BidomainSolver - Class featuring the usual solver for bidomain equations. More...

#include <ElectroETABidomainSolver.hpp>

Collaboration diagram for ElectroETABidomainSolver< Mesh, IonicModel >:

Protected Member Functions
void	importFibers (vectorPtr_Type M_fiberPtr, std::string fibersFile, meshPtr_Type M_localMeshPtr)

Private Member Functions
void	setParameters ()

void	init ()

void	init (commPtr_Type comm)

void	init (meshPtr_Type meshPtr)

void	init (ionicModelPtr_Type model)

void	init (commPtr_Type comm, ionicModelPtr_Type model)

void	init (meshPtr_Type meshPtr, ionicModelPtr_Type model)

Private Attributes
Real	M_surfaceVolumeRatio

ionicModelPtr_Type	M_ionicModelPtr

commPtr_Type	M_commPtr

meshPtr_Type	M_localMeshPtr

meshPtr_Type	M_fullMeshPtr

ETFESpacePtr_Type	M_ETFESpacePtr

feSpacePtr_Type	M_feSpacePtr

blockMatrixPtr_Type	M_massMatrixPtr

blockMatrixPtr_Type	M_stiffnessMatrixPtr

blockMatrixPtr_Type	M_globalMatrixPtr

Real	M_initialTime

Real	M_endTime

Real	M_timeStep

VectorSmall< 3 >	M_diffusionTensorIntra

VectorSmall< 3 >	M_diffusionTensorExtra

blockVectorPtr_Type	M_rhsPtr

blockVectorPtr_Type	M_rhsPtrUnique

blockVectorPtr_Type	M_potentialGlobalPtr

vectorPtr_Type	M_potentialTransPtr

vectorPtr_Type	M_potentialExtraPtr

linearSolverPtr_Type	M_linearSolverPtr

vectorOfPtr_Type	M_globalSolution

vectorOfPtr_Type	M_globalRhs

std::string	M_elementsOrder

vectorPtr_Type	M_fiberPtr

vectorPtr_Type	M_displacementPtr

matrixSmall_Type	M_identity

ETFESpaceVectorialPtr_Type	M_displacementETFESpacePtr

bool	M_lumpedMassMatrix

Type definitions
Bidomain Solver The Bidomain equation reads
typedef Mesh	mesh_Type

typedef std::shared_ptr< mesh_Type >	meshPtr_Type

typedef VectorEpetra	vector_Type

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef VectorEpetraStructured	blockVector_Type

typedef std::shared_ptr< blockVector_Type >	blockVectorPtr_Type

typedef std::vector< vectorPtr_Type >	vectorOfPtr_Type

typedef MatrixEpetra< Real >	matrix_Type

typedef std::shared_ptr< matrix_Type >	matrixPtr_Type

typedef MatrixEpetraStructured< Real >	blockMatrix_Type

typedef std::shared_ptr< blockMatrix_Type >	blockMatrixPtr_Type

typedef Epetra_Comm	comm_Type

typedef std::shared_ptr< comm_Type >	commPtr_Type

typedef ETFESpace< mesh_Type, MapEpetra, 3, 1 >	ETFESpace_Type

typedef std::shared_ptr< ETFESpace< mesh_Type, MapEpetra, 3, 1 > >	ETFESpacePtr_Type

typedef ETFESpace< mesh_Type, MapEpetra, 3, 3 >	ETFESpaceVectorial_Type

typedef std::shared_ptr< ETFESpaceVectorial_Type >	ETFESpaceVectorialPtr_Type

typedef FESpace< mesh_Type, MapEpetra >	feSpace_Type

typedef std::shared_ptr< feSpace_Type >	feSpacePtr_Type

typedef LinearSolver	linearSolver_Type

typedef std::shared_ptr< LinearSolver >	linearSolverPtr_Type

typedef Exporter< mesh_Type >	IOFile_Type

typedef std::shared_ptr< IOFile_Type >	IOFilePtr_Type

typedef ExporterData< mesh_Type >	IOData_Type

typedef ExporterEnsight< mesh_Type >	ensightIOFile_Type

typedef ExporterHDF5< mesh_Type >	hdf5IOFile_Type

typedef LifeV::Preconditioner	basePrec_Type

typedef std::shared_ptr< basePrec_Type >	basePrecPtr_Type

typedef LifeV::PreconditionerML	prec_Type

typedef std::shared_ptr< prec_Type >	precPtr_Type

typedef IonicModel	ionicModel_Type

typedef ElectroIonicModel	superIonicModel

typedef std::shared_ptr< ionicModel_Type >	ionicModelPtr_Type

typedef Teuchos::ParameterList	list_Type

typedef std::function< Real(const Real &t, const Real &x, const Real &y, const Real &z, const ID &i) >	function_Type

typedef MatrixSmall< 3, 3 >	matrixSmall_Type

Constructors & Destructor
	ElectroETABidomainSolver ()
	Empty Constructor. More...

	ElectroETABidomainSolver (list_Type list, GetPot &dataFile, ionicModelPtr_Type model)
	Constructor. More...

	ElectroETABidomainSolver (GetPot &dataFile, ionicModelPtr_Type model, meshPtr_Type meshPtr)
	Constructor. More...

	ElectroETABidomainSolver (list_Type list, GetPot &dataFile, ionicModelPtr_Type model, commPtr_Type comm)
	Constructor. More...

	ElectroETABidomainSolver (list_Type list, GetPot &dataFile, ionicModelPtr_Type model, meshPtr_Type meshPtr)
	Constructor. More...

	ElectroETABidomainSolver (std::string meshName, std::string meshPath, GetPot &dataFile, ionicModelPtr_Type model)
	Constructor. More...

	ElectroETABidomainSolver (std::string meshName, std::string meshPath, GetPot &dataFile, ionicModelPtr_Type model, commPtr_Type comm)
	Constructor. More...

	ElectroETABidomainSolver (const ElectroETABidomainSolver &solver)
	Copy Constructor. More...

ElectroETABidomainSolver< Mesh, IonicModel > &	operator= (const ElectroETABidomainSolver &solver)
	Operator=() More...

virtual	~ElectroETABidomainSolver ()
	Destructor. More...

Get Methods
const Real &	surfaceVolumeRatio () const
	get the surface to volume ratio More...

const Real &	initialTime () const
	get the initial time (by default 0) More...

const Real &	timeStep () const
	get the final time More...

const Real &	endTime () const
	get the time step More...

const VectorSmall< 3 > &	diffusionTensorIntra () const
	get the diagonal intra cellular diffusion tensor More...

const VectorSmall< 3 > &	diffusionTensorExtra () const
	get the diagonal extra cellular diffusion tensor More...

const std::string	elementsOrder () const
	get the order of the elements More...

const ionicModelPtr_Type	ionicModelPtr () const
	get the pointer to the ionic model More...

const commPtr_Type	commPtr () const
	get the pointer to the Epetra communicator More...

const meshPtr_Type	localMeshPtr () const
	get the pointer to the partitioned mesh More...

const meshPtr_Type	fullMeshPtr () const
	get the pointer to the partitioned mesh More...

const ETFESpacePtr_Type	ETFESpacePtr () const
	get the pointer to the ETA finite element space More...

const feSpacePtr_Type	feSpacePtr () const
	get the pointer to the usual finite element space More...

const blockMatrixPtr_Type	massMatrixPtr () const
	get the pointer to the mass matrix More...

const blockMatrixPtr_Type	stiffnessMatrixPtr () const
	get the pointer to the stiffness matrix More...

const blockMatrixPtr_Type	globalMatrixPtr () const
	get the pointer to the global matrix More...

const blockVectorPtr_Type	rhsPtr () const
	get the pointer to the right hand side More...

const blockVectorPtr_Type	rhsPtrUnique () const
	get the pointer to the unique version of the right hand side More...

const vectorPtr_Type	potentialTransPtr () const
	get the pointer to the transmembrane potential More...

blockVectorPtr_Type	potentialGlobalPtr ()
	get the pointer to the potential More...

const vectorPtr_Type	potentialExtraPtr () const
	get the pointer to the extra cellular potential More...

const vectorPtr_Type	fiberPtr () const
	get the pointer to the fiber vector More...

const vectorPtr_Type	appliedCurrentIntraPtr ()
	get the pointer to the applied intra cellular current vector More...

const linearSolverPtr_Type	linearSolverPtr () const
	get the pointer to the linear solver More...

const vectorOfPtr_Type &	globalSolution () const
	get the pointer to the vector of pointers containing the transmembrane potential (at 0) and the gating variables More...

const vectorOfPtr_Type &	globalRhs () const
	get the pointer to the vector of pointers containing the rhs for transmembrane potential (at 0) and the gating variables More...

vectorPtr_Type	displacementPtr () const
	get the pointer to the transmembrane potential More...

ETFESpaceVectorialPtr_Type	displacementETFESpacePtr () const

bool	lumpedMassMatrix () const

Set Methods
void	setSurfaceVolumeRatio (const Real &p)
	set the surface to volume ratio More...

void	setInitialTime (const Real &p)
	set the starting time More...

void	setTimeStep (const Real &p)
	set the ending time More...

void	setEndTime (const Real &p)
	set the time step More...

void	setDiffusionTensorIntra (const VectorSmall< 3 > &p)
	set the intra cellular diagonal diffusion tensor More...

void	setDiffusionTensorExtra (const VectorSmall< 3 > &p)
	set the extra cellular diagonal diffusion tensor More...

void	setIonicModelPtr (const ionicModelPtr_Type p)
	set the pointer to the ionic model More...

void	setCommPtr (const commPtr_Type p)
	set the pointer to the Epetra communicator More...

void	setLocalMeshPtr (const meshPtr_Type p)
	set the pointer to the partitioned mesh More...

void	setFullMeshPtr (const meshPtr_Type p)
	set the pointer to the partitioned mesh More...

void	setETFESpacePtr (const ETFESpacePtr_Type p)
	set the pointer to the ETA fe space More...

void	setFeSpacePtr (const feSpacePtr_Type p)
	set the pointer to the usual fe space More...

void	setMassMatrixPtr (const blockMatrixPtr_Type p)
	set the pointer to the mass matrix More...

void	setStiffnessMatrixPtr (const blockMatrixPtr_Type p)
	set the pointer to the stiffness matrix More...

void	setGlobalMatrixPtr (const blockMatrixPtr_Type p)
	set the pointer to the global matrix More...

void	setRhsPtr (const blockVectorPtr_Type p)
	set the pointer to the right hand side More...

void	setRhsPtrUnique (const blockVectorPtr_Type p)
	set the pointer to the unique version of the right hand side More...

void	setPotentialExtraPtr (const vectorPtr_Type p)

void	setPotentialTransPtr (const vectorPtr_Type p)

void	setAppliedCurrentIntraPtr (const vectorPtr_Type p)
	set the pointer to the intra cell applied current vector More...

void	setLinearSolverPtr (const linearSolverPtr_Type p)
	set the pointer to the linear solver More...

void	setGlobalSolution (const vectorOfPtr_Type &p)
	set the vector of pointers containing the transmembrane potential (at 0) and the gating variables More...

void	setGlobalRhs (const vectorOfPtr_Type &p)
	set the vector of pointers containing the rhs for the transmembrane potential (at 0) and the gating variables More...

void	setFiberPtr (const vectorPtr_Type p)
	set the pointer to the fiber direction vector More...

void	setDisplacementPtr (const vectorPtr_Type p)
	set the pointer to displacement of the tissue More...

Copy Methods
void	setIonicModel (const ionicModel_Type &p)

void	setComm (const comm_Type &p)

void	setLocalMesh (const mesh_Type &p)

void	setFullMesh (const mesh_Type &p)

void	setETFESpace (const ETFESpace_Type &p)

void	setFeSpace (const feSpace_Type &p)

void	setMassMatrix (const matrix_Type &p)

void	setStiffnessMatrix (const matrix_Type &p)

void	setGlobalMatrix (const matrix_Type &p)

void	setRhs (const vector_Type &p)

void	setRhsUnique (const vector_Type &p)

void	setPotentialTrans (const vector_Type &p)

void	setPotentialExtra (const blockVector_Type &p)

void	setFiber (const vector_Type &p)

void	setDisplacement (const vector_Type &p)

void	setAppliedCurrentIntra (const vector_Type &p)

void	setLinearSolver (const linearSolver_Type &p)

void	copyGlobalSolution (const vectorOfPtr_Type &p)

void	setVariablePtr (const vectorPtr_Type p, int j)

void	copyGlobalRhs (const vectorOfPtr_Type &p)

void	setLumpedMassMatrix (bool p) const

Methods
void	setup (GetPot &dataFile, short int ionicSize)

void	setup (std::string meshName, std::string meshPath, GetPot &dataFile, short int ionicSize)

void	setupMassMatrix ()
	create mass matrix More...

void	setupMassMatrix (vector_Type &disp)
	create mass matrix More...

void	setupLumpedMassMatrix ()
	create mass matrix More...

void	setupLumpedMassMatrix (vector_Type &disp)

void	setupStiffnessMatrix ()
	create stiffness matrix More...

void	setupStiffnessMatrix (vectorPtr_Type disp)
	create stiffness matrix in a moving domain More...

void	setupStiffnessMatrix (VectorSmall< 3 > diffusionIntra, VectorSmall< 3 > diffusionExtra)
	create stiffness matrix given a diagonal diffusion tensor More...

void	setupGlobalMatrix ()
	create stiffness matrix given the fiber direction and a diagonal diffusion tensor More...

void	setupLinearSolver (GetPot dataFile)
	setup the linear solver More...

void	setupLinearSolver (GetPot dataFile, list_Type list)
	setup the linear solver More...

void	initializePotential ()
	Initialize the potentials to zero. More...

void	initializePotentialTrans (Real k)
	Initialize the potential to the value k. More...

void	initializePotentialExtra (Real k)

void	initializeAppliedCurrentIntra ()
	Initialize the applied current to zero. More...

void	initializeAppliedCurrentIntra (Real k)
	Initialize the intra cellular applied current to the value k. More...

void	setupGlobalSolution (short int ionicSize)
	creates a vector of pointers to store the solution More...

void	setupGlobalRhs (short int ionicSize)
	creates a vector of pointers to store the rhs More...

void	setParameters (list_Type list)
	Set parameters from an xml file. More...

void	partitionMesh (std::string meshName, std::string meshPath)
	partition the mesh More...

void	setPotentialFromFunctionTrans (function_Type &f, Real time=0.0)
	given a boost function initialize the transmembrane potential More...

void	setPotentialFromFunctionExtra (function_Type &f, Real time=0.0)
	given a boost function initialize the extra cellular potential More...

void	setAppliedCurrentFromFunctionIntra (function_Type &f, Real time=0.0)
	given a boost function initialize the applied intra cellular current More...

void	solveOneReactionStepFE (int subiterations=1)
	Solves one reaction step using the forward Euler scheme. More...

void	solveOneReactionStepFE (matrix_Type &mass, int subiterations=1)

void	solveOneReactionStepRL (int subiterations=1)

void	updateRhs ()
	Update the rhs. More...

void	solveOneDiffusionStepBDF2 (vectorPtr_Type previousPotentialGlobalPtr)
	Solves one diffusion step using the BDF2 scheme. More...

void	solveOneDiffusionStepBE ()
	Solves one diffusion step using the backward Euler scheme. More...

void	solveOneSplittingStep ()
	Solve one full step with operator splitting. More...

void	solveSplitting ()
	Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep. More...

void	solveOneSplittingStep (IOFile_Type &exporter, Real t)
	Solve one full step with operator splitting and export the solution. More...

void	solveSplitting (IOFile_Type &exporter)
	Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep and export the solution. More...

void	solveSplitting (IOFile_Type &exporter, Real dt)
	Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep and export the solution every dt. More...

void	setupPotentialExporter (IOFile_Type &exporter)
	add to a given exporter the pointer to the potential More...

void	setupPotentialExporter (IOFile_Type &exporter, std::string fileName)
	add to a given exporter the pointer to the potential saved with name fileName More...

void	setupExporter (IOFile_Type &exporter, std::string fileName="output", std::string folder="./")
	add to a given exporter the pointer to the potential and to the gating variables saved with name fileName More...

void	setupFibers ()
	Generates a default fiber direction (0,1,0) More...

void	setupFibers (VectorSmall< 3 > fibers)
	Generates the fiber direction given the three component of the vector (F_x,F_y,F_z) More...

void	setupFibers (std::string fibersFile)
	Imports the fiber direction from a hdf5 file. More...

void	setupFibers (std::string fibersFile, std::string directory, int format=0)
	Imports the fiber direction from a vtk file ( format = 0), or text file. More...

void	solveOneStepGatingVariablesFE ()
	Solves the gating variables with forward Euler. More...

void	solveOneStepGatingVariablesRL ()

void	computeRhsSVI ()
	Compute the rhs using state variable interpolation. More...

void	computeRhsICI ()
	Compute the rhs using ionic current interpolation. More...

void	computeRhsICI (matrix_Type &mass)

void	solveOneICIStep ()
	Solve one full step with ionic current interpolation. More...

void	solveOneICIStep (matrix_Type &mass)

void	solveOneSVIStep ()
	Solve one full step with ionic current interpolation. More...

void	solveICI ()
	solve system using ICI from M_initialTime to the M_endTime with time step M_timeStep More...

void	solveSVI ()
	solve system using SVI from M_initialTime to the M_endTime with time step M_timeStep More...

void	solveOneICIStep (IOFile_Type &exporter, Real t)
	Solve one full step with ionic current interpolation and export the solution. More...

void	solveOneSVIStep (IOFile_Type &exporter, Real t)
	Solve one full step with ionic current interpolation and export the solution. More...

void	solveICI (IOFile_Type &exporter)
	solve system using ICI from M_initialTime to the M_endTime with time step M_timeStep and export the solution More...

void	solveSVI (IOFile_Type &exporter)
	solve system using SVI from M_initialTime to the M_endTime with time step M_timeStep and export the solution More...

void	solveICI (IOFile_Type &exporter, Real dt)
	Solve the system using ICI from M_initialTime to the M_endTime with time step M_timeStep and export the solution every dt. More...

void	solveSVI (IOFile_Type &exporter, Real dt)
	Solve the using SVI from M_initialTime to the M_endTime with time step M_timeStep and export the solution every dt. More...

void	exportFiberDirection (std::string postDir="./")
	Generates a file where the fiber direction is saved. More...

void	exportFiberDirection (IOFile_Type &exporter)
	save the fiber direction into the given exporter More...

void	exportSolution (IOFile_Type &exporter, Real t)
	Save the solution in the exporter. More...

void	importSolution (GetPot &dataFile, std::string prefix, std::string postDir, Real time)
	Import solution. More...

void	setInitialConditions ()

void	registerActivationTime (vector_Type &activationTimeVector, Real time, Real threshold=0.0)
	save the fiber direction into the given exporter More...

Detailed Description

template<typename Mesh, typename IonicModel>
class LifeV::ElectroETABidomainSolver< Mesh, IonicModel >

BidomainSolver - Class featuring the usual solver for bidomain equations.

Definition at line 106 of file ElectroETABidomainSolver.hpp.

Member Typedef Documentation

◆ mesh_Type

typedef Mesh mesh_Type

Definition at line 121 of file ElectroETABidomainSolver.hpp.

◆ meshPtr_Type

typedef std::shared_ptr<mesh_Type> meshPtr_Type

Definition at line 122 of file ElectroETABidomainSolver.hpp.

◆ vector_Type

typedef VectorEpetra vector_Type

Definition at line 124 of file ElectroETABidomainSolver.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 125 of file ElectroETABidomainSolver.hpp.

◆ blockVector_Type

typedef VectorEpetraStructured blockVector_Type

Definition at line 127 of file ElectroETABidomainSolver.hpp.

◆ blockVectorPtr_Type

typedef std::shared_ptr<blockVector_Type> blockVectorPtr_Type

Definition at line 128 of file ElectroETABidomainSolver.hpp.

◆ vectorOfPtr_Type

typedef std::vector<vectorPtr_Type> vectorOfPtr_Type

Definition at line 130 of file ElectroETABidomainSolver.hpp.

◆ matrix_Type

typedef MatrixEpetra<Real> matrix_Type

Definition at line 134 of file ElectroETABidomainSolver.hpp.

◆ matrixPtr_Type

typedef std::shared_ptr<matrix_Type> matrixPtr_Type

Definition at line 135 of file ElectroETABidomainSolver.hpp.

◆ blockMatrix_Type

typedef MatrixEpetraStructured<Real> blockMatrix_Type

Definition at line 137 of file ElectroETABidomainSolver.hpp.

◆ blockMatrixPtr_Type

typedef std::shared_ptr<blockMatrix_Type> blockMatrixPtr_Type

Definition at line 138 of file ElectroETABidomainSolver.hpp.

◆ comm_Type

typedef Epetra_Comm comm_Type

Definition at line 140 of file ElectroETABidomainSolver.hpp.

◆ commPtr_Type

typedef std::shared_ptr<comm_Type> commPtr_Type

Definition at line 141 of file ElectroETABidomainSolver.hpp.

◆ ETFESpace_Type

typedef ETFESpace<mesh_Type, MapEpetra, 3, 1> ETFESpace_Type

Definition at line 143 of file ElectroETABidomainSolver.hpp.

◆ ETFESpacePtr_Type

typedef std::shared_ptr<ETFESpace<mesh_Type, MapEpetra, 3, 1> > ETFESpacePtr_Type

Definition at line 144 of file ElectroETABidomainSolver.hpp.

◆ ETFESpaceVectorial_Type

typedef ETFESpace<mesh_Type, MapEpetra, 3, 3> ETFESpaceVectorial_Type

Definition at line 146 of file ElectroETABidomainSolver.hpp.

◆ ETFESpaceVectorialPtr_Type

typedef std::shared_ptr<ETFESpaceVectorial_Type> ETFESpaceVectorialPtr_Type

Definition at line 147 of file ElectroETABidomainSolver.hpp.

◆ feSpace_Type

typedef FESpace<mesh_Type, MapEpetra> feSpace_Type

Definition at line 149 of file ElectroETABidomainSolver.hpp.

◆ feSpacePtr_Type

typedef std::shared_ptr<feSpace_Type> feSpacePtr_Type

Definition at line 150 of file ElectroETABidomainSolver.hpp.

◆ linearSolver_Type

typedef LinearSolver linearSolver_Type

Definition at line 152 of file ElectroETABidomainSolver.hpp.

◆ linearSolverPtr_Type

typedef std::shared_ptr<LinearSolver> linearSolverPtr_Type

Definition at line 153 of file ElectroETABidomainSolver.hpp.

◆ IOFile_Type

typedef Exporter<mesh_Type> IOFile_Type

Definition at line 156 of file ElectroETABidomainSolver.hpp.

◆ IOFilePtr_Type

typedef std::shared_ptr<IOFile_Type> IOFilePtr_Type

Definition at line 157 of file ElectroETABidomainSolver.hpp.

◆ IOData_Type

typedef ExporterData<mesh_Type> IOData_Type

Definition at line 158 of file ElectroETABidomainSolver.hpp.

◆ ensightIOFile_Type

typedef ExporterEnsight<mesh_Type> ensightIOFile_Type

Definition at line 159 of file ElectroETABidomainSolver.hpp.

◆ hdf5IOFile_Type

typedef ExporterHDF5< mesh_Type > hdf5IOFile_Type

Definition at line 161 of file ElectroETABidomainSolver.hpp.

◆ basePrec_Type

typedef LifeV::Preconditioner basePrec_Type

Definition at line 164 of file ElectroETABidomainSolver.hpp.

◆ basePrecPtr_Type

typedef std::shared_ptr<basePrec_Type> basePrecPtr_Type

Definition at line 165 of file ElectroETABidomainSolver.hpp.

◆ prec_Type

typedef LifeV::PreconditionerML prec_Type

Definition at line 166 of file ElectroETABidomainSolver.hpp.

◆ precPtr_Type

typedef std::shared_ptr<prec_Type> precPtr_Type

Definition at line 167 of file ElectroETABidomainSolver.hpp.

◆ ionicModel_Type

typedef IonicModel ionicModel_Type

Definition at line 169 of file ElectroETABidomainSolver.hpp.

◆ superIonicModel

typedef ElectroIonicModel superIonicModel

Definition at line 170 of file ElectroETABidomainSolver.hpp.

◆ ionicModelPtr_Type

typedef std::shared_ptr<ionicModel_Type> ionicModelPtr_Type

Definition at line 171 of file ElectroETABidomainSolver.hpp.

◆ list_Type

typedef Teuchos::ParameterList list_Type

Definition at line 173 of file ElectroETABidomainSolver.hpp.

◆ function_Type

typedef std::function< Real (const Real& t, const Real& x, const Real& y, const Real& z, const ID& i) > function_Type

Definition at line 177 of file ElectroETABidomainSolver.hpp.

◆ matrixSmall_Type

typedef MatrixSmall<3, 3> matrixSmall_Type

Definition at line 179 of file ElectroETABidomainSolver.hpp.

Constructor & Destructor Documentation

◆ ElectroETABidomainSolver() [1/8]

ElectroETABidomainSolver ( )

Empty Constructor.

Constructors.

Definition at line 1093 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [2/8]

ElectroETABidomainSolver	(	list_Type	list,
		GetPot &	dataFile,
		ionicModelPtr_Type	model
	)

Constructor.

Parameters

Teuchos::ParameterList	parameter list
GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer

Definition at line 1100 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [3/8]

ElectroETABidomainSolver	(	GetPot &	dataFile,
		ionicModelPtr_Type	model,
		meshPtr_Type	meshPtr
	)

Constructor.

Parameters

GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer
std::shared_ptr<Mesh>	Pointer to the partitioned mesh

Definition at line 1152 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [4/8]

ElectroETABidomainSolver	(	list_Type	list,
		GetPot &	dataFile,
		ionicModelPtr_Type	model,
		commPtr_Type	comm
	)

Constructor.

Parameters

Teuchos::ParameterList	parameter list
GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer
std::shared_ptr<Epetra_Comm>	Epetra communicator

Definition at line 1110 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [5/8]

ElectroETABidomainSolver	(	list_Type	list,
		GetPot &	dataFile,
		ionicModelPtr_Type	model,
		meshPtr_Type	meshPtr
	)

Constructor.

Parameters

Teuchos::ParameterList	parameter list
GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer
std::shared_ptr<Mesh>	Pointer to the partitioned mesh

Definition at line 1121 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [6/8]

ElectroETABidomainSolver	(	std::string	meshName,
		std::string	meshPath,
		GetPot &	dataFile,
		ionicModelPtr_Type	model
	)

Constructor.

Parameters

string	file name of the mesh
string	path to the mesh
GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer

Definition at line 1131 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [7/8]

ElectroETABidomainSolver	(	std::string	meshName,
		std::string	meshPath,
		GetPot &	dataFile,
		ionicModelPtr_Type	model,
		commPtr_Type	comm
	)

Constructor.

Parameters

string	file name of the mesh
string	path to the mesh
GetPot	datafile (for preconditioner)
std::shared_ptr<IonicModel>	chosen ionic model pointer
std::shared_ptr<Epetra_Comm>	Epetra communicator

Definition at line 1141 of file ElectroETABidomainSolver.hpp.

◆ ElectroETABidomainSolver() [8/8]

ElectroETABidomainSolver ( const ElectroETABidomainSolver< Mesh, IonicModel > & solver )

Copy Constructor.

Parameters

ElectroETABidomainSolver object

Definition at line 1162 of file ElectroETABidomainSolver.hpp.

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◆ ~ElectroETABidomainSolver()

virtual ~ElectroETABidomainSolver ( )

inlinevirtual

Destructor.

Definition at line 272 of file ElectroETABidomainSolver.hpp.

Member Function Documentation

◆ operator=()

ElectroETABidomainSolver< Mesh, IonicModel > & operator= ( const ElectroETABidomainSolver< Mesh, IonicModel > & solver )

Operator=()

Parameters

ElectroETABidomainSolver object

Definition at line 1197 of file ElectroETABidomainSolver.hpp.

◆ surfaceVolumeRatio()

const Real& surfaceVolumeRatio ( ) const

inline

get the surface to volume ratio

Not used in the code ( implicit definition inside the diffusion tensor)

Definition at line 285 of file ElectroETABidomainSolver.hpp.

◆ initialTime()

const Real& initialTime ( ) const

inline

get the initial time (by default 0)

Definition at line 291 of file ElectroETABidomainSolver.hpp.

◆ timeStep()

const Real& timeStep ( ) const

inline

get the final time

Definition at line 296 of file ElectroETABidomainSolver.hpp.

◆ endTime()

const Real& endTime ( ) const

inline

get the time step

Definition at line 301 of file ElectroETABidomainSolver.hpp.

◆ diffusionTensorIntra()

const VectorSmall<3>& diffusionTensorIntra ( ) const

inline

get the diagonal intra cellular diffusion tensor

Definition at line 306 of file ElectroETABidomainSolver.hpp.

◆ diffusionTensorExtra()

const VectorSmall<3>& diffusionTensorExtra ( ) const

inline

get the diagonal extra cellular diffusion tensor

Definition at line 311 of file ElectroETABidomainSolver.hpp.

◆ elementsOrder()

const std::string elementsOrder ( ) const

inline

get the order of the elements

Definition at line 316 of file ElectroETABidomainSolver.hpp.

◆ ionicModelPtr()

const ionicModelPtr_Type ionicModelPtr ( ) const

inline

get the pointer to the ionic model

Definition at line 321 of file ElectroETABidomainSolver.hpp.

◆ commPtr()

const commPtr_Type commPtr ( ) const

inline

get the pointer to the Epetra communicator

Definition at line 326 of file ElectroETABidomainSolver.hpp.

◆ localMeshPtr()

const meshPtr_Type localMeshPtr ( ) const

inline

get the pointer to the partitioned mesh

Definition at line 331 of file ElectroETABidomainSolver.hpp.

◆ fullMeshPtr()

const meshPtr_Type fullMeshPtr ( ) const

inline

get the pointer to the partitioned mesh

Definition at line 336 of file ElectroETABidomainSolver.hpp.

◆ ETFESpacePtr()

const ETFESpacePtr_Type ETFESpacePtr ( ) const

inline

get the pointer to the ETA finite element space

Definition at line 341 of file ElectroETABidomainSolver.hpp.

◆ feSpacePtr()

const feSpacePtr_Type feSpacePtr ( ) const

inline

get the pointer to the usual finite element space

Definition at line 346 of file ElectroETABidomainSolver.hpp.

◆ massMatrixPtr()

const blockMatrixPtr_Type massMatrixPtr ( ) const

inline

get the pointer to the mass matrix

Definition at line 351 of file ElectroETABidomainSolver.hpp.

◆ stiffnessMatrixPtr()

const blockMatrixPtr_Type stiffnessMatrixPtr ( ) const

inline

get the pointer to the stiffness matrix

Definition at line 356 of file ElectroETABidomainSolver.hpp.

◆ globalMatrixPtr()

const blockMatrixPtr_Type globalMatrixPtr ( ) const

inline

get the pointer to the global matrix

$A = \frac{M}{\Delta t} + K(\mathbf{f})$

Definition at line 367 of file ElectroETABidomainSolver.hpp.

◆ rhsPtr()

const blockVectorPtr_Type rhsPtr ( ) const

inline

get the pointer to the right hand side

Definition at line 372 of file ElectroETABidomainSolver.hpp.

◆ rhsPtrUnique()

const blockVectorPtr_Type rhsPtrUnique ( ) const

inline

get the pointer to the unique version of the right hand side

Definition at line 377 of file ElectroETABidomainSolver.hpp.

◆ potentialTransPtr()

const vectorPtr_Type potentialTransPtr ( ) const

inline

get the pointer to the transmembrane potential

Definition at line 382 of file ElectroETABidomainSolver.hpp.

◆ potentialGlobalPtr()

blockVectorPtr_Type potentialGlobalPtr ( )

inline

get the pointer to the potential

Definition at line 387 of file ElectroETABidomainSolver.hpp.

◆ potentialExtraPtr()

const vectorPtr_Type potentialExtraPtr ( ) const

inline

get the pointer to the extra cellular potential

Definition at line 392 of file ElectroETABidomainSolver.hpp.

◆ fiberPtr()

const vectorPtr_Type fiberPtr ( ) const

inline

get the pointer to the fiber vector

Definition at line 398 of file ElectroETABidomainSolver.hpp.

◆ appliedCurrentIntraPtr()

const vectorPtr_Type appliedCurrentIntraPtr ( )

inline

get the pointer to the applied intra cellular current vector

Definition at line 403 of file ElectroETABidomainSolver.hpp.

◆ linearSolverPtr()

const linearSolverPtr_Type linearSolverPtr ( ) const

inline

get the pointer to the linear solver

Definition at line 409 of file ElectroETABidomainSolver.hpp.

◆ globalSolution()

const vectorOfPtr_Type& globalSolution ( ) const

inline

get the pointer to the vector of pointers containing the transmembrane potential (at 0) and the gating variables

Definition at line 414 of file ElectroETABidomainSolver.hpp.

◆ globalRhs()

const vectorOfPtr_Type& globalRhs ( ) const

inline

get the pointer to the vector of pointers containing the rhs for transmembrane potential (at 0) and the gating variables

Definition at line 419 of file ElectroETABidomainSolver.hpp.

◆ displacementPtr()

vectorPtr_Type displacementPtr ( ) const

inline

get the pointer to the transmembrane potential

Definition at line 424 of file ElectroETABidomainSolver.hpp.

◆ displacementETFESpacePtr()

ETFESpaceVectorialPtr_Type displacementETFESpacePtr ( ) const

inline

Definition at line 429 of file ElectroETABidomainSolver.hpp.

◆ lumpedMassMatrix()

bool lumpedMassMatrix ( ) const

inline

Definition at line 434 of file ElectroETABidomainSolver.hpp.

◆ setSurfaceVolumeRatio()

void setSurfaceVolumeRatio ( const Real & p )

inline

set the surface to volume ratio

Parameters

Real	surface to volume ratio

Definition at line 448 of file ElectroETABidomainSolver.hpp.

◆ setInitialTime()

void setInitialTime ( const Real & p )

inline

set the starting time

Parameters

Real	initial time

Definition at line 457 of file ElectroETABidomainSolver.hpp.

◆ setTimeStep()

void setTimeStep ( const Real & p )

inline

set the ending time

Parameters

Real	ending time

Definition at line 465 of file ElectroETABidomainSolver.hpp.

◆ setEndTime()

void setEndTime ( const Real & p )

inline

set the time step

Parameters

Real time step

Definition at line 473 of file ElectroETABidomainSolver.hpp.

◆ setDiffusionTensorIntra()

void setDiffusionTensorIntra ( const VectorSmall< 3 > & p )

inline

set the intra cellular diagonal diffusion tensor

Parameters

VectorSmall<3> diagonal intra cellular diffusion tensor

Definition at line 481 of file ElectroETABidomainSolver.hpp.

◆ setDiffusionTensorExtra()

void setDiffusionTensorExtra ( const VectorSmall< 3 > & p )

inline

set the extra cellular diagonal diffusion tensor

Parameters

VectorSmall<3> diagonal extra cellular diffusion tensor

Definition at line 489 of file ElectroETABidomainSolver.hpp.

◆ setIonicModelPtr()

void setIonicModelPtr ( const ionicModelPtr_Type p )

inline

set the pointer to the ionic model

Parameters

std::shared_ptr<IonicModel> pointer to the ionic model

Definition at line 498 of file ElectroETABidomainSolver.hpp.

◆ setCommPtr()

void setCommPtr ( const commPtr_Type p )

inline

set the pointer to the Epetra communicator

Parameters

std::shared_ptr<Epetra_Comm> pointer to the Epetra communicator

Definition at line 507 of file ElectroETABidomainSolver.hpp.

◆ setLocalMeshPtr()

void setLocalMeshPtr ( const meshPtr_Type p )

inline

set the pointer to the partitioned mesh

Parameters

std::shared_ptr<Mesh> pointer to the partitioned mesh

Definition at line 515 of file ElectroETABidomainSolver.hpp.

◆ setFullMeshPtr()

void setFullMeshPtr ( const meshPtr_Type p )

inline

set the pointer to the partitioned mesh

Parameters

std::shared_ptr<Mesh> pointer to the partitioned mesh

Definition at line 523 of file ElectroETABidomainSolver.hpp.

◆ setETFESpacePtr()

void setETFESpacePtr ( const ETFESpacePtr_Type p )

inline

set the pointer to the ETA fe space

Parameters

std::shared_ptr<ETFESpace<Mesh,MapEpetra,3,1>> pointer to the ETA fe space

Definition at line 531 of file ElectroETABidomainSolver.hpp.

◆ setFeSpacePtr()

void setFeSpacePtr ( const feSpacePtr_Type p )

inline

set the pointer to the usual fe space

Parameters

std::shared_ptr<IFESpace<Mesh,MapEpetra>> pointer to the usual fe space

Definition at line 539 of file ElectroETABidomainSolver.hpp.

◆ setMassMatrixPtr()

void setMassMatrixPtr ( const blockMatrixPtr_Type p )

inline

set the pointer to the mass matrix

Parameters

std::shared_ptr<MatrixEpetra<Real>> pointer to the mass matrix

Definition at line 548 of file ElectroETABidomainSolver.hpp.

◆ setStiffnessMatrixPtr()

void setStiffnessMatrixPtr ( const blockMatrixPtr_Type p )

inline

set the pointer to the stiffness matrix

Parameters

std::shared_ptr<MatrixEpetra<Real>> pointer to the stiffness matrix

Definition at line 556 of file ElectroETABidomainSolver.hpp.

◆ setGlobalMatrixPtr()

void setGlobalMatrixPtr ( const blockMatrixPtr_Type p )

inline

set the pointer to the global matrix

Parameters

std::shared_ptr<MatrixEpetra<Real>> pointer to the global matrix

Definition at line 564 of file ElectroETABidomainSolver.hpp.

◆ setRhsPtr()

void setRhsPtr ( const blockVectorPtr_Type p )

inline

set the pointer to the right hand side

Parameters

std::shared_ptr<VectorEpetra> pointer to the right hand side

Definition at line 572 of file ElectroETABidomainSolver.hpp.

◆ setRhsPtrUnique()

void setRhsPtrUnique ( const blockVectorPtr_Type p )

inline

set the pointer to the unique version of the right hand side

Parameters

std::shared_ptr<VectorEpetra> pointer to the unique version of the right hand side

Definition at line 580 of file ElectroETABidomainSolver.hpp.

◆ setPotentialExtraPtr()

void setPotentialExtraPtr ( const vectorPtr_Type p )

inline

Definition at line 585 of file ElectroETABidomainSolver.hpp.

◆ setPotentialTransPtr()

void setPotentialTransPtr ( const vectorPtr_Type p )

inline

Definition at line 591 of file ElectroETABidomainSolver.hpp.

◆ setAppliedCurrentIntraPtr()

void setAppliedCurrentIntraPtr ( const vectorPtr_Type p )

inline

set the pointer to the intra cell applied current vector

Parameters

std::shared_ptr<VectorEpetra> pointer to the intra cellular applied current vector

Definition at line 602 of file ElectroETABidomainSolver.hpp.

◆ setLinearSolverPtr()

void setLinearSolverPtr ( const linearSolverPtr_Type p )

inline

set the pointer to the linear solver

Parameters

std::shared_ptr<LinearSolver> pointer to the linear solver

Definition at line 611 of file ElectroETABidomainSolver.hpp.

◆ setGlobalSolution()

void setGlobalSolution ( const vectorOfPtr_Type & p )

inline

set the vector of pointers containing the transmembrane potential (at 0) and the gating variables

Parameters

std::vector<std::shared_ptr<VectorEpetra>> vector of pointers containing the transmembrane potential (at 0) and the gating variables

Definition at line 619 of file ElectroETABidomainSolver.hpp.

◆ setGlobalRhs()

void setGlobalRhs ( const vectorOfPtr_Type & p )

inline

set the vector of pointers containing the rhs for the transmembrane potential (at 0) and the gating variables

Parameters

std::vector<std::shared_ptr<VectorEpetra>> vector of pointers containing the rhs for the transmembrane potential (at 0) and the gating variables

Definition at line 627 of file ElectroETABidomainSolver.hpp.

◆ setFiberPtr()

void setFiberPtr ( const vectorPtr_Type p )

inline

set the pointer to the fiber direction vector

Parameters

std::shared_ptr<VectorEpetra> pointer to the fiber direction vector

Definition at line 635 of file ElectroETABidomainSolver.hpp.

◆ setDisplacementPtr()

void setDisplacementPtr ( const vectorPtr_Type p )

inline

set the pointer to displacement of the tissue

Definition at line 640 of file ElectroETABidomainSolver.hpp.

◆ setIonicModel()

void setIonicModel ( const ionicModel_Type & p )

inline

Definition at line 649 of file ElectroETABidomainSolver.hpp.

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◆ setComm()

void setComm ( const comm_Type & p )

inline

Definition at line 653 of file ElectroETABidomainSolver.hpp.

◆ setLocalMesh()

void setLocalMesh ( const mesh_Type & p )

inline

Definition at line 657 of file ElectroETABidomainSolver.hpp.

◆ setFullMesh()

void setFullMesh ( const mesh_Type & p )

inline

Definition at line 661 of file ElectroETABidomainSolver.hpp.

◆ setETFESpace()

void setETFESpace ( const ETFESpace_Type & p )

inline

Definition at line 665 of file ElectroETABidomainSolver.hpp.

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◆ setFeSpace()

void setFeSpace ( const feSpace_Type & p )

inline

Definition at line 669 of file ElectroETABidomainSolver.hpp.

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◆ setMassMatrix()

void setMassMatrix ( const matrix_Type & p )

inline

Definition at line 673 of file ElectroETABidomainSolver.hpp.

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◆ setStiffnessMatrix()

void setStiffnessMatrix ( const matrix_Type & p )

inline

Definition at line 677 of file ElectroETABidomainSolver.hpp.

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◆ setGlobalMatrix()

void setGlobalMatrix ( const matrix_Type & p )

inline

Definition at line 681 of file ElectroETABidomainSolver.hpp.

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◆ setRhs()

void setRhs ( const vector_Type & p )

inline

Definition at line 685 of file ElectroETABidomainSolver.hpp.

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◆ setRhsUnique()

void setRhsUnique ( const vector_Type & p )

inline

Definition at line 689 of file ElectroETABidomainSolver.hpp.

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◆ setPotentialTrans()

void setPotentialTrans ( const vector_Type & p )

inline

Definition at line 693 of file ElectroETABidomainSolver.hpp.

◆ setPotentialExtra()

void setPotentialExtra ( const blockVector_Type & p )

inline

Definition at line 698 of file ElectroETABidomainSolver.hpp.

◆ setFiber()

void setFiber ( const vector_Type & p )

inline

Definition at line 703 of file ElectroETABidomainSolver.hpp.

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◆ setDisplacement()

void setDisplacement ( const vector_Type & p )

inline

Definition at line 707 of file ElectroETABidomainSolver.hpp.

◆ setAppliedCurrentIntra()

void setAppliedCurrentIntra ( const vector_Type & p )

inline

Definition at line 711 of file ElectroETABidomainSolver.hpp.

◆ setLinearSolver()

void setLinearSolver ( const linearSolver_Type & p )

inline

Definition at line 715 of file ElectroETABidomainSolver.hpp.

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◆ copyGlobalSolution()

void copyGlobalSolution ( const vectorOfPtr_Type & p )

inline

Definition at line 719 of file ElectroETABidomainSolver.hpp.

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◆ setVariablePtr()

void setVariablePtr	(	const vectorPtr_Type	p,
		int	j
	)

inline

Definition at line 727 of file ElectroETABidomainSolver.hpp.

◆ copyGlobalRhs()

void copyGlobalRhs ( const vectorOfPtr_Type & p )

inline

Definition at line 732 of file ElectroETABidomainSolver.hpp.

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◆ setLumpedMassMatrix()

void setLumpedMassMatrix ( bool p ) const

inline

Definition at line 740 of file ElectroETABidomainSolver.hpp.

◆ setup() [1/2]

void setup	(	GetPot &	dataFile,
		short int	ionicSize
	)

Definition at line 1325 of file ElectroETABidomainSolver.hpp.

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◆ setup() [2/2]

void setup	(	std::string	meshName,
		std::string	meshPath,
		GetPot &	dataFile,
		short int	ionicSize
	)

Definition at line 1367 of file ElectroETABidomainSolver.hpp.

◆ setupMassMatrix() [1/2]

void setupMassMatrix ( )

create mass matrix

Definition at line 1377 of file ElectroETABidomainSolver.hpp.

◆ setupMassMatrix() [2/2]

void setupMassMatrix ( vector_Type & disp )

create mass matrix

Definition at line 1416 of file ElectroETABidomainSolver.hpp.

◆ setupLumpedMassMatrix() [1/2]

void setupLumpedMassMatrix ( )

create mass matrix

Definition at line 1443 of file ElectroETABidomainSolver.hpp.

◆ setupLumpedMassMatrix() [2/2]

void setupLumpedMassMatrix ( vector_Type & disp )

Definition at line 1474 of file ElectroETABidomainSolver.hpp.

◆ setupStiffnessMatrix() [1/3]

void setupStiffnessMatrix ( )

create stiffness matrix

Definition at line 1566 of file ElectroETABidomainSolver.hpp.

◆ setupStiffnessMatrix() [2/3]

void setupStiffnessMatrix ( vectorPtr_Type disp )

create stiffness matrix in a moving domain

Definition at line 1655 of file ElectroETABidomainSolver.hpp.

◆ setupStiffnessMatrix() [3/3]

void setupStiffnessMatrix	(	VectorSmall< 3 >	diffusionIntra,
		VectorSmall< 3 >	diffusionExtra
	)

create stiffness matrix given a diagonal diffusion tensor

Definition at line 1584 of file ElectroETABidomainSolver.hpp.

◆ setupGlobalMatrix()

void setupGlobalMatrix ( )

create stiffness matrix given the fiber direction and a diagonal diffusion tensor

setup the total matrix

$A = \frac{M}{\Delta t} + K(\mathbf{f})$

Definition at line 1729 of file ElectroETABidomainSolver.hpp.

◆ setupLinearSolver() [1/2]

void setupLinearSolver ( GetPot dataFile )

setup the linear solver

A file named BidomainSolverParamList.xml must be in the execution folder with the parameters to set the linear solver

Definition at line 1740 of file ElectroETABidomainSolver.hpp.

◆ setupLinearSolver() [2/2]

void setupLinearSolver	(	GetPot	dataFile,
		list_Type	list
	)

setup the linear solver

Definition at line 1766 of file ElectroETABidomainSolver.hpp.

◆ initializePotential()

void initializePotential ( )

inline

Initialize the potentials to zero.

Definition at line 786 of file ElectroETABidomainSolver.hpp.

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◆ initializePotentialTrans()

void initializePotentialTrans ( Real k )

inline

Initialize the potential to the value k.

Definition at line 793 of file ElectroETABidomainSolver.hpp.

◆ initializePotentialExtra()

void initializePotentialExtra ( Real k )

inline

Definition at line 799 of file ElectroETABidomainSolver.hpp.

◆ initializeAppliedCurrentIntra() [1/2]

void initializeAppliedCurrentIntra ( )

inline

Initialize the applied current to zero.

Definition at line 807 of file ElectroETABidomainSolver.hpp.

◆ initializeAppliedCurrentIntra() [2/2]

void initializeAppliedCurrentIntra ( Real k )

inline

Initialize the intra cellular applied current to the value k.

Definition at line 813 of file ElectroETABidomainSolver.hpp.

◆ setupGlobalSolution()

void setupGlobalSolution ( short int ionicSize )

creates a vector of pointers to store the solution

The first pointer points to the vector of the transmembrane potential, while the others point to the gating variables

Definition at line 1783 of file ElectroETABidomainSolver.hpp.

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◆ setupGlobalRhs()

void setupGlobalRhs ( short int ionicSize )

creates a vector of pointers to store the rhs

The first pointer points to the rhs of the transmembrane potential, while the others point to the rhs of the gating variables

Definition at line 1797 of file ElectroETABidomainSolver.hpp.

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◆ setParameters() [1/2]

void setParameters ( list_Type list )

Set parameters from an xml file.

Definition at line 2011 of file ElectroETABidomainSolver.hpp.

◆ partitionMesh()

void partitionMesh	(	std::string	meshName,
		std::string	meshPath
	)

inline

partition the mesh

Definition at line 832 of file ElectroETABidomainSolver.hpp.

◆ setPotentialFromFunctionTrans()

void setPotentialFromFunctionTrans	(	function_Type &	f,
		Real	time = `0.0`
	)

inline

given a boost function initialize the transmembrane potential

Definition at line 838 of file ElectroETABidomainSolver.hpp.

◆ setPotentialFromFunctionExtra()

void setPotentialFromFunctionExtra	(	function_Type &	f,
		Real	time = `0.0`
	)

inline

given a boost function initialize the extra cellular potential

Definition at line 845 of file ElectroETABidomainSolver.hpp.

◆ setAppliedCurrentFromFunctionIntra()

void setAppliedCurrentFromFunctionIntra	(	function_Type &	f,
		Real	time = `0.0`
	)

inline

given a boost function initialize the applied intra cellular current

Definition at line 852 of file ElectroETABidomainSolver.hpp.

◆ solveOneReactionStepFE() [1/2]

void solveOneReactionStepFE ( int subiterations = 1 )

Solves one reaction step using the forward Euler scheme.

$\mathbf{V}^* = \mathbf{V}^n + \Delta t I_{ion}(\mathbf{V}^n).$

Definition at line 1811 of file ElectroETABidomainSolver.hpp.

◆ solveOneReactionStepFE() [2/2]

void solveOneReactionStepFE	(	matrix_Type &	mass,
		int	subiterations = `1`
	)

◆ solveOneReactionStepRL()

void solveOneReactionStepRL ( int subiterations = 1 )

Definition at line 1830 of file ElectroETABidomainSolver.hpp.

◆ updateRhs()

void updateRhs ( )

inline

Update the rhs.

$rhs \leftarrow C_m \frac{M}{\Delta t} \mathbf{V}^n$

Definition at line 873 of file ElectroETABidomainSolver.hpp.

◆ solveOneDiffusionStepBDF2()

void solveOneDiffusionStepBDF2 ( vectorPtr_Type previousPotentialGlobalPtr )

Solves one diffusion step using the BDF2 scheme.

$( \frac{3}{\Delta t}M + A ) V^{n+1} = \frac{1}{\Delta t}M(4 V^n -V^{n-1})$

◆ solveOneDiffusionStepBE()

void solveOneDiffusionStepBE ( )

Solves one diffusion step using the backward Euler scheme.

$A\mathbf{V}^{n+1} = \left( C_m \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^*.$

Definition at line 1850 of file ElectroETABidomainSolver.hpp.

◆ solveOneSplittingStep() [1/2]

void solveOneSplittingStep ( )

Solve one full step with operator splitting.

$\mathbf{V}^* = \mathbf{V}^n + \Delta t I_{ion}(\mathbf{V}^n).$

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^*.$

Definition at line 1864 of file ElectroETABidomainSolver.hpp.

◆ solveSplitting() [1/3]

void solveSplitting ( )

Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep.

◆ solveOneSplittingStep() [2/2]

void solveOneSplittingStep	(	IOFile_Type &	exporter,
		Real	t
	)

Solve one full step with operator splitting and export the solution.

$\mathbf{V}^* = \mathbf{V}^n + \Delta t I_{ion}(\mathbf{V}^n).$

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^*.$

◆ solveSplitting() [2/3]

void solveSplitting ( IOFile_Type & exporter )

Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep and export the solution.

◆ solveSplitting() [3/3]

void solveSplitting	(	IOFile_Type &	exporter,
		Real	dt
	)

Solve the system with operator splitting from M_initialTime to the M_endTime with time step M_timeStep and export the solution every dt.

◆ setupPotentialExporter() [1/2]

void setupPotentialExporter ( IOFile_Type & exporter )

add to a given exporter the pointer to the potential

Definition at line 1876 of file ElectroETABidomainSolver.hpp.

◆ setupPotentialExporter() [2/2]

void setupPotentialExporter	(	IOFile_Type &	exporter,
		std::string	fileName
	)

add to a given exporter the pointer to the potential saved with name fileName

Definition at line 1889 of file ElectroETABidomainSolver.hpp.

◆ setupExporter()

void setupExporter	(	IOFile_Type &	exporter,
		std::string	fileName = `"output"`,
		std::string	folder = `"./"`
	)

add to a given exporter the pointer to the potential and to the gating variables saved with name fileName

Definition at line 1902 of file ElectroETABidomainSolver.hpp.

◆ setupFibers() [1/4]

void setupFibers ( )

Generates a default fiber direction (0,1,0)

Definition at line 1235 of file ElectroETABidomainSolver.hpp.

◆ setupFibers() [2/4]

void setupFibers ( VectorSmall< 3 > fibers )

Generates the fiber direction given the three component of the vector (F_x,F_y,F_z)

Definition at line 1255 of file ElectroETABidomainSolver.hpp.

◆ setupFibers() [3/4]

void setupFibers ( std::string fibersFile )

inline

Imports the fiber direction from a hdf5 file.

Definition at line 935 of file ElectroETABidomainSolver.hpp.

◆ setupFibers() [4/4]

void setupFibers	(	std::string	fibersFile,
		std::string	directory,
		int	format = `0`
	)

inline

Imports the fiber direction from a vtk file ( format = 0), or text file.

Definition at line 941 of file ElectroETABidomainSolver.hpp.

◆ solveOneStepGatingVariablesFE()

void solveOneStepGatingVariablesFE ( )

Solves the gating variables with forward Euler.

◆ solveOneStepGatingVariablesRL()

void solveOneStepGatingVariablesRL ( )

◆ computeRhsSVI()

void computeRhsSVI ( )

Compute the rhs using state variable interpolation.

◆ computeRhsICI() [1/2]

void computeRhsICI ( )

Compute the rhs using ionic current interpolation.

◆ computeRhsICI() [2/2]

void computeRhsICI ( matrix_Type & mass )

◆ solveOneICIStep() [1/3]

void solveOneICIStep ( )

Solve one full step with ionic current interpolation.

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^n+M\mathbf{I},$

where ${I}$ is the vector of the ionic currents $I_j = I_{ion}(V_j^n)$

◆ solveOneICIStep() [2/3]

void solveOneICIStep ( matrix_Type & mass )

◆ solveOneSVIStep() [1/2]

void solveOneSVIStep ( )

Solve one full step with ionic current interpolation.

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^n+\mathbf{I}_{ion}(\mathbf{V}^n).$

◆ solveICI() [1/3]

void solveICI ( )

solve system using ICI from M_initialTime to the M_endTime with time step M_timeStep

◆ solveSVI() [1/3]

void solveSVI ( )

solve system using SVI from M_initialTime to the M_endTime with time step M_timeStep

◆ solveOneICIStep() [3/3]

void solveOneICIStep	(	IOFile_Type &	exporter,
		Real	t
	)

Solve one full step with ionic current interpolation and export the solution.

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^n+M\mathbf{I},$

where ${I}$ is the vector of the ionic currents $I_j = I_{ion}(V_j^n)$

◆ solveOneSVIStep() [2/2]

void solveOneSVIStep	(	IOFile_Type &	exporter,
		Real	t
	)

Solve one full step with ionic current interpolation and export the solution.

$A\mathbf{V}^{n+1} = \left( \frac{M}{\Delta t} + K(\mathbf{f}) \right)\mathbf{V}^{n+1} =\frac{M}{\Delta t} \mathbf{V}^n+\mathbf{I}_{ion}(\mathbf{V}^n).$