#include <ElectrodesStimulusFactory.hpp>

Inheritance diagram for ElectrodesStimulusFactory< DIM >:

Collaboration diagram for ElectrodesStimulusFactory< DIM >:

Public Member Functions
	ElectrodesStimulusFactory (std::vector< std::pair< AbstractChasteRegion< DIM > , AbstractChasteRegion< DIM > > > &rElectrodePairs, std::vector< double > &rStimulusMagnitudes, std::vector< double > &rDurations, std::vector< double > &rPeriods, std::vector< double > &rStarts, std::vector< double > &rEnds)

boost::shared_ptr< AbstractStimulusFunction >	CreateStimulusForNode (Node< DIM > *pNode)

	~ElectrodesStimulusFactory ()

void	SetCompatibleExtracellularStimulus ()

void	GroundSecondElectrode (bool grounded)

Public Member Functions inherited from AbstractStimulusFactory< DIM >
virtual boost::shared_ptr< AbstractStimulusFunction >	CreateStimulusForNode (Node< ELEMENT_DIM > *pNode)

virtual unsigned	GetNumberOfCells ()

	AbstractStimulusFactory ()

virtual	~AbstractStimulusFactory ()

void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > *pMesh)

AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > *	GetMesh ()

std::vector< AbstractChasteRegion< ELEMENT_DIM > * >	GetRegionsToBeGrounded ()

Protected Types
typedef LinearBasisFunction< DIM >	BasisFunction

Protected Member Functions
void	CheckForElectrodesIntersection ()

double	ComputeElectrodeTotalFlux (AbstractChasteRegion< DIM > *pRegion, double stimulusMagnitude)

Protected Attributes
std::vector< std::pair< AbstractChasteRegion< DIM > , AbstractChasteRegion< DIM > > > &	mrElectrodePairs

std::vector< double > &	mrMagnitudes

std::vector< double > &	mrDurations

std::vector< double > &	mrPeriods

std::vector< double > &	mrStarts

std::vector< double > &	mrEnds

std::vector< double >	mMagnitudesElectrode1

std::vector< double >	mMagnitudesElectrode2

bool	mGroundSecondElectrode

Protected Attributes inherited from AbstractStimulusFactory< DIM >
AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > *	mpMesh

std::vector< AbstractChasteRegion< ELEMENT_DIM > * >	mGroundedRegions

Friends
class	TestStimulusFactory

Detailed Description

template<unsigned DIM>
class ElectrodesStimulusFactory< DIM >

This class implements the specification of tow electrodes with a RegularStimulus applied to them. It makes sure the compatibility conditions is verified by scaling the magnitude of the second electrode according to the flux flowing thorugh each of them.

User needs to pass in a vector of pairs of electrodes and, for each pair, the stimulation parameters. This class will then implement the CreateStimulusForNode accordingly by creating a RegularStimulus object for each node. Each node belonging to any "first electrode" will have an extracellular volume stimulus equals to the value that is passed in, while each node belonging to any "second elecrode" will have an extracellular volume stimulus corrected by the flux (proportional to electrode volume) in such a way that compatibility conditions of the extended bidomain equations are followed.

It is possible to ground all second electrodes by calling GroundSecondElectrode. In this case, the member variable mGroundSecondElectrode will have size > 0 and other classes can behave accordingly (e.g., problem class will set Dirichlet boundary conditions accordingly).

Definition at line 67 of file ElectrodesStimulusFactory.hpp.

Member Typedef Documentation

template<unsigned DIM>

typedef LinearBasisFunction<DIM> ElectrodesStimulusFactory< DIM >::BasisFunction

protected

typedef for basis function

Definition at line 121 of file ElectrodesStimulusFactory.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

ElectrodesStimulusFactory< DIM >::ElectrodesStimulusFactory	(	std::vector< std::pair< AbstractChasteRegion< DIM > , AbstractChasteRegion< DIM > > > &	rElectrodePairs,
		std::vector< double > &	rStimulusMagnitudes,
		std::vector< double > &	rDurations,
		std::vector< double > &	rPeriods,
		std::vector< double > &	rStarts,
		std::vector< double > &	rEnds
	)

Constructor. Electrodes and stimulation parameters need to be passed in.

Parameters

rElectrodePairs	the pairs of electrodes
rStimulusMagnitudes	the magnitudes of the stimuli (microA / cm^3). First electrode will have magnitude value and second electrode will have -magnitude (before being corrected to ensure equal flux).
rDurations	the duration of each stimulus (ms)
rPeriods	the period of each stimulus (ms)
rStarts	the start time of each stimulus (ms).
rEnds	the end of each stimulation (ms)

Definition at line 44 of file ElectrodesStimulusFactory.cpp.

References EXCEPTION, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode1, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode2, and ElectrodesStimulusFactory< DIM >::mrMagnitudes.

template<unsigned DIM>

ElectrodesStimulusFactory< DIM >::~ElectrodesStimulusFactory ( )

Destructor

Definition at line 72 of file ElectrodesStimulusFactory.cpp.

Member Function Documentation

template<unsigned DIM>

void ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection ( )

protected

Helper method to check if any of the electrodes intersects with the other. it needs to check whether any element that conatins any node of electrode 1 does not conatin also nodes of eledtrode 2

Definition at line 77 of file ElectrodesStimulusFactory.cpp.

References PetscTools::Barrier(), EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), DistributedVectorFactory::IsGlobalIndexLocal(), AbstractStimulusFactory< DIM >::mpMesh, and ElectrodesStimulusFactory< DIM >::mrElectrodePairs.

Referenced by ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus().

template<unsigned DIM>

double ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux	(	AbstractChasteRegion< DIM > *	pRegion,
		double	stimulusMagnitude
	)

protected

Helper method to compute electrode flux. This method is the main functionality of this class.

It essentially computes the contribution of each electrode to the RHS vector of the linear system. The loops over elements and gauss points mimicks the ones in AssembleOnElement. Interpolation is done for the value of the magnitude of the electrode.

NOTE that this method assumes the use of a 2nd order Gauss quadrature rule (the default value of Chaste FE assemblers).

Parameters