CEPS: IonicSolver Class Reference

Detailed Description

Groups two ODE solvers for ionic variables and interacts with cardiac problem.

The goal of this solver is to return a distributed halo vector with values of the ionic current on the rows of the unknown set in the AbstractIonicModel

Definition at line 43 of file IonicSolver.hpp.

#include <IonicSolver.hpp>

Public Types
using	EvolFunction = ceps::Function< void(CepsReal, CepsReal , CepsReal , CepsUInt)>
	Typedef for evolution functions of the ionic model converted into ceps::Function objects. More...

Public Member Functions
	IonicSolver (CepsString opts, AbstractIonicModel m, AbstractDiscretization discr)
	Constructor with parameters from input file and ionic model to be linked with The constructor also sets the passed vector of TMV data to the initial values of the ionic model. More...

	~IonicSolver ()
	Destructor. More...

void	setActionPotential (DHVecPtr vPde)
	Copies values of TMV from PDE vector to local array. Call this method prior to takeOneStep or takeOneSubStep. More...

void	takeOneStep (CepsReal t, CepsReal dt, DHVecPtr vPde)
	Advance the ODE system by one full step each (not substep) More...

void	takeOneSubStep (CepsReal t, CepsReal dt, DHVecPtr vPde)
	Advance the ODE system by one sub step (for RK solvers) More...

void	addDtv (DHVecPtr dtv, CepsReal t=0) const
	Fills the given distributed vector with values of ionic current from ODE system. Does the unit conversion. More...

void	fillPdeVm (DHVecPtr vPde) const
	Fills the linked PDE vector for vm with current values of m_v. Can be used to get initial condition. More...

CepsReal	getVm (CepsBool convert) const
	Get TMV for testing purposes. More...

CepsReal *	getStates () const
	Get pointer on state vars for testing purposes. More...

CepsReal *	getDtv () const
	Get pointer on ionic current for testing purposes. More...

CepsUInt	getNbMultiSteps () const
	Number of multi steps of the inner solver. More...

Protected Member Functions
void	computeIndexMapping ()
	Sets the map from instance-local indices of points to global indices, then allocates arrays and sets initial condition. More...

void	createSolvers (CepsString opts)
	Instantiates ODE solvers from options. More...

void	initializeSolver ()
	Set the initial conditions and required intermediate arrays of the ODE solvers. More...

void	computeModelRates (CepsReal t, CepsReal *y)
	Computes the evolution function and ionic current on all dofs, calls the model. More...

void	computeRatesLin (CepsReal t, CepsReal w, CepsReal dtw, CepsUInt n)
	Call the linear part of evolution function of the model. More...

void	computeRatesNonLin (CepsReal t, CepsReal w, CepsReal dtw, CepsUInt n)
	Get the non linear part of evolution function of the model. More...

Protected Attributes
AbstractIonicModel *	m_model
	Link to ionic model equations. More...

EvolFunction *	m_fLin
	Evolution function (linear part -1/tau) More...

EvolFunction *	m_fNLin
	Evolution function (non linear part winf/tau + others) More...

AbstractDiscretization *	m_sDiscr
	Link to spatial discretization. More...

AbstractOdeSolver *	m_solver
	internal ODE solver More...

CepsReal *	m_y
	Values of state variables. More...

CepsReal *	m_dtyLin
	Linear part of rates. More...

CepsReal *	m_dtyNLin
	Non-linear part of rates. More...

CepsReal *	m_v
	Transmembrane voltage. More...

CepsReal *	m_dtv
	Total ionic current. More...

CepsBool	m_tauOk
	Flag to avoid to compute tau and winf twice per iteration. More...

DHVecPtr *	m_vPde
	Pointer on pointer with v data from the PDE. More...

CepsVector< CepsIndex >	m_localToGlobal
	Mapping between local index of dof and index in PDE. More...

CepsUInt	m_size
	Number of dofs for this solver. More...

Member Typedef Documentation

◆ EvolFunction

using IonicSolver::EvolFunction = ceps::Function<void(CepsReal,CepsReal*,CepsReal*,CepsUInt)>

Typedef for evolution functions of the ionic model converted into ceps::Function objects.

Definition at line 50 of file IonicSolver.hpp.

Constructor & Destructor Documentation

◆ IonicSolver()

IonicSolver::IonicSolver	(	CepsString	opts,
		AbstractIonicModel *	m,
		AbstractDiscretization *	discr
	)

Constructor with parameters from input file and ionic model to be linked with The constructor also sets the passed vector of TMV data to the initial values of the ionic model.

See Ionic Models for information on available parameters

See also: InputParameters

Definition at line 34 of file IonicSolver.cpp.

◆ ~IonicSolver()

IonicSolver::~IonicSolver ( )

Destructor.

Definition at line 71 of file IonicSolver.cpp.

Member Function Documentation

◆ addDtv()

void IonicSolver::addDtv	(	DHVecPtr	dtv,
		CepsReal	t = `0`
	)		const

Fills the given distributed vector with values of ionic current from ODE system. Does the unit conversion.

Parameters

[out]	dtv	vector in which data will be put
[in]	t	time for evaluation of Cm, if needed

Definition at line 112 of file IonicSolver.cpp.

◆ computeIndexMapping()

void IonicSolver::computeIndexMapping ( )

protected

Sets the map from instance-local indices of points to global indices, then allocates arrays and sets initial condition.

Definition at line 163 of file IonicSolver.cpp.

◆ computeModelRates()

void IonicSolver::computeModelRates	(	CepsReal	t,
		CepsReal *	y
	)

protected

Computes the evolution function and ionic current on all dofs, calls the model.

Definition at line 274 of file IonicSolver.cpp.

◆ computeRatesLin()

void IonicSolver::computeRatesLin	(	CepsReal	t,
		CepsReal *	w,
		CepsReal *	dtw,
		CepsUInt	n
	)

protected

Call the linear part of evolution function of the model.

Definition at line 298 of file IonicSolver.cpp.

◆ computeRatesNonLin()

void IonicSolver::computeRatesNonLin	(	CepsReal	t,
		CepsReal *	w,
		CepsReal *	dtw,
		CepsUInt	n
	)

protected

Get the non linear part of evolution function of the model.

Definition at line 306 of file IonicSolver.cpp.

◆ createSolvers()

void IonicSolver::createSolvers ( CepsString opts )

protected

Instantiates ODE solvers from options.

Definition at line 177 of file IonicSolver.cpp.

◆ fillPdeVm()

void IonicSolver::fillPdeVm ( DHVecPtr vPde ) const

Fills the linked PDE vector for vm with current values of m_v. Can be used to get initial condition.

Definition at line 126 of file IonicSolver.cpp.

◆ getDtv()

CepsReal * IonicSolver::getDtv ( ) const

Get pointer on ionic current for testing purposes.

Definition at line 149 of file IonicSolver.cpp.

◆ getNbMultiSteps()

CepsUInt IonicSolver::getNbMultiSteps ( ) const

Number of multi steps of the inner solver.

Definition at line 155 of file IonicSolver.cpp.

◆ getStates()

CepsReal * IonicSolver::getStates ( ) const

Get pointer on state vars for testing purposes.

Definition at line 143 of file IonicSolver.cpp.

◆ getVm()

CepsReal IonicSolver::getVm ( CepsBool convert ) const

Get TMV for testing purposes.

Definition at line 135 of file IonicSolver.cpp.

◆ initializeSolver()

void IonicSolver::initializeSolver ( )

protected

Set the initial conditions and required intermediate arrays of the ODE solvers.

Definition at line 245 of file IonicSolver.cpp.

◆ setActionPotential()

void IonicSolver::setActionPotential ( DHVecPtr vPde )

Copies values of TMV from PDE vector to local array. Call this method prior to takeOneStep or takeOneSubStep.

Definition at line 86 of file IonicSolver.cpp.

◆ takeOneStep()

void IonicSolver::takeOneStep	(	CepsReal	t,
		CepsReal	dt,
		DHVecPtr	vPde
	)

Advance the ODE system by one full step each (not substep)

Definition at line 96 of file IonicSolver.cpp.

◆ takeOneSubStep()

void IonicSolver::takeOneSubStep	(	CepsReal	t,
		CepsReal	dt,
		DHVecPtr	vPde
	)

Advance the ODE system by one sub step (for RK solvers)

Definition at line 104 of file IonicSolver.cpp.

Field Documentation

◆ m_dtv

CepsReal* IonicSolver::m_dtv

protected

Total ionic current.

Definition at line 158 of file IonicSolver.hpp.

◆ m_dtyLin

CepsReal* IonicSolver::m_dtyLin

protected

Linear part of rates.

Definition at line 155 of file IonicSolver.hpp.

◆ m_dtyNLin

CepsReal* IonicSolver::m_dtyNLin

protected

Non-linear part of rates.

Definition at line 156 of file IonicSolver.hpp.

◆ m_fLin

EvolFunction* IonicSolver::m_fLin

protected

Evolution function (linear part -1/tau)

Definition at line 145 of file IonicSolver.hpp.

◆ m_fNLin

EvolFunction* IonicSolver::m_fNLin

protected

Evolution function (non linear part winf/tau + others)

Definition at line 146 of file IonicSolver.hpp.

◆ m_localToGlobal

CepsVector<CepsIndex> IonicSolver::m_localToGlobal

protected

Mapping between local index of dof and index in PDE.

Definition at line 165 of file IonicSolver.hpp.

◆ m_model

AbstractIonicModel* IonicSolver::m_model

protected

Link to ionic model equations.

Definition at line 144 of file IonicSolver.hpp.

◆ m_sDiscr

AbstractDiscretization* IonicSolver::m_sDiscr

protected

Link to spatial discretization.

Definition at line 149 of file IonicSolver.hpp.

◆ m_size

CepsUInt IonicSolver::m_size

protected

Number of dofs for this solver.

Definition at line 167 of file IonicSolver.hpp.

◆ m_solver

AbstractOdeSolver* IonicSolver::m_solver

protected

internal ODE solver

Definition at line 151 of file IonicSolver.hpp.

◆ m_tauOk

CepsBool IonicSolver::m_tauOk

protected

Flag to avoid to compute tau and winf twice per iteration.

Definition at line 160 of file IonicSolver.hpp.

◆ m_v

CepsReal* IonicSolver::m_v

protected

Transmembrane voltage.

Definition at line 157 of file IonicSolver.hpp.

◆ m_vPde

DHVecPtr* IonicSolver::m_vPde

protected

Pointer on pointer with v data from the PDE.

Definition at line 163 of file IonicSolver.hpp.

◆ m_y

CepsReal* IonicSolver::m_y

protected

Values of state variables.

Definition at line 154 of file IonicSolver.hpp.

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

/builds/xxjFYZX3/0/carmen/ceps/src/ode/solver/IonicSolver.hpp
/builds/xxjFYZX3/0/carmen/ceps/src/ode/solver/IonicSolver.cpp

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Member Typedef Documentation

◆ EvolFunction

Constructor & Destructor Documentation

◆ IonicSolver()

◆ ~IonicSolver()

Member Function Documentation

◆ addDtv()

◆ computeIndexMapping()

◆ computeModelRates()

◆ computeRatesLin()

◆ computeRatesNonLin()

◆ createSolvers()

◆ fillPdeVm()

◆ getDtv()

◆ getNbMultiSteps()

◆ getStates()

◆ getVm()

◆ initializeSolver()

◆ setActionPotential()

◆ takeOneStep()

◆ takeOneSubStep()

Field Documentation

◆ m_dtv

◆ m_dtyLin

◆ m_dtyNLin

◆ m_fLin

◆ m_fNLin

◆ m_localToGlobal

◆ m_model

◆ m_sDiscr

◆ m_size

◆ m_solver

◆ m_tauOk

◆ m_v

◆ m_vPde

◆ m_y