CEPS: CardiacSolver Class Reference

Detailed Description

Solves cardiac problems, that all share the same structure.

The class regroups the solving algorithms for various numerical schemes (SBDF, Runge-Kutta, Crank-Nicolson). Whatever the dimension of the unknown U (one or two scalars), the problems can be written in the weak form

[M + alpha K] U = 1/Cm (Iion+Iapp) + 1/(AmCm) src

where M and K are respectively the mass and stiffness matrix

The ionic models return directly 1/Cm (Iion+Iapp), as long as the stimulations were correctly set with the Stimulation flag (TYPE IAPP input parameter), and linked to the ionic models

Definition at line 53 of file CardiacSolver.hpp.

#include <CardiacSolver.hpp>

Inheritance diagram for CardiacSolver:

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Public Member Functions
virtual	~CardiacSolver ()
	Destructor. More...

	CardiacSolver (CardiacProblem *problem)
	Constructor with associated PDE problem. More...

void	solve () override
	Performs all iterations of the PDE solver. More...

CepsString	getResultsLocationMessage () const
	To be displayed at the end of computation. More...

CardiacProblem *	getCardiacProblem () const
	Converts own pointer to abstract pde problem to cardiac problem. More...

ActivationTracker *	getActivationTracker () const
	Link to activation tracker. More...

Public Member Functions inherited from HeatSolver
	HeatSolver ()=delete
	Deleted constructor. More...

	HeatSolver (HeatProblem *problem)
	Constructor (valid with HeatProblem and PseudoWaveFrontProblem) More...

	~HeatSolver () override
	Destructor. More...

Public Member Functions inherited from FETimedSolver
	FETimedSolver ()=delete
	Deleted constructor. More...

	FETimedSolver (AbstractTimedPdeProblem *problem)
	Constructor (valid with HeatProblem and PseudoWaveFrontProblem) More...

	~FETimedSolver () override
	Destructor. More...

Public Member Functions inherited from AbstractTimedPdeSolver
	AbstractTimedPdeSolver (AbstractTimedPdeProblem *pb)
	Default constructor. More...

virtual	~AbstractTimedPdeSolver ()
	Destructor. More...

void	solve () override
	Solves the all PDE (all iterations) More...

void	setupWithParameters (InputParameters *params) override
	Set attributes from input file. Parameters are passed as arguments in case one wants to use other parameters. More...

CepsUInt	getExpectedNumberOfOutputs () const override
	Number of files written. More...

DHVecPtr	getSolution () const
	Returns a copy of the distributed vector containing the current solution. More...

void	enableErrorComputation ()
	Sets the comparison with analytic solution. More...

CepsArray2< CepsArray3< CepsArray3< CepsReal > > >	getErrors () const
	Gets the currently computed errors. First index selects absolute(0) or relative(1) second index select max on t(0), integral on t(1), or error at end of time interval(2) third index is L-inf, L1, L2 selector. More...

Public Member Functions inherited from AbstractPdeSolver
	AbstractPdeSolver ()=delete
	Deleted default constructor. More...

	AbstractPdeSolver (AbstractPdeProblem *pb)
	Constructor with problem. More...

	AbstractPdeSolver (const AbstractPdeSolver &that)=delete
	No copy. More...

AbstractPdeSolver &	operator= (const AbstractPdeSolver &that)=delete
	No assignment. More...

	~AbstractPdeSolver () override
	Destructor. More...

void	disableOutput ()
	Stops output. More...

void	enableOutput ()
	Starts output. More...

TimeWriter *	getTimeWriter () const
	Access to Time Writer to be able to add data. More...

void	disableErrorComputation ()
	Sets the comparison with analytic solution. More...

Public Member Functions inherited from CepsObject
	CepsObject ()=default
	default constructor More...

	CepsObject (const CepsObject &)=default
	Copy constructor. More...

virtual	~CepsObject ()=default
	Destructor. More...

CepsObject &	operator= (const CepsObject &)=default
	Assignment operator. More...

CepsObject *	toBaseObject ()
	Returns a pointer to CepsObject class. More...

const CepsObject *	toBaseObject () const
	Returns a pointer to CepsObject class, const version. More...

Profiler *	getProfiler () const
	Access to profiler. More...

Protected Member Functions
void	assembleAndSolve () override
	Performs one iteration of the solver. More...

CepsBool	finished () const override
	Tells if simulation reached end time or, if enabled, all points have seen an AP. More...

void	fillSourceTermsVector (CepsReal tn) override
	Computes all contributions to source terms (ionic current, stimcurrent, field sources) with a loop on source terms. More...

void	output (DHVecPtr dummy, CepsBool immediatWriting=true) override
	Calls the appropriate post-processing and writing methods. More...

Protected Member Functions inherited from HeatSolver
void	initializeAssemblers () override
	Creates the right type of assemblers for LHS and BCs. Needs to be overriden. More...

HeatProblem *	getHeatProblem () const
	Returns a pointer to the pb with appropriate type. More...

Protected Member Functions inherited from FETimedSolver
void	assembleAndSolve () override
	Main routine used during solving, assemble the system depending on the scheme and solve the linear system. More...

void	assembleAndSolveSBDF (CepsUInt nSteps)
	Updates matrix and RHS for the SBDF numerical scheme. More...

void	assembleAndSolveCN (CepsUInt nSteps)
	Updates matrix and RHS for the CN numerical scheme. More...

Protected Member Functions inherited from AbstractTimedPdeSolver
AbstractTimedPdeProblem *	getTimedProblem () const
	Returns a pointer with the appropriate type of pb. More...

virtual void	displayProgress () const
	Tells time. More...

void	determineSolverType (CepsString s)
	Initialize the type from parameter string. More...

virtual void	allocateArrays ()
	Allocates the arrays with the correct number of multistep. More...

void	updateAssemblers () override
	Update assemblers and recompute everything is needed. More...

virtual void	swapMultiStepPointers ()
	Swaps vectors of array pointers for next step (for multistep methods) More...

Protected Member Functions inherited from AbstractPdeSolver
virtual void	initializeWriter ()
	Creates the solution writer. More...

Protected Attributes
ActivationTracker *	m_activationTracker
	Output computation and writing. More...

CepsVector< IonicSolver * >	m_ionSolvers
	One solver per ionic model in the problem. More...

CepsString	m_ionSolvOpts
	Options for ionic ODE solvers. More...

CepsBool	m_writeIIon
	Flag for additional output. More...

CepsBool	m_writeIapp
	Flag for additional output. More...

CepsReal	m_postProcessPeriod
	Period of post process calculations. More...

std::set< CepsUInt >	m_saveDepolarizationTime
	Components of which to save depolarization times. More...

CepsBool	m_stopAtCompleteActivation
	stop when all points have activation time computed More...

CepsBool	m_stopAtCompleteRepolarization
	stop when all points have APD computed More...

Protected Attributes inherited from FETimedSolver
FiniteElements *	m_fe
	Geometry and reference FE. More...

DHVecPtr	m_temp1
	Temporary vector for assembly of source terms. More...

DHVecPtr	m_temp2
	Temporary vector for assembly of source terms. More...

Protected Attributes inherited from AbstractTimedPdeSolver
DMatPtr	m_dtMat
	Matrix of time derivative of the system. More...

DVecPtr	m_timeDerEqsVec
	Vector of 1 or 0, depending on whether the dof equation has a time derivative or not. More...

DVecPtr	m_noTimeDerEqsVec
	The opposite version of m_timeDerEqsVec, such as m_timeDerEqsVec + m_noTimeDerEqsVec = vec(1) More...

DHVecPtr	m_uNp1
	Vectors of unknowns at time t^n+1. More...

CepsVector< DHVecPtr >	m_uNm
	Solution vectors at different time steps. Several vectors are needed for multi-step methods. (read u^{n-k}). m_uNm[0] is current solution. More...

CepsString	m_type
	Numerical scheme descriptor. More...

CepsString	m_rkType
	RK Method if the solver is of type "RK". More...

CepsUInt	m_nbMultiSteps
	Maximum number of steps needed to compute next solution (eg CN:2) More...

TimeStepper *	m_timeStepper
	Monitors time evolution. More...

CepsVector< DHVecPtr >	m_regSourcesNm
	Sources at previous steps (if problem has source terms) More...

CepsVector< DHVecPtr >	m_lapSourcesNm
	Sources at previous steps (if problem has laplace source terms) More...

CepsVector< DHVecPtr >	m_rkF
	RK methods: intermediate rates. More...

CepsVector< DHVecPtr >	m_rkU
	RK methods: intermediate evaluations. More...

CepsReal	m_scaleSystem
	A factor for both matrix and vector (typically 1/dt) More...

CepsBool	m_cheatConvergence
	If true, use exact solution for first steps of multi steps methods. More...

CepsUInt	m_nbIterSnapshot
	Output perdiodicity. More...

Protected Attributes inherited from AbstractPdeSolver
AbstractPdeProblem *	m_problem
	Link to PDE to solve. More...

AbstractDiscretization *	m_discretization
	Link to PDE discretization. More...

LinearSystem *	m_linearSystem
	Linear system. More...

DMatPtr	m_lhs
	Left hand side of the system. More...

DVecPtr	m_rhs
	Right hand side of the system. More...

AbstractAssembler *	m_opAsb
	Assembler for the operator matrix. More...

DMatPtr	m_opMat
	Matrix of operator. More...

AbstractAssembler *	m_bcAsb
	Assembler for Robin and Neumann BCs. More...

DMatPtr	m_bcMat
	Matrix of boundary conditions. More...

DVecPtr	m_bcVec
	Vector of boundary conditions. More...

AbstractAssembler *	m_lapSrcAsb
	Assembler for laplace source terms. More...

DMatPtr	m_lapSrcMat
	Matrix used for laplace source terms. More...

CepsBool	m_hasRegSrc
	Flag telling if there are regular source terms. More...

CepsBool	m_hasLapSrc
	Flag telling if there are Delta f source terms. More...

CepsBool	m_useMassLumping
	Put the mass on the diagonal of the matrix. More...

CepsBool	m_doOutput
	Enables/disables outputs. More...

VtkWriter *	m_writer
	Manages output. More...

TimeWriter *	m_timeWriter
	Writer for time dependant data (even for static problems...) More...

CepsBool	m_doError
	Compute error wrt analytic solution or reference. More...

PdeErrorCalculator *	m_errors
	Error computation. More...

Additional Inherited Members
Static Protected Attributes inherited from AbstractTimedPdeSolver
static constexpr CepsReal	c_alphaSBDF [5] = {0., 1., 2. / 3., 6. / 11., 12. / 25.}
	LHS coeffcients of the SBDF schemes. More...

static constexpr CepsReal	c_alphaCN [3] = {0., 1., 1. / 2.}
	LHS coeffcients of the CN scheme. More...

static constexpr CepsReal	c_akSBDF [4][4] = {{1.}, {4. / 3., -1. / 3.}, {18. / 11., -9. / 11., 2. / 11.}, {48. / 25., -36. / 25., 16. / 25., -3. / 25.}}
	RHS coeffcients of the SBDF schemes. More...

Static Protected Attributes inherited from CepsObject
static Profiler	m_profiler
	The same profiler for each big object. More...

Constructor & Destructor Documentation

◆ ~CardiacSolver()

CardiacSolver::~CardiacSolver ( )

virtual

Destructor.

Definition at line 71 of file CardiacSolver.cpp.

◆ CardiacSolver()

CardiacSolver::CardiacSolver ( CardiacProblem * problem )

Constructor with associated PDE problem.

Definition at line 32 of file CardiacSolver.cpp.

Member Function Documentation

◆ assembleAndSolve()

void CardiacSolver::assembleAndSolve ( )

overrideprotectedvirtual

Performs one iteration of the solver.

Implements AbstractPdeSolver.

Definition at line 109 of file CardiacSolver.cpp.

◆ fillSourceTermsVector()

void CardiacSolver::fillSourceTermsVector ( CepsReal tn )

overrideprotectedvirtual

Computes all contributions to source terms (ionic current, stimcurrent, field sources) with a loop on source terms.

Parameters

[in] tn time at which source terms will be evaluated

Reimplemented from AbstractTimedPdeSolver.

Definition at line 127 of file CardiacSolver.cpp.

◆ finished()

CepsBool CardiacSolver::finished ( ) const

overrideprotectedvirtual

Tells if simulation reached end time or, if enabled, all points have seen an AP.

Reimplemented from AbstractTimedPdeSolver.

Definition at line 94 of file CardiacSolver.cpp.

◆ getActivationTracker()

ActivationTracker * CardiacSolver::getActivationTracker ( ) const

Link to activation tracker.

Definition at line 87 of file CardiacSolver.cpp.

◆ getCardiacProblem()

CardiacProblem * CardiacSolver::getCardiacProblem ( ) const

Converts own pointer to abstract pde problem to cardiac problem.

Definition at line 103 of file CardiacSolver.cpp.

◆ getResultsLocationMessage()

CepsString CardiacSolver::getResultsLocationMessage ( ) const

To be displayed at the end of computation.

◆ output()

void CardiacSolver::output	(	DHVecPtr	dummy,
		CepsBool	immediatWriting = `true`
	)

overrideprotectedvirtual

Calls the appropriate post-processing and writing methods.

Reimplemented from AbstractTimedPdeSolver.

Definition at line 161 of file CardiacSolver.cpp.

◆ solve()

void CardiacSolver::solve ( )

overridevirtual

Performs all iterations of the PDE solver.

Implements AbstractPdeSolver.

Definition at line 79 of file CardiacSolver.cpp.

Field Documentation

◆ m_activationTracker

ActivationTracker* CardiacSolver::m_activationTracker

protected

Output computation and writing.

Definition at line 120 of file CardiacSolver.hpp.

◆ m_ionSolvers

CepsVector<IonicSolver*> CardiacSolver::m_ionSolvers

protected

One solver per ionic model in the problem.

Definition at line 123 of file CardiacSolver.hpp.

◆ m_ionSolvOpts

CepsString CardiacSolver::m_ionSolvOpts

protected

Options for ionic ODE solvers.

Definition at line 124 of file CardiacSolver.hpp.

◆ m_postProcessPeriod

CepsReal CardiacSolver::m_postProcessPeriod

protected

Period of post process calculations.

Definition at line 129 of file CardiacSolver.hpp.

◆ m_saveDepolarizationTime

std::set<CepsUInt> CardiacSolver::m_saveDepolarizationTime

protected

Components of which to save depolarization times.

Definition at line 130 of file CardiacSolver.hpp.

◆ m_stopAtCompleteActivation

CepsBool CardiacSolver::m_stopAtCompleteActivation

protected

stop when all points have activation time computed

Definition at line 133 of file CardiacSolver.hpp.

◆ m_stopAtCompleteRepolarization

CepsBool CardiacSolver::m_stopAtCompleteRepolarization

protected

stop when all points have APD computed

Definition at line 134 of file CardiacSolver.hpp.

◆ m_writeIapp

CepsBool CardiacSolver::m_writeIapp

protected

Flag for additional output.

Definition at line 128 of file CardiacSolver.hpp.

◆ m_writeIIon

CepsBool CardiacSolver::m_writeIIon

protected

Flag for additional output.

Definition at line 127 of file CardiacSolver.hpp.

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

/builds/xxjFYZX3/0/carmen/ceps/src/cardiac/solver/CardiacSolver.hpp
/builds/xxjFYZX3/0/carmen/ceps/src/cardiac/solver/CardiacSolver.cpp

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ~CardiacSolver()

◆ CardiacSolver()

Member Function Documentation

◆ assembleAndSolve()

◆ fillSourceTermsVector()

◆ finished()

◆ getActivationTracker()

◆ getCardiacProblem()

◆ getResultsLocationMessage()

◆ output()

◆ solve()

Field Documentation

◆ m_activationTracker

◆ m_ionSolvers

◆ m_ionSolvOpts

◆ m_postProcessPeriod

◆ m_saveDepolarizationTime

◆ m_stopAtCompleteActivation

◆ m_stopAtCompleteRepolarization

◆ m_writeIapp

◆ m_writeIIon