) (const Real &, const Real &, const Real &, const Real &, const ID &)

typedef std::function< Real(const Real &, const Real &, const Real &, const Real &, const ID &) >	source_Type

typedef Mesh	mesh_Type

typedef BCHandler	bchandlerRaw_Type

typedef SolverType::matrix_type	matrix_Type

typedef std::shared_ptr< matrix_Type >	matrixPtr_Type

typedef SolverType::vector_type	vector_Type

typedef SolverType::prec_raw_type	precRaw_Type

typedef SolverType::prec_type	prec_Type

Constructors & Destructor
	HeartBidomainSolver (const data_type &dataType, FESpace< Mesh, MapEpetra > &pFESpace, FESpace< Mesh, MapEpetra > &uFESpace, BCHandler &bcHandler, std::shared_ptr< Epetra_Comm > &comm)
	Constructor. More...

virtual	~HeartBidomainSolver ()
	Destructor. More...

Methods
virtual void	PDEiterate (bchandlerRaw_Type &bch)
	Updates sources, bc treatment and solve the bidomain system. More...

virtual void	setup (const GetPot &dataFile)
	Sets up the system solver. More...

virtual void	buildSystem ()
	Builds time independent parts of PDE system. More...

virtual void	updatePDESystem (Real alpha, vector_Type &sourceVec)
	Updates time dependent parts of PDE system. More...

virtual void	updatePDESystem (vector_Type &sourceVec)
	Updates time dependent parts of PDE system. More...

void	initialize (const source_Type &, const source_Type &)
	Initialize. More...

void	initialize (const Function &, const Function &)

void	initialize (const vector_Type &, const vector_Type &)

const vector_Type &	solutionTransmembranePotential () const
	Returns the local solution vector. More...

const vector_Type &	solutionExtraPotential () const

const vector_Type &	solutionIntraExtraPotential () const

const vector_Type &	solutionTransmembranePotentialExtrapolated () const

const vector_Type &	fiberVector () const

const vector_Type &	residual () const
	Returns the local residual vector. More...

FESpace< Mesh, MapEpetra > &	potentialFESpace ()
	Returns u FE space. More...

void	setBC (BCHandler &BCh_u)
	Sets Bidomain BCs. More...

void	resetPreconditioner ()

Epetra_Map const &	getRepeatedMapEpetra () const
	Return maps getMap. More...

Epetra_Map const &	getRepeatedMapEpetraVec () const

MapEpetra const &	getMap () const

void	recomputeMatrix (bool const recomp)

matrix_Type &	matrMass ()

TimeAdvanceBDF< vector_Type > &	BDFIntraExtraPotential ()

Detailed Description

template<typename Mesh, typename SolverType = LifeV::SolverAztecOO>
class LifeV::HeartBidomainSolver< Mesh, SolverType >

Definition at line 67 of file HeartBidomainSolver.hpp.

Member Typedef Documentation

◆ data_type

typedef HeartBidomainData data_type

Definition at line 74 of file HeartBidomainSolver.hpp.

◆ Function

typedef Real( * Function) (const Real &, const Real &, const Real &, const Real &, const ID &)

Definition at line 76 of file HeartBidomainSolver.hpp.

◆ source_Type

typedef std::function< Real ( const Real&, const Real&, const Real&, const Real&, const ID& ) > source_Type

Definition at line 79 of file HeartBidomainSolver.hpp.

◆ mesh_Type

typedef Mesh mesh_Type

Definition at line 81 of file HeartBidomainSolver.hpp.

◆ bchandlerRaw_Type

typedef BCHandler bchandlerRaw_Type

Definition at line 83 of file HeartBidomainSolver.hpp.

◆ matrix_Type

typedef SolverType::matrix_type matrix_Type

Definition at line 86 of file HeartBidomainSolver.hpp.

◆ matrixPtr_Type

typedef std::shared_ptr<matrix_Type> matrixPtr_Type

Definition at line 87 of file HeartBidomainSolver.hpp.

◆ vector_Type

typedef SolverType::vector_type vector_Type

Definition at line 88 of file HeartBidomainSolver.hpp.

◆ precRaw_Type

typedef SolverType::prec_raw_type precRaw_Type

Definition at line 90 of file HeartBidomainSolver.hpp.

◆ prec_Type

typedef SolverType::prec_type prec_Type

Definition at line 91 of file HeartBidomainSolver.hpp.

Constructor & Destructor Documentation

◆ HeartBidomainSolver()

HeartBidomainSolver	(	const data_type &	dataType,
		FESpace< Mesh, MapEpetra > &	pFESpace,
		FESpace< Mesh, MapEpetra > &	uFESpace,
		BCHandler &	bcHandler,
		std::shared_ptr< Epetra_Comm > &	comm
	)

Constructor.

Constructors.

Parameters

dataType
potential	FE space
bcHandler	boundary conditions for potential
Epetra	communicator

Definition at line 332 of file HeartBidomainSolver.hpp.

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◆ ~HeartBidomainSolver()

~HeartBidomainSolver ( )

virtual

Destructor.

Definition at line 407 of file HeartBidomainSolver.hpp.

Member Function Documentation

◆ PDEiterate()

void PDEiterate ( bchandlerRaw_Type & bch )

virtual

Updates sources, bc treatment and solve the bidomain system.

Solving the system

Definition at line 750 of file HeartBidomainSolver.hpp.

◆ setup()

void setup ( const GetPot & dataFile )

virtual

Sets up the system solver.

Definition at line 412 of file HeartBidomainSolver.hpp.

◆ buildSystem()

void buildSystem ( )

virtual

Builds time independent parts of PDE system.

Elementary computation and matrix assembling Loop on elements

Computing 1.0/dt * M + K

Definition at line 426 of file HeartBidomainSolver.hpp.

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◆ updatePDESystem() [1/2]

void updatePDESystem	(	Real	alpha,
		vector_Type &	sourceVec
	)

virtual

Updates time dependent parts of PDE system.

Definition at line 680 of file HeartBidomainSolver.hpp.

◆ updatePDESystem() [2/2]

void updatePDESystem ( vector_Type & sourceVec )

virtual

Updates time dependent parts of PDE system.

Definition at line 729 of file HeartBidomainSolver.hpp.

◆ initialize() [1/3]

void initialize	(	const source_Type &	ui0,
		const source_Type &	ue0
	)

Initialize.

Definition at line 634 of file HeartBidomainSolver.hpp.

◆ initialize() [2/3]

void initialize	(	const Function &	ui0,
		const Function &	ue0
	)

Definition at line 647 of file HeartBidomainSolver.hpp.

◆ initialize() [3/3]

void initialize	(	const vector_Type &	ui0,
		const vector_Type &	ue0
	)

Definition at line 659 of file HeartBidomainSolver.hpp.

◆ solutionTransmembranePotential()

const vector_Type& solutionTransmembranePotential ( ) const

inline

Returns the local solution vector.

Definition at line 144 of file HeartBidomainSolver.hpp.

◆ solutionExtraPotential()

const vector_Type& solutionExtraPotential ( ) const

inline

Definition at line 148 of file HeartBidomainSolver.hpp.

◆ solutionIntraExtraPotential()

const vector_Type& solutionIntraExtraPotential ( ) const

inline

Definition at line 152 of file HeartBidomainSolver.hpp.

◆ solutionTransmembranePotentialExtrapolated()

const vector_Type& solutionTransmembranePotentialExtrapolated ( ) const

inline

Definition at line 156 of file HeartBidomainSolver.hpp.

◆ fiberVector()

const vector_Type& fiberVector ( ) const

inline

Definition at line 160 of file HeartBidomainSolver.hpp.

◆ residual()

const vector_Type& residual ( ) const

inline

Returns the local residual vector.

Definition at line 166 of file HeartBidomainSolver.hpp.

◆ potentialFESpace()

FESpace<Mesh, MapEpetra>& potentialFESpace ( )

inline

Returns u FE space.

Definition at line 172 of file HeartBidomainSolver.hpp.

◆ setBC()

void setBC ( BCHandler & BCh_u )

inline

Sets Bidomain BCs.

Definition at line 178 of file HeartBidomainSolver.hpp.

◆ resetPreconditioner()

void resetPreconditioner ( )

inline

Definition at line 184 of file HeartBidomainSolver.hpp.

◆ getRepeatedMapEpetra()

Epetra_Map const& getRepeatedMapEpetra ( ) const

inline

Return maps getMap.

Definition at line 190 of file HeartBidomainSolver.hpp.

◆ getRepeatedMapEpetraVec()

Epetra_Map const& getRepeatedMapEpetraVec ( ) const

inline

Definition at line 195 of file HeartBidomainSolver.hpp.

◆ getMap()

MapEpetra const& getMap ( ) const

inline

Definition at line 200 of file HeartBidomainSolver.hpp.

◆ recomputeMatrix()

void recomputeMatrix ( bool const recomp )

inline

Definition at line 205 of file HeartBidomainSolver.hpp.

◆ matrMass()

matrix_Type& matrMass ( )

inline

Definition at line 210 of file HeartBidomainSolver.hpp.

◆ BDFIntraExtraPotential()

TimeAdvanceBDF<vector_Type>& BDFIntraExtraPotential ( )

inline

Definition at line 215 of file HeartBidomainSolver.hpp.

◆ solveSystem()

void solveSystem	(	matrixPtr_Type	matrFull,
		vector_Type &	rhsFull
	)

protected

Solves PDE system.

Definition at line 792 of file HeartBidomainSolver.hpp.

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◆ applyBoundaryConditions()

void applyBoundaryConditions	(	matrix_Type &	matrix,
		vector_Type &	rhs,
		bchandlerRaw_Type &	BCh
	)

protected

Apply BC.

Definition at line 890 of file HeartBidomainSolver.hpp.

◆ computeMean()

Real computeMean ( vector_Type & x )

protected

compute mean of vector x

Definition at line 919 of file HeartBidomainSolver.hpp.

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◆ removeValue()

void removeValue	(	vector_Type &	x,
		Real &	value
	)

protected

removes a scalar from each entry of vector x

Definition at line 927 of file HeartBidomainSolver.hpp.

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◆ potentialFESpaceDimension()

UInt potentialFESpaceDimension ( ) const

inlineprivate

Definition at line 317 of file HeartBidomainSolver.hpp.

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Field Documentation

◆ M_data

const data_type& M_data

protected

Data.

Definition at line 240 of file HeartBidomainSolver.hpp.

◆ M_pFESpace

FESpace<Mesh, MapEpetra>& M_pFESpace

protected

u FE space

Definition at line 243 of file HeartBidomainSolver.hpp.

◆ M_uFESpace

FESpace<Mesh, MapEpetra>& M_uFESpace

protected

Definition at line 244 of file HeartBidomainSolver.hpp.

◆ M_comm

const std::shared_ptr<Epetra_Comm> M_comm

protected

MPI communicator.

Definition at line 247 of file HeartBidomainSolver.hpp.

◆ M_me

Int M_me

protected

Definition at line 248 of file HeartBidomainSolver.hpp.

◆ M_BCh_electric

BCHandler* M_BCh_electric

protected

Bidomain BC.

Definition at line 251 of file HeartBidomainSolver.hpp.

◆ M_setBC

bool M_setBC

protected

Definition at line 252 of file HeartBidomainSolver.hpp.

◆ M_localMap

MapEpetra M_localMap

protected

Map.

Definition at line 255 of file HeartBidomainSolver.hpp.

◆ M_localMap_u

MapEpetra M_localMap_u

protected

Definition at line 256 of file HeartBidomainSolver.hpp.

◆ M_localMapVec

MapEpetra M_localMapVec

protected

Definition at line 257 of file HeartBidomainSolver.hpp.

◆ M_matrMass

matrixPtr_Type M_matrMass

protected

mass matrix

Definition at line 260 of file HeartBidomainSolver.hpp.

◆ M_matrStiff

matrixPtr_Type M_matrStiff

protected

Stiff matrix: D*stiff.

Definition at line 263 of file HeartBidomainSolver.hpp.

◆ M_matrNoBC

matrixPtr_Type M_matrNoBC

protected

Definition at line 265 of file HeartBidomainSolver.hpp.

◆ M_rhsNoBC

vector_Type M_rhsNoBC

protected

Right hand side for the PDE.

Definition at line 268 of file HeartBidomainSolver.hpp.

◆ M_solutionIntraExtraPotential

vector_Type M_solutionIntraExtraPotential

protected

Global solution _u.

Definition at line 271 of file HeartBidomainSolver.hpp.

◆ M_solutionTransmembranePotential

vector_Type M_solutionTransmembranePotential

protected

Definition at line 273 of file HeartBidomainSolver.hpp.

◆ M_solutionExtraPotential

vector_Type M_solutionExtraPotential

protected

Definition at line 275 of file HeartBidomainSolver.hpp.

◆ M_solutionIntraExtraPotentialExtrapolated

vector_Type M_solutionIntraExtraPotentialExtrapolated

protected

Definition at line 277 of file HeartBidomainSolver.hpp.

◆ M_solutionTransmembranePotentialExtrapolated

vector_Type M_solutionTransmembranePotentialExtrapolated

protected

Definition at line 279 of file HeartBidomainSolver.hpp.

◆ M_fiberVector

vector_Type M_fiberVector

protected

Local fibers vector.

Definition at line 282 of file HeartBidomainSolver.hpp.

◆ M_residual

vector_Type M_residual

protected

residual

Definition at line 285 of file HeartBidomainSolver.hpp.

◆ M_linearSolver

SolverType M_linearSolver

protected

Solver.

Definition at line 288 of file HeartBidomainSolver.hpp.

◆ M_prec

prec_Type M_prec

protected

Definition at line 290 of file HeartBidomainSolver.hpp.

◆ M_diagonalize

Real M_diagonalize

protected

Definition at line 292 of file HeartBidomainSolver.hpp.

◆ M_verbose

bool M_verbose

protected

Boolean that indicates if output is sent to cout.

Definition at line 295 of file HeartBidomainSolver.hpp.

◆ M_updated

bool M_updated

protected

Boolean that indicates if the matrix is updated for the current iteration.

Definition at line 298 of file HeartBidomainSolver.hpp.

◆ M_reusePrec

bool M_reusePrec

protected

Boolean that indicates if the precond has to be recomputed.

Definition at line 301 of file HeartBidomainSolver.hpp.

◆ M_resetPreconditioner

bool M_resetPreconditioner

protected

Definition at line 302 of file HeartBidomainSolver.hpp.

◆ M_maxIterSolver

Int M_maxIterSolver

protected

Integer storing the max number of solver iteration with prec recomputing.

Definition at line 305 of file HeartBidomainSolver.hpp.

◆ M_recomputeMatrix

bool M_recomputeMatrix

protected

Boolean that indicates if the matrix has to be recomputed.

Definition at line 308 of file HeartBidomainSolver.hpp.

◆ M_BDFIntraExtraPotential

TimeAdvanceBDF<vector_Type> M_BDFIntraExtraPotential

protected

Definition at line 310 of file HeartBidomainSolver.hpp.

◆ M_elmatStiff

MatrixElemental M_elmatStiff

private

Elementary matrices.

Definition at line 314 of file HeartBidomainSolver.hpp.

◆ M_elmatMass

MatrixElemental M_elmatMass

private

Definition at line 315 of file HeartBidomainSolver.hpp.

◆ massCoeff

Real massCoeff

private

Definition at line 316 of file HeartBidomainSolver.hpp.

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

HeartBidomainSolver.hpp

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Type definitions

Constructors & Destructor

Methods

Detailed Description

template<typename Mesh, typename SolverType = LifeV::SolverAztecOO> class LifeV::HeartBidomainSolver< Mesh, SolverType >

Member Typedef Documentation

◆ data_type

◆ Function

◆ source_Type

◆ mesh_Type

◆ bchandlerRaw_Type

◆ matrix_Type

◆ matrixPtr_Type

◆ vector_Type

◆ precRaw_Type

◆ prec_Type

Constructor & Destructor Documentation

◆ HeartBidomainSolver()

◆ ~HeartBidomainSolver()

Member Function Documentation

◆ PDEiterate()

◆ setup()

◆ buildSystem()

◆ updatePDESystem() [1/2]

◆ updatePDESystem() [2/2]

◆ initialize() [1/3]

◆ initialize() [2/3]

◆ initialize() [3/3]

◆ solutionTransmembranePotential()

◆ solutionExtraPotential()

◆ solutionIntraExtraPotential()

◆ solutionTransmembranePotentialExtrapolated()

◆ fiberVector()

◆ residual()

◆ potentialFESpace()

◆ setBC()

◆ resetPreconditioner()

◆ getRepeatedMapEpetra()

◆ getRepeatedMapEpetraVec()

◆ getMap()

◆ recomputeMatrix()

◆ matrMass()

◆ BDFIntraExtraPotential()

◆ solveSystem()

◆ applyBoundaryConditions()

◆ computeMean()

◆ removeValue()

◆ potentialFESpaceDimension()

Field Documentation

◆ M_data

◆ M_pFESpace

◆ M_uFESpace

◆ M_comm

◆ M_me

◆ M_BCh_electric

◆ M_setBC

◆ M_localMap

◆ M_localMap_u

◆ M_localMapVec

◆ M_matrMass

◆ M_matrStiff

◆ M_matrNoBC

◆ M_rhsNoBC

◆ M_solutionIntraExtraPotential

◆ M_solutionTransmembranePotential

◆ M_solutionExtraPotential

◆ M_solutionIntraExtraPotentialExtrapolated

◆ M_solutionTransmembranePotentialExtrapolated

◆ M_fiberVector

◆ M_residual

◆ M_linearSolver

◆ M_prec

◆ M_diagonalize

◆ M_verbose

◆ M_updated

◆ M_reusePrec

template<typename Mesh, typename SolverType = LifeV::SolverAztecOO>
class LifeV::HeartBidomainSolver< Mesh, SolverType >