monodomainSolver - Class featuring the solver for monodomain equations More...

#include <ElectroETAMonodomainSolver.hpp>

Collaboration diagram for ElectroETAMonodomainSolver< Mesh, IonicModel >:

Protected 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

matrixPtr_Type	M_massMatrixPtr

matrixPtr_Type	M_fullMassMatrixPtr

matrixPtr_Type	M_stiffnessMatrixPtr

matrixPtr_Type	M_globalMatrixPtr

Real	M_initialTime

Real	M_endTime

Real	M_timeStep

VectorSmall< 3 >	M_diffusionTensor

vectorPtr_Type	M_rhsPtr

vectorPtr_Type	M_rhsPtrUnique

vectorPtr_Type	M_potentialPtr

linearSolverPtr_Type	M_linearSolverPtr

vectorOfPtr_Type	M_globalSolution

vectorOfPtr_Type	M_globalRhs

std::string	M_elementsOrder

vectorPtr_Type	M_fiberPtr

matrixSmall_Type	M_identity

bool	M_lumpedMassMatrix

bool	M_verbose

Private Member Functions
void	setParameters ()
	Set default parameters. More...

void	init ()
	initialization in constructor More...

void	init (commPtr_Type comm)
	initialization in constructor More...

void	init (meshPtr_Type meshPtr)
	initialization in constructor More...

void	init (ionicModelPtr_Type model)
	initialization in constructor More...

Type definitions
Monodomain Solver The monodomain equation reads
typedef Mesh	mesh_Type
	Mesh. More...

typedef std::shared_ptr< mesh_Type >	meshPtr_Type

typedef VectorEpetra	vector_Type
	Distributed vector // For parallel usage. More...

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef vector_Type	solution_Type

typedef vectorPtr_Type	solutionPtr_Type

typedef std::vector< vectorPtr_Type >	vectorOfPtr_Type

typedef MatrixEpetra< Real >	matrix_Type
	Distributed Matrix // For parallel usage. More...

typedef std::shared_ptr< matrix_Type >	matrixPtr_Type

typedef Epetra_Comm	comm_Type
	Communicator to exchange informations among processes. More...

typedef std::shared_ptr< comm_Type >	commPtr_Type

typedef ETFESpace< mesh_Type, MapEpetra, 3, 1 >	ETFESpace_Type
	Expression template scalar finite element space To be used in the expression assembly namespace. More...

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

typedef ETFESpace< mesh_Type, MapEpetra, 3, 3 >	ETFESpaceVectorial_Type
	Expression template vectorial finite element space To be used in the expression assembly namespace. More...

typedef std::shared_ptr< ETFESpaceVectorial_Type >	ETFESpaceVectorialPtr_Type

typedef FESpace< mesh_Type, MapEpetra >	feSpace_Type
	Finite element space. More...

typedef std::shared_ptr< feSpace_Type >	feSpacePtr_Type

typedef LinearSolver	linearSolver_Type
	Linear Solver. More...

typedef std::shared_ptr< LinearSolver >	linearSolverPtr_Type

typedef Exporter< mesh_Type >	IOFile_Type
	Exporter to save the solution. More...

typedef std::shared_ptr< IOFile_Type >	IOFilePtr_Type

typedef ExporterData< mesh_Type >	IOData_Type
	Exporter data. More...

typedef ExporterEnsight< mesh_Type >	ensightIOFile_Type

typedef ExporterHDF5< mesh_Type >	hdf5IOFile_Type

typedef LifeV::Preconditioner	basePrec_Type
	Preconditioner. More...

typedef std::shared_ptr< basePrec_Type >	basePrecPtr_Type

typedef LifeV::PreconditionerML	prec_Type
	MultiLevel Preconditioner. More...

typedef std::shared_ptr< prec_Type >	precPtr_Type

typedef IonicModel	ionicModel_Type
	Ionic model. More...

typedef ElectroIonicModel	superIonicModel
	Base class of the ionic model. More...

typedef std::shared_ptr< superIonicModel >	ionicModelPtr_Type

typedef Teuchos::ParameterList	list_Type
	xml list to read parameters More...

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

typedef MatrixSmall< 3, 3 >	matrixSmall_Type
	3x3 matrix More...

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

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

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

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

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

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

virtual	~ElectroETAMonodomainSolver ()
	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 > &	diffusionTensor () const
	get the diagonal 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...

meshPtr_Type	localMeshPtr ()
	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 matrixPtr_Type	massMatrixPtr () const
	get the pointer to the mass matrix More...

const matrixPtr_Type	fullMassMatrixPtr () const
	get the pointer to the mass matrix More...

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

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

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

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

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

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

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

const vectorPtr_Type	appliedCurrentPtr ()
	get the pointer to the applied 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...

bool	lumpedMassMatrix () const
	getter for the boolean to know if we want a lumped matrix More...

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

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

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

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

void	setDiffusionTensor (const VectorSmall< 3 > &diffusionTensor)
	set the diagonal diffusion tensor More...

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

void	setIonicModel (const ionicModel_Type &ionicModel)
	set ionic model More...

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

void	setComm (const comm_Type &comm)
	set the Epetra communicator More...

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

void	setLocalMesh (const mesh_Type &localMesh)
	set the partitioned mesh More...

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

void	setFullMesh (const mesh_Type &fullMesh)
	set the non partitioned mesh More...

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

void	setETFESpace (const ETFESpace_Type &ETFESpace)
	set the scalar ETA fe space More...

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

void	setFeSpace (const feSpace_Type &feSpace)
	set the fe space More...

void	setMassMatrixPtr (const matrixPtr_Type massMatrixPtr)
	set the pointer to the mass matrix More...

void	setMassMatrix (const matrix_Type &massMatrix)
	set the mass matrix More...

void	setFullMassMatrixPtr (const matrixPtr_Type fullMassMatrixPtr)
	set the pointer to the full mass matrix More...

void	setFullMassMatrix (const matrix_Type &fullMassMatrix)
	set the full mass matrix More...

void	setStiffnessMatrixPtr (const matrixPtr_Type stiffnessMatrixPtr)
	set the pointer to the stiffness matrix More...

void	setStiffnessMatrix (const matrix_Type &stiffnessMatrix)
	set the stiffness matrix More...

void	setGlobalMatrixPtr (const matrixPtr_Type globalMatrixPtr)
	set the pointer to the global matrix More...

void	setGlobalMatrix (const matrix_Type &globalMatrix)
	set the global matrix More...

void	setRhsPtr (const vectorPtr_Type rhsPtr)
	set the pointer to the right hand side More...

void	setRhs (const vector_Type &rhs)
	set the right hand side More...

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

void	setRhsUnique (const vector_Type &rhsPtrUnique)
	set the unique version of the right hand side More...

void	setPotentialPtr (const vectorPtr_Type potentialPtr)
	set the pointer to the potential More...

void	setPotential (const vector_Type &potential)
	set the potential More...

void	setAppliedCurrentPtr (const vectorPtr_Type appliedCurrentPtr)
	set the pointer to the applied current vector More...

void	setAppliedCurrent (const vector_Type &appliedCurrent)
	set the applied current vector More...

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

void	setLinearSolver (const linearSolver_Type &linearSolver)
	set the linear solver More...

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

void	setGlobalSolution (const vectorOfPtr_Type &globalSolution)
	set the vectors of unknowns: containing the transmembrane potential (at 0) and the gating variables More...

void	setVariablePtr (const vectorPtr_Type gatingVariable, int j)
	set the pointer to the [j]-th gating variable More...

void	setVariablePtr (const vector_Type &gatingVariable, int j)
	set the [j]-th gating variable More...

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

void	setGlobalRhs (const vectorOfPtr_Type &globalRhs)
	set the vectors containing the rhs for the transmembrane potential (at 0) and the gating variables More...

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

void	setFiber (const vector_Type &fiber)
	set the fiber direction vector More...

void	setLumpedMassMatrix (bool isLumped)
	set the the choice of lumping More...

Methods
virtual void	setup (GetPot &dataFile, short int ionicSize)
	setup method used in the constructor More...

virtual void	setup (std::string meshName, std::string meshPath, GetPot &dataFile, short int ionicSize)
	setup method used in the constructor More...

void	setupMassMatrix ()
	create mass matrix More...

void	setupLumpedMassMatrix ()
	create mass matrix More...

virtual void	setupStiffnessMatrix ()
	create stiffness matrix More...

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

void	setupGlobalMatrix ()
	setup the total matrix More...

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

void	initializePotential (Real k=0.0)
	Initialize the potential to the value k. More...

void	initializeAppliedCurrent (Real k=0.0)
	Initialize the 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	setPotentialFromFunction (function_Type &f, Real time=0.0)
	given a boost function initialize the potential More...

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

void	setAppliedCurrentFromElectroStimulus (ElectroStimulus &stimulus, Real time=0.0)
	given a ElectroStimulus object initialize the applied current More...

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

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

void	solveOneReactionStepRL (int subiterations=1)
	Solves one reaction step using the Rush-Larsen scheme. More...

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

void	solveOneDiffusionStepBDF2 (vectorPtr_Type previousPotentialPtr)
	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, std::string fileName="Potential")
	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, const std::string &filePath="./")
	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 ()
	Solves the gating variables with Rush-Larsen scheme. More...

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

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

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

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

void	solveOneICIStepWithFullMass ()
	solves using ionic current interpolation More...

void	solveOneSVIStep ()
	Solve one full step with state variable 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	solveOneICIStepWithFullMass (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	solveICIWithFullMass (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 (std::string prefix, std::string postDir, Real time=0.0)
	Importer: lead a solution from an hdf5 file. More...

void	setInitialConditions ()
	Initialize the solution with resting values of the ionic model. More...

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

void	setVerbosity (bool verbose)
	set the verbosity More...

Detailed Description

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

monodomainSolver - Class featuring the solver for monodomain equations

Definition at line 87 of file ElectroETAMonodomainSolver.hpp.

Member Typedef Documentation

◆ mesh_Type

typedef Mesh mesh_Type

Mesh.

Definition at line 103 of file ElectroETAMonodomainSolver.hpp.

◆ meshPtr_Type

typedef std::shared_ptr<mesh_Type> meshPtr_Type

Definition at line 105 of file ElectroETAMonodomainSolver.hpp.

◆ vector_Type

typedef VectorEpetra vector_Type

Distributed vector // For parallel usage.

Definition at line 108 of file ElectroETAMonodomainSolver.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 110 of file ElectroETAMonodomainSolver.hpp.

◆ solution_Type

typedef vector_Type solution_Type

Definition at line 112 of file ElectroETAMonodomainSolver.hpp.

◆ solutionPtr_Type

typedef vectorPtr_Type solutionPtr_Type

Definition at line 114 of file ElectroETAMonodomainSolver.hpp.

◆ vectorOfPtr_Type

typedef std::vector<vectorPtr_Type> vectorOfPtr_Type

Definition at line 116 of file ElectroETAMonodomainSolver.hpp.

◆ matrix_Type

typedef MatrixEpetra<Real> matrix_Type

Distributed Matrix // For parallel usage.

Definition at line 119 of file ElectroETAMonodomainSolver.hpp.

◆ matrixPtr_Type

typedef std::shared_ptr<matrix_Type> matrixPtr_Type

Definition at line 121 of file ElectroETAMonodomainSolver.hpp.

◆ comm_Type

typedef Epetra_Comm comm_Type

Communicator to exchange informations among processes.

Definition at line 124 of file ElectroETAMonodomainSolver.hpp.

◆ commPtr_Type

typedef std::shared_ptr<comm_Type> commPtr_Type

Definition at line 126 of file ElectroETAMonodomainSolver.hpp.

◆ ETFESpace_Type

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

Expression template scalar finite element space To be used in the expression assembly namespace.

Definition at line 130 of file ElectroETAMonodomainSolver.hpp.

◆ ETFESpacePtr_Type

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

Definition at line 132 of file ElectroETAMonodomainSolver.hpp.

◆ ETFESpaceVectorial_Type

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

Expression template vectorial finite element space To be used in the expression assembly namespace.

Definition at line 136 of file ElectroETAMonodomainSolver.hpp.

◆ ETFESpaceVectorialPtr_Type

typedef std::shared_ptr<ETFESpaceVectorial_Type> ETFESpaceVectorialPtr_Type

Definition at line 138 of file ElectroETAMonodomainSolver.hpp.

◆ feSpace_Type

typedef FESpace<mesh_Type, MapEpetra> feSpace_Type

Finite element space.

Definition at line 141 of file ElectroETAMonodomainSolver.hpp.

◆ feSpacePtr_Type

typedef std::shared_ptr<feSpace_Type> feSpacePtr_Type

Definition at line 143 of file ElectroETAMonodomainSolver.hpp.

◆ linearSolver_Type

typedef LinearSolver linearSolver_Type

Linear Solver.

Definition at line 146 of file ElectroETAMonodomainSolver.hpp.

◆ linearSolverPtr_Type

typedef std::shared_ptr<LinearSolver> linearSolverPtr_Type

Definition at line 148 of file ElectroETAMonodomainSolver.hpp.

◆ IOFile_Type

typedef Exporter<mesh_Type> IOFile_Type

Exporter to save the solution.

Definition at line 151 of file ElectroETAMonodomainSolver.hpp.

◆ IOFilePtr_Type

typedef std::shared_ptr<IOFile_Type> IOFilePtr_Type

Definition at line 153 of file ElectroETAMonodomainSolver.hpp.

◆ IOData_Type

typedef ExporterData<mesh_Type> IOData_Type

Exporter data.

Definition at line 156 of file ElectroETAMonodomainSolver.hpp.

◆ ensightIOFile_Type

typedef ExporterEnsight<mesh_Type> ensightIOFile_Type

Definition at line 158 of file ElectroETAMonodomainSolver.hpp.

◆ hdf5IOFile_Type

typedef ExporterHDF5< mesh_Type > hdf5IOFile_Type

Definition at line 161 of file ElectroETAMonodomainSolver.hpp.

◆ basePrec_Type

typedef LifeV::Preconditioner basePrec_Type

Preconditioner.

Definition at line 165 of file ElectroETAMonodomainSolver.hpp.

◆ basePrecPtr_Type

typedef std::shared_ptr<basePrec_Type> basePrecPtr_Type

Definition at line 167 of file ElectroETAMonodomainSolver.hpp.

◆ prec_Type

typedef LifeV::PreconditionerML prec_Type

MultiLevel Preconditioner.

Definition at line 170 of file ElectroETAMonodomainSolver.hpp.

◆ precPtr_Type

typedef std::shared_ptr<prec_Type> precPtr_Type

Definition at line 172 of file ElectroETAMonodomainSolver.hpp.

◆ ionicModel_Type

typedef IonicModel ionicModel_Type

Ionic model.

Definition at line 175 of file ElectroETAMonodomainSolver.hpp.

◆ superIonicModel

typedef ElectroIonicModel superIonicModel

Base class of the ionic model.

Definition at line 178 of file ElectroETAMonodomainSolver.hpp.

◆ ionicModelPtr_Type

typedef std::shared_ptr<superIonicModel> ionicModelPtr_Type

Definition at line 180 of file ElectroETAMonodomainSolver.hpp.

◆ list_Type

typedef Teuchos::ParameterList list_Type

xml list to read parameters

Definition at line 183 of file ElectroETAMonodomainSolver.hpp.

◆ function_Type

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

boost function

Definition at line 190 of file ElectroETAMonodomainSolver.hpp.

◆ matrixSmall_Type

typedef MatrixSmall<3, 3> matrixSmall_Type

3x3 matrix

Definition at line 193 of file ElectroETAMonodomainSolver.hpp.

Constructor & Destructor Documentation

◆ ElectroETAMonodomainSolver() [1/5]

ElectroETAMonodomainSolver ( )

Empty Constructor.

Constructors.

Empty constructor

Definition at line 1419 of file ElectroETAMonodomainSolver.hpp.

◆ ElectroETAMonodomainSolver() [2/5]

ElectroETAMonodomainSolver	(	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 1451 of file ElectroETAMonodomainSolver.hpp.

◆ ElectroETAMonodomainSolver() [3/5]

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

Constructor.

constructor

Parameters

meshName	file name of the mesh
meshPath	path to the mesh
datafile	GetPot file to setup the preconditioner
model	shared pointer to the chosen ionic model

Definition at line 1428 of file ElectroETAMonodomainSolver.hpp.

◆ ElectroETAMonodomainSolver() [4/5]

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

Constructor.

constructor with communicator

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 1440 of file ElectroETAMonodomainSolver.hpp.

◆ ElectroETAMonodomainSolver() [5/5]

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

Copy Constructor.

Copy constructor.

Parameters

ElectroETAmonodomainSolver object

Definition at line 1462 of file ElectroETAMonodomainSolver.hpp.

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◆ ~ElectroETAMonodomainSolver()

virtual ~ElectroETAMonodomainSolver ( )

inlinevirtual

Destructor.

Definition at line 249 of file ElectroETAMonodomainSolver.hpp.

Member Function Documentation

◆ operator=()

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

Operator=()

Assignment operator.

Parameters

ElectroETAmonodomainSolver object

Definition at line 1497 of file ElectroETAMonodomainSolver.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 262 of file ElectroETAMonodomainSolver.hpp.

◆ initialTime()

const Real& initialTime ( ) const

inline

get the initial time (by default 0)

Definition at line 268 of file ElectroETAMonodomainSolver.hpp.

◆ timeStep()

const Real& timeStep ( ) const

inline

get the final time

Definition at line 274 of file ElectroETAMonodomainSolver.hpp.

◆ endTime()

const Real& endTime ( ) const

inline

get the time step

Definition at line 280 of file ElectroETAMonodomainSolver.hpp.

◆ diffusionTensor()

const VectorSmall<3>& diffusionTensor ( ) const

inline

get the diagonal diffusion tensor

Definition at line 286 of file ElectroETAMonodomainSolver.hpp.

◆ elementsOrder()

const std::string elementsOrder ( ) const

inline

get the order of the elements

Definition at line 292 of file ElectroETAMonodomainSolver.hpp.

◆ ionicModelPtr()

const ionicModelPtr_Type ionicModelPtr ( ) const

inline

get the pointer to the ionic model

Definition at line 298 of file ElectroETAMonodomainSolver.hpp.

◆ commPtr()

const commPtr_Type commPtr ( ) const

inline

get the pointer to the Epetra communicator

Definition at line 304 of file ElectroETAMonodomainSolver.hpp.

◆ localMeshPtr() [1/2]

const meshPtr_Type localMeshPtr ( ) const

inline

get the pointer to the partitioned mesh

Definition at line 310 of file ElectroETAMonodomainSolver.hpp.

◆ localMeshPtr() [2/2]

meshPtr_Type localMeshPtr ( )

inline

get the pointer to the partitioned mesh

Definition at line 316 of file ElectroETAMonodomainSolver.hpp.

◆ fullMeshPtr()

const meshPtr_Type fullMeshPtr ( ) const

inline

get the pointer to the partitioned mesh

Definition at line 322 of file ElectroETAMonodomainSolver.hpp.

◆ ETFESpacePtr()

const ETFESpacePtr_Type ETFESpacePtr ( ) const

inline

get the pointer to the ETA finite element space

Definition at line 328 of file ElectroETAMonodomainSolver.hpp.

◆ feSpacePtr()

const feSpacePtr_Type feSpacePtr ( ) const

inline

get the pointer to the usual finite element space

Definition at line 334 of file ElectroETAMonodomainSolver.hpp.

◆ massMatrixPtr()

const matrixPtr_Type massMatrixPtr ( ) const

inline

get the pointer to the mass matrix

Definition at line 340 of file ElectroETAMonodomainSolver.hpp.

◆ fullMassMatrixPtr()

const matrixPtr_Type fullMassMatrixPtr ( ) const

inline

get the pointer to the mass matrix

Definition at line 346 of file ElectroETAMonodomainSolver.hpp.

◆ stiffnessMatrixPtr()

const matrixPtr_Type stiffnessMatrixPtr ( ) const

inline

get the pointer to the stiffness matrix

Definition at line 352 of file ElectroETAMonodomainSolver.hpp.

◆ globalMatrixPtr()

const matrixPtr_Type globalMatrixPtr ( ) const

inline

get the pointer to the global matrix

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

Definition at line 363 of file ElectroETAMonodomainSolver.hpp.

◆ rhsPtr()

const vectorPtr_Type rhsPtr ( ) const

inline

get the pointer to the right hand side

Definition at line 369 of file ElectroETAMonodomainSolver.hpp.

◆ rhsPtrUnique()

const vectorPtr_Type rhsPtrUnique ( ) const

inline

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

Definition at line 375 of file ElectroETAMonodomainSolver.hpp.

◆ potentialPtr()

const vectorPtr_Type potentialPtr ( ) const

inline

get the pointer to the transmembrane potential

Definition at line 381 of file ElectroETAMonodomainSolver.hpp.

◆ fiberPtr() [1/2]

const vectorPtr_Type fiberPtr ( ) const

inline

get the pointer to the fiber vector

Definition at line 387 of file ElectroETAMonodomainSolver.hpp.

◆ fiberPtr() [2/2]

vectorPtr_Type fiberPtr ( )

inline

get the pointer to the fiber vector

Definition at line 393 of file ElectroETAMonodomainSolver.hpp.

◆ appliedCurrentPtr()

const vectorPtr_Type appliedCurrentPtr ( )

inline

get the pointer to the applied current vector

Definition at line 399 of file ElectroETAMonodomainSolver.hpp.

◆ linearSolverPtr()

const linearSolverPtr_Type linearSolverPtr ( ) const

inline

get the pointer to the linear solver

Definition at line 405 of file ElectroETAMonodomainSolver.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 411 of file ElectroETAMonodomainSolver.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 417 of file ElectroETAMonodomainSolver.hpp.

◆ lumpedMassMatrix()

bool lumpedMassMatrix ( ) const

inline

getter for the boolean to know if we want a lumped matrix

Definition at line 423 of file ElectroETAMonodomainSolver.hpp.

◆ setSurfaceVolumeRatio()

void setSurfaceVolumeRatio ( const Real & surfaceVolumeRatio )

inline

set the surface to volume ratio

Parameters

surfaceVolumeRatio surface to volume ratio

Definition at line 436 of file ElectroETAMonodomainSolver.hpp.

◆ setInitialTime()

void setInitialTime ( const Real & initialTime )

inline

set the starting time

Parameters

initialTime initial time

Definition at line 445 of file ElectroETAMonodomainSolver.hpp.

◆ setTimeStep()

void setTimeStep ( const Real & timeStep )

inline

set the ending time

Parameters

timeStep ending time

Definition at line 454 of file ElectroETAMonodomainSolver.hpp.

◆ setEndTime()

void setEndTime ( const Real & endTime )

inline

set the time step

Parameters

endTime time step

Definition at line 463 of file ElectroETAMonodomainSolver.hpp.

◆ setDiffusionTensor()

void setDiffusionTensor ( const VectorSmall< 3 > & diffusionTensor )

inline

set the diagonal diffusion tensor

Parameters

diffusionTensor diagonal diffusion tensor

Definition at line 472 of file ElectroETAMonodomainSolver.hpp.

◆ setIonicModelPtr()

void setIonicModelPtr ( const ionicModelPtr_Type ionicModelPtr )

inline

set the pointer to the ionic model

Parameters

ionicModelPtr pointer to the ionic model

Definition at line 481 of file ElectroETAMonodomainSolver.hpp.

◆ setIonicModel()

void setIonicModel ( const ionicModel_Type & ionicModel )

inline

set ionic model

Parameters

ionicModel ionic model

Definition at line 490 of file ElectroETAMonodomainSolver.hpp.

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◆ setCommPtr()

void setCommPtr ( const commPtr_Type commPtr )

inline

set the pointer to the Epetra communicator

Parameters

commPtr pointer to the Epetra communicator

Definition at line 500 of file ElectroETAMonodomainSolver.hpp.

◆ setComm()

void setComm ( const comm_Type & comm )

inline

set the Epetra communicator

Parameters

comm	Epetra communicator

Definition at line 508 of file ElectroETAMonodomainSolver.hpp.

◆ setLocalMeshPtr()

void setLocalMeshPtr ( const meshPtr_Type localMeshPtr )

inline

set the pointer to the partitioned mesh

Parameters

localMeshPtr pointer to the partitioned mesh

Definition at line 517 of file ElectroETAMonodomainSolver.hpp.

◆ setLocalMesh()

void setLocalMesh ( const mesh_Type & localMesh )

inline

set the partitioned mesh

Parameters

localMesh partitioned mesh

Definition at line 526 of file ElectroETAMonodomainSolver.hpp.

◆ setFullMeshPtr()

void setFullMeshPtr ( const meshPtr_Type fullMeshPtr )

inline

set the pointer to the non partitioned mesh

Parameters

fullMeshPtr pointer to the partitioned mesh

Definition at line 536 of file ElectroETAMonodomainSolver.hpp.

◆ setFullMesh()

void setFullMesh ( const mesh_Type & fullMesh )

inline

set the non partitioned mesh

Parameters

fullMesh pointer to the partitioned mesh

Definition at line 544 of file ElectroETAMonodomainSolver.hpp.

◆ setETFESpacePtr()

void setETFESpacePtr ( const ETFESpacePtr_Type ETFESpacePtr )

inline

set the pointer to the ETA fe space

Parameters

ETFESpacePtr pointer to the ETA fe space

Definition at line 554 of file ElectroETAMonodomainSolver.hpp.

◆ setETFESpace()

void setETFESpace ( const ETFESpace_Type & ETFESpace )

inline

set the scalar ETA fe space

Parameters

ETFESpace scalar ETA fe space

Definition at line 563 of file ElectroETAMonodomainSolver.hpp.

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◆ setFeSpacePtr()

void setFeSpacePtr ( const feSpacePtr_Type feSpacePtr )

inline

set the pointer to the usual fe space

Parameters

feSpacePtr pointer to the usual fe space

Definition at line 572 of file ElectroETAMonodomainSolver.hpp.

◆ setFeSpace()

void setFeSpace ( const feSpace_Type & feSpace )

inline

set the fe space

Parameters

feSpace the fe space

Definition at line 581 of file ElectroETAMonodomainSolver.hpp.

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◆ setMassMatrixPtr()

void setMassMatrixPtr ( const matrixPtr_Type massMatrixPtr )

inline

set the pointer to the mass matrix

Parameters

massMatrixPtr pointer to the mass matrix

Definition at line 591 of file ElectroETAMonodomainSolver.hpp.

◆ setMassMatrix()

void setMassMatrix ( const matrix_Type & massMatrix )

inline

set the mass matrix

Parameters

massMatrix the mass matrix

Definition at line 600 of file ElectroETAMonodomainSolver.hpp.

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◆ setFullMassMatrixPtr()

void setFullMassMatrixPtr ( const matrixPtr_Type fullMassMatrixPtr )

inline

set the pointer to the full mass matrix

Parameters

massMatrixPtr pointer to the mass matrix

Definition at line 609 of file ElectroETAMonodomainSolver.hpp.

◆ setFullMassMatrix()

void setFullMassMatrix ( const matrix_Type & fullMassMatrix )

inline

set the full mass matrix

Parameters

massMatrix the mass matrix

Definition at line 618 of file ElectroETAMonodomainSolver.hpp.

◆ setStiffnessMatrixPtr()

void setStiffnessMatrixPtr ( const matrixPtr_Type stiffnessMatrixPtr )

inline

set the pointer to the stiffness matrix

Parameters

stiffnessMatrixPtr pointer to the stiffness matrix

Definition at line 627 of file ElectroETAMonodomainSolver.hpp.

◆ setStiffnessMatrix()

void setStiffnessMatrix ( const matrix_Type & stiffnessMatrix )

inline

set the stiffness matrix

Parameters

stiffnessMatrix the stiffness matrix

Definition at line 636 of file ElectroETAMonodomainSolver.hpp.

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◆ setGlobalMatrixPtr()

void setGlobalMatrixPtr ( const matrixPtr_Type globalMatrixPtr )

inline

set the pointer to the global matrix

Parameters

globalMatrix pointer to the global matrix

Definition at line 646 of file ElectroETAMonodomainSolver.hpp.

◆ setGlobalMatrix()

void setGlobalMatrix ( const matrix_Type & globalMatrix )

inline

set the global matrix

Parameters

globalMatrix the global matrix

Definition at line 655 of file ElectroETAMonodomainSolver.hpp.

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◆ setRhsPtr()

void setRhsPtr ( const vectorPtr_Type rhsPtr )

inline

set the pointer to the right hand side

Parameters

rhsPtr pointer to the right hand side

Definition at line 665 of file ElectroETAMonodomainSolver.hpp.

◆ setRhs()

void setRhs ( const vector_Type & rhs )

inline

set the right hand side

Parameters

rhs	the right hand side

Definition at line 674 of file ElectroETAMonodomainSolver.hpp.

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◆ setRhsPtrUnique()

void setRhsPtrUnique ( const vectorPtr_Type rhsPtrUnique )

inline

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

Parameters

rhsPtrUnique pointer to the unique version of the right hand side

Definition at line 684 of file ElectroETAMonodomainSolver.hpp.

◆ setRhsUnique()

void setRhsUnique ( const vector_Type & rhsPtrUnique )

inline

set the unique version of the right hand side

Parameters

rhsPtrUnique the unique version of the right hand side

Definition at line 694 of file ElectroETAMonodomainSolver.hpp.

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◆ setPotentialPtr()

void setPotentialPtr ( const vectorPtr_Type potentialPtr )

inline

set the pointer to the potential

Parameters

potentialPtr pointer to the potential

Definition at line 703 of file ElectroETAMonodomainSolver.hpp.

◆ setPotential()

void setPotential ( const vector_Type & potential )

inline

set the potential

Parameters

potential the potential

Definition at line 713 of file ElectroETAMonodomainSolver.hpp.

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◆ setAppliedCurrentPtr()

void setAppliedCurrentPtr ( const vectorPtr_Type appliedCurrentPtr )

inline

set the pointer to the applied current vector

Parameters

appliedCurrentPtr pointer to the applied current vector

Definition at line 722 of file ElectroETAMonodomainSolver.hpp.

◆ setAppliedCurrent()

void setAppliedCurrent ( const vector_Type & appliedCurrent )

inline

set the applied current vector

Parameters

appliedCurrent the applied current vector

Definition at line 731 of file ElectroETAMonodomainSolver.hpp.

◆ setLinearSolverPtr()

void setLinearSolverPtr ( const linearSolverPtr_Type linearSolverPtr )

inline

set the pointer to the linear solver

Parameters

linearSolverPtr pointer to the linear solver

Definition at line 740 of file ElectroETAMonodomainSolver.hpp.

◆ setLinearSolver()

void setLinearSolver ( const linearSolver_Type & linearSolver )

inline

set the linear solver

Parameters

linearSolver the linear solver

Definition at line 749 of file ElectroETAMonodomainSolver.hpp.

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◆ setGlobalSolutionPtrs()

void setGlobalSolutionPtrs ( const vectorOfPtr_Type & globalSolution )

inline

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

Parameters

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

Definition at line 758 of file ElectroETAMonodomainSolver.hpp.

◆ setGlobalSolution()

void setGlobalSolution ( const vectorOfPtr_Type & globalSolution )

inline

set the vectors of unknowns: containing the transmembrane potential (at 0) and the gating variables

Parameters

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

Definition at line 767 of file ElectroETAMonodomainSolver.hpp.

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◆ setVariablePtr() [1/2]

void setVariablePtr	(	const vectorPtr_Type	gatingVariable,
		int	j
	)

inline

set the pointer to the [j]-th gating variable

Parameters

gatingVariable	pointer to the gating variable
j	index of the gating variable

Definition at line 780 of file ElectroETAMonodomainSolver.hpp.

◆ setVariablePtr() [2/2]

void setVariablePtr	(	const vector_Type &	gatingVariable,
		int	j
	)

inline

set the [j]-th gating variable

Parameters

gatingVariable	the gating variable
j	index of the gating variable

Definition at line 790 of file ElectroETAMonodomainSolver.hpp.

◆ setGlobalRhsPtrs()

void setGlobalRhsPtrs ( const vectorOfPtr_Type & globalRhs )

inline

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

Parameters

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

Definition at line 799 of file ElectroETAMonodomainSolver.hpp.

◆ setGlobalRhs()

void setGlobalRhs ( const vectorOfPtr_Type & globalRhs )

inline

set the vectors containing the rhs for the transmembrane potential (at 0) and the gating variables

Parameters

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

Definition at line 808 of file ElectroETAMonodomainSolver.hpp.

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◆ setFiberPtr()

void setFiberPtr ( const vectorPtr_Type fiberPtr )

inline

set the pointer to the fiber direction vector

Parameters

fiberPtr pointer to the fiber direction vector

Definition at line 820 of file ElectroETAMonodomainSolver.hpp.

◆ setFiber()

void setFiber ( const vector_Type & fiber )

inline

set the fiber direction vector

Parameters

fiber the fiber direction vector

Definition at line 829 of file ElectroETAMonodomainSolver.hpp.

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◆ setLumpedMassMatrix()

void setLumpedMassMatrix ( bool isLumped )

inline

set the the choice of lumping

Parameters

isLumped true if you want to lump the mass matrix

Definition at line 838 of file ElectroETAMonodomainSolver.hpp.

◆ setup() [1/2]

void setup	(	GetPot &	dataFile,
		short int	ionicSize
	)

virtual

setup method used in the constructor

Parameters

dataFile	needed to set up the preconditioner
ionicSize	number of equation in the ionic model

Definition at line 1619 of file ElectroETAMonodomainSolver.hpp.

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◆ setup() [2/2]

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

virtual

setup method used in the constructor

Parameters

meshFile	filename of the mesh
meshPath	directory where we have the mesh
dataFile	needed to set up the preconditioner
ionicSize	number of equation in the ionic model

Definition at line 1659 of file ElectroETAMonodomainSolver.hpp.

◆ setupMassMatrix()

void setupMassMatrix ( )

create mass matrix

Computes the mass matrix calling different methods if the mass should be lumped

Definition at line 1670 of file ElectroETAMonodomainSolver.hpp.

◆ setupLumpedMassMatrix()

void setupLumpedMassMatrix ( )

create mass matrix

Computes the lumped mass matrix by nodal integration.

Definition at line 1697 of file ElectroETAMonodomainSolver.hpp.

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◆ setupStiffnessMatrix() [1/2]

void setupStiffnessMatrix ( )

virtual

create stiffness matrix

Computes the stiffness matrix calling different methods

Definition at line 1719 of file ElectroETAMonodomainSolver.hpp.

◆ setupStiffnessMatrix() [2/2]

void setupStiffnessMatrix ( VectorSmall< 3 > diffusion )

create stiffness matrix given a diagonal diffusion tensor

Parameters

diffusion vector defining the conductivities

Definition at line 1725 of file ElectroETAMonodomainSolver.hpp.

◆ setupGlobalMatrix()

void setupGlobalMatrix ( )

setup the total matrix

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

where is the membrane capacitance, t the timestep, M is the mass matrix and K is the stiffness matrix which depends on the fiber direction.

Definition at line 1759 of file ElectroETAMonodomainSolver.hpp.

◆ setupLinearSolver()

void setupLinearSolver ( GetPot dataFile )

setup the linear solver

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

Parameters

dataFile GetPot to setup the preconditioners

Definition at line 1768 of file ElectroETAMonodomainSolver.hpp.

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◆ initializePotential()

void initializePotential ( Real k = 0.0 )

inline

Initialize the potential to the value k.

Parameters

k	value to intialize the potential

Definition at line 913 of file ElectroETAMonodomainSolver.hpp.

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◆ initializeAppliedCurrent()

void initializeAppliedCurrent ( Real k = 0.0 )

inline

Initialize the applied current to the value k.

Parameters

k	value to intialize the applied current

Definition at line 922 of file ElectroETAMonodomainSolver.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

Parameters

ionicSize number of unknowns in the ionic model

Definition at line 1791 of file ElectroETAMonodomainSolver.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

Parameters

ionicSize number of unknowns in the ionic model

Definition at line 1803 of file ElectroETAMonodomainSolver.hpp.

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◆ setParameters() [1/2]

void setParameters ( list_Type list )

Set parameters from an xml file.

Parameters

list	Teuchos parameter list with the monodomain parameters

Definition at line 2356 of file ElectroETAMonodomainSolver.hpp.

◆ partitionMesh()

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

inline

partition the mesh

Parameters

meshName	filename of the mesh
meshPath	path to the folder where you have the mesh

Definition at line 954 of file ElectroETAMonodomainSolver.hpp.

◆ setPotentialFromFunction()

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

inline

given a boost function initialize the potential

Parameters

f	function defining the potential
time	time at which we want to evaluate the function

Definition at line 964 of file ElectroETAMonodomainSolver.hpp.

◆ setAppliedCurrentFromFunction()

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

inline

given a boost function initialize the applied current

Parameters

f	function defining the applied current
time	time at which we want to evaluate the function

Definition at line 976 of file ElectroETAMonodomainSolver.hpp.

◆ setAppliedCurrentFromElectroStimulus()

void setAppliedCurrentFromElectroStimulus	(	ElectroStimulus &	stimulus,
		Real	time = `0.0`
	)

inline

given a ElectroStimulus object initialize the applied current

Parameters

stimulus	pacing protocol
time	time at which we want to evaluate the stimulus

Definition at line 987 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneReactionStepFE() [1/2]

void solveOneReactionStepFE ( int subiterations = 1 )

Solves one reaction step using the forward Euler scheme and N subiterations.

$\mathbf{V}^* = \mathbf{V}^{n+k/N} + \frac{\Delta t}{N} I_{ion}(\mathbf{V}^{n+k/N}), \quad k=0,\dots,N-1.$

Parameters

int	number of subiterations

Definition at line 1845 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneReactionStepFE() [2/2]

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

Solves one reaction step using the forward Euler scheme.

$\mathbf{V}^* = \mathbf{V}^{n+k/N} + \frac{\Delta t}{N} M I_{ion}(\mathbf{V}^{n+k/N}), \quad k=0,\dots,N-1.$

Parameters

matrix_Type	full mass matrix
int	number of subiterations

Definition at line 1863 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneReactionStepRL()

void solveOneReactionStepRL ( int subiterations = 1 )

Solves one reaction step using the Rush-Larsen scheme.

Parameters

int	number of subiterations

Definition at line 1886 of file ElectroETAMonodomainSolver.hpp.

◆ updateRhs()

void updateRhs ( )

inline

Update the rhs.

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

Definition at line 1029 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneDiffusionStepBDF2()

void solveOneDiffusionStepBDF2 ( vectorPtr_Type previousPotentialPtr )

Solves one diffusion step using the BDF2 scheme.

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

Parameters

previousPotentialPtr potential at n-1

Definition at line 1906 of file ElectroETAMonodomainSolver.hpp.

◆ 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 1925 of file ElectroETAMonodomainSolver.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 1932 of file ElectroETAMonodomainSolver.hpp.

◆ solveSplitting() [1/3]

void solveSplitting ( )

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

Definition at line 1949 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneSplittingStep() [2/2]

void solveOneSplittingStep	(	IOFile_Type &	exporter,
		Real	t
	)

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

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

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

Parameters

exporter	where you want to save the solution
t	time at which we save the solution

Definition at line 1941 of file ElectroETAMonodomainSolver.hpp.

◆ 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.

Parameters

exporter where you want to save the solution

Definition at line 1959 of file ElectroETAMonodomainSolver.hpp.

◆ 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.

Parameters

exporter	where you want to save the solution
t	time at which we save the solution

Definition at line 1973 of file ElectroETAMonodomainSolver.hpp.

◆ setupPotentialExporter()

void setupPotentialExporter	(	IOFile_Type &	exporter,
		std::string	fileName = `"Potential"`
	)

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

Parameters

exporter	where you want to save the solution
t	time at which we save the solution

Definition at line 1816 of file ElectroETAMonodomainSolver.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

Parameters

exporter	where you want to save the solution
fileName	name of the file we wish to export
folder	directory where to save the solution

Definition at line 1827 of file ElectroETAMonodomainSolver.hpp.

◆ setupFibers() [1/4]

void setupFibers ( )

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

Definition at line 1535 of file ElectroETAMonodomainSolver.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)

Parameters

fibers vector with the fiber direction

Definition at line 1555 of file ElectroETAMonodomainSolver.hpp.

◆ setupFibers() [3/4]

void setupFibers	(	std::string	fibersFile,
		const std::string &	filePath = `"./"`
	)

inline

Imports the fiber direction from a hdf5 file.

Parameters

fibersFile name of the hdf5 file with the fibers

Definition at line 1125 of file ElectroETAMonodomainSolver.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.

Parameters

fibersFile	name of the file with the fibers
directory	folder in which we have the file for the fibers
format	format in which fibers are saved

format 0 = fibers saved as (fx, fy, fz) in each row

format 1 = fibers saved as fx in each row for all the mesh fy in each row for all the mesh fz in each row for all the mesh

Definition at line 1142 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneStepGatingVariablesFE()

void solveOneStepGatingVariablesFE ( )

Solves the gating variables with forward Euler.

Definition at line 2002 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneStepGatingVariablesRL()

void solveOneStepGatingVariablesRL ( )

Solves the gating variables with Rush-Larsen scheme.

Definition at line 2014 of file ElectroETAMonodomainSolver.hpp.

◆ computeRhsSVI()

void computeRhsSVI ( )

Compute the rhs using state variable interpolation.

Definition at line 2053 of file ElectroETAMonodomainSolver.hpp.

◆ computeRhsICI()

void computeRhsICI ( )

Compute the rhs using ionic current interpolation.

Definition at line 2030 of file ElectroETAMonodomainSolver.hpp.

◆ computeRhsICIWithFullMass()

void computeRhsICIWithFullMass ( )

Compute the rhs using ionic current interpolation.

This method is useful to solve ICI without lumping the mass matrix in fron of the reaction term. Lump the mass matrix, and pass as argument a full mass matrix

Definition at line 2038 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneICIStep() [1/2]

void solveOneICIStep ( )

virtual

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 $I_j = I_{ion}(V_j^n)$

Definition at line 2065 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneICIStepWithFullMass() [1/2]

void solveOneICIStepWithFullMass ( )

solves using ionic current interpolation

This method is useful to solve ICI without lumping the mass matrix in front of the reaction term. Lump the mass matrix, and pass as argument a full mass matrix

Definition at line 2073 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneSVIStep() [1/2]

void solveOneSVIStep ( )

Solve one full step with state variable interpolation.

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

Definition at line 2081 of file ElectroETAMonodomainSolver.hpp.

◆ solveICI() [1/3]

void solveICI ( )

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

Definition at line 2089 of file ElectroETAMonodomainSolver.hpp.

◆ solveSVI() [1/3]

void solveSVI ( )

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

Definition at line 2100 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneICIStep() [2/2]

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 $I_j = I_{ion}(V_j^n)$

Parameters

exporter	where we want to save the solution
t	time at wich we save the solution

Definition at line 2111 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneICIStepWithFullMass() [2/2]

void solveOneICIStepWithFullMass	(	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 $I_j = I_{ion}(V_j^n)$ This method is useful to solve ICI without lumping the mass matrix in front of the reaction term. Lump the mass matrix, and pass as argument a full mass matrix

Parameters

exporter	where we want to save the solution
t	time at wich we save the solution

Definition at line 2119 of file ElectroETAMonodomainSolver.hpp.

◆ solveOneSVIStep() [2/2]

void solveOneSVIStep	(	IOFile_Type &	exporter,
		Real	t
	)

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

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

Parameters

exporter	where we want to save the solution
t	time at wich we save the solution

Definition at line 2127 of file ElectroETAMonodomainSolver.hpp.

◆ solveICI() [2/3]

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

Parameters

exporter where we want to save the solution

Definition at line 2135 of file ElectroETAMonodomainSolver.hpp.

◆ solveSVI() [2/3]

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

Parameters

exporter where we want to save the solution

Definition at line 2153 of file ElectroETAMonodomainSolver.hpp.

◆ solveICI() [3/3]

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.

Parameters

exporter	where we want to save the solution
t	time at wich we save the solution

Definition at line 2165 of file ElectroETAMonodomainSolver.hpp.

◆ solveICIWithFullMass()

void solveICIWithFullMass	(	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.

This method is useful to solve ICI without lumping the mass matrix in front of the reaction term. Lump the mass matrix, and pass as argument a full mass matrix

Parameters