Electrodes< DIM > Class Template Reference

#include <Electrodes.hpp>

Collaboration diagram for Electrodes< DIM >:

Public Member Functions
	Electrodes (AbstractTetrahedralMesh< DIM, DIM > &rMesh, bool groundSecondElectrode, unsigned index, double lowerValue, double upperValue, double magnitude, double startTime, double duration)
boost::shared_ptr < BoundaryConditionsContainer < DIM, DIM, 2 > >	GetBoundaryConditionsContainer ()
bool	SwitchOff (double time)
bool	SwitchOn (double time)
double	GetSwitchOnTime ()
double	GetSwitchOffTime ()
bool	HasGroundedElectrode ()
Private Member Functions
void	ComputeElectrodesAreasAndCheckEquality (unsigned index, double lowerValue, double upperValue)
template<class Archive >
void	save (Archive &archive, const unsigned int version) const
template<class Archive >
void	load (Archive &archive, const unsigned int version)
	Electrodes ()
Private Attributes
bool	mGroundSecondElectrode
boost::shared_ptr < BoundaryConditionsContainer < DIM, DIM, 2 > >	mpBoundaryConditionsContainer
double	mStartTime
double	mEndTime
bool	mAreActive
AbstractTetrahedralMesh< DIM, DIM > *	mpMesh
double	mLeftElectrodeArea
double	mRightElectrodeArea
Friends
class	TestBidomainWithBathAssembler
class	TestElectrodes
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class Electrodes< DIM >

A class for setting up the boundary conditions associated with electrodes. There are two modes: grounding the second electrode, in which case the first electrode has an input flux (Neumann boundary condition) of the specified magnitude, the extracellular potential is fixed on the second electrode; or not grounded, in which case the opposite electrode has an equal and opposite output flux.

This class assumes the given mesh is cuboid, and the electrodes are taken to be the specified opposite surfaces.

Note the class now includes a pointer to the mesh as a member variable, as this is required to archive (reconstruct) itself. Because boost is clever it will still only archive one copy of the mesh.

Definition at line 58 of file Electrodes.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

Electrodes< DIM >::Electrodes ( ) [inline, private]

Private default constructor for archiving only.

Definition at line 141 of file Electrodes.hpp.

template<unsigned DIM>

Electrodes< DIM >::Electrodes	(	AbstractTetrahedralMesh< DIM, DIM > &	rMesh,
		bool	groundSecondElectrode,
		unsigned	index,
		double	lowerValue,
		double	upperValue,
		double	magnitude,
		double	startTime,
		double	duration
	)			`[inline]`

Constructor.

Parameters:

	rMesh	The mesh, assumed to be a cuboid.
	groundSecondElectrode	Whether to ground the second electrode (see class documentation)
	index	The value i when applying the electrodes to x_i=a and x_i=b (a<b)
	lowerValue	The value a when applying the electrodes to x_i=a and x_i=b (a<b) (should be the minimum value of x_i for the given mesh)
	upperValue	The value b when applying the electrodes to x_i=a and x_i=b (a<b) (should be the maximum value of x_i for the given mesh)
	magnitude	Magnitude of the stimulus
	startTime	Switch on time
	duration	Duration of the stimulus.

Definition at line 33 of file Electrodes.cpp.

Member Function Documentation

template<unsigned DIM>

void Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality	(	unsigned	index,
		double	lowerValue,
		double	upperValue
	)			`[inline, private]`

Helper method to compute electrodes area and check they are equal. Throws if they are not.

Parameters:

	index	The value i when applying the electrodes to x_i=a and x_i=b (a<b)
	lowerValue	The value a when applying the electrodes to x_i=a and x_i=b (a<b) (should be the minimum value of x_i for the given mesh)
	upperValue	The value b when applying the electrodes to x_i=a and x_i=b (a<b) (should be the maximum value of x_i for the given mesh)

Definition at line 197 of file Electrodes.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement(), Electrodes< DIM >::mLeftElectrodeArea, Electrodes< DIM >::mpMesh, and Electrodes< DIM >::mRightElectrodeArea.

Referenced by Electrodes< DIM >::Electrodes().

template<unsigned DIM>

boost::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 2 > > Electrodes< DIM >::GetBoundaryConditionsContainer ( ) [inline]

Get the boundary conditions container in which is set up the Neumann fluxes for the first electrode, and the opposite fluxes for the second electrode if the the second electrode isn't grounded

Definition at line 161 of file Electrodes.cpp.

References Electrodes< DIM >::mpBoundaryConditionsContainer.

template<unsigned DIM>

double Electrodes< DIM >::GetSwitchOffTime ( ) [inline]

Get the time the electrodes are switched off

Definition at line 193 of file Electrodes.hpp.

References Electrodes< DIM >::mEndTime.

template<unsigned DIM>

double Electrodes< DIM >::GetSwitchOnTime ( ) [inline]

Get the time the electrodes are switched on

Definition at line 187 of file Electrodes.hpp.

References Electrodes< DIM >::mStartTime.

template<unsigned DIM>

bool Electrodes< DIM >::HasGroundedElectrode ( ) [inline]

Whether the second electrode is grounded or not

Definition at line 199 of file Electrodes.hpp.

References Electrodes< DIM >::mGroundSecondElectrode.

template<unsigned DIM>

template<class Archive >

void Electrodes< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Load the Electrodes class

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 123 of file Electrodes.hpp.

References Electrodes< DIM >::mAreActive, Electrodes< DIM >::mEndTime, Electrodes< DIM >::mGroundSecondElectrode, Electrodes< DIM >::mpBoundaryConditionsContainer, Electrodes< DIM >::mpMesh, and Electrodes< DIM >::mStartTime.

template<unsigned DIM>

template<class Archive >

void Electrodes< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)			const `[inline, private]`

Save the Electrodes class

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 107 of file Electrodes.hpp.

References Electrodes< DIM >::mAreActive, Electrodes< DIM >::mEndTime, Electrodes< DIM >::mGroundSecondElectrode, Electrodes< DIM >::mpBoundaryConditionsContainer, Electrodes< DIM >::mpMesh, and Electrodes< DIM >::mStartTime.

template<unsigned DIM>

bool Electrodes< DIM >::SwitchOff ( double time ) [inline]

Whether it is time to switch off the electrodes yet. THIS ONLY RETURNS TRUE ONCE - the first appropriate time. After that the electrodes assume they have been switched off and therefore this returns false.

Parameters:

time

the current time

Definition at line 169 of file Electrodes.cpp.

References Electrodes< DIM >::mAreActive, and Electrodes< DIM >::mEndTime.

template<unsigned DIM>

bool Electrodes< DIM >::SwitchOn ( double time ) [inline]

Whether it is time to switch on the electrodes yet. THIS ONLY RETURNS TRUE ONCE - the first appropriate time. After that the electrodes assume they have been switched on and therefore this returns false.

Parameters:

time

the current time

Definition at line 183 of file Electrodes.cpp.

References Electrodes< DIM >::mAreActive, Electrodes< DIM >::mEndTime, and Electrodes< DIM >::mStartTime.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 99 of file Electrodes.hpp.

Member Data Documentation

template<unsigned DIM>

bool Electrodes< DIM >::mAreActive [private]

Whether the electrodes are currently switched on

Definition at line 73 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::Electrodes(), Electrodes< DIM >::load(), Electrodes< DIM >::save(), Electrodes< DIM >::SwitchOff(), and Electrodes< DIM >::SwitchOn().

template<unsigned DIM>

double Electrodes< DIM >::mEndTime [private]

The time the electrodes are switched off

Definition at line 71 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::Electrodes(), Electrodes< DIM >::GetSwitchOffTime(), Electrodes< DIM >::load(), Electrodes< DIM >::save(), Electrodes< DIM >::SwitchOff(), and Electrodes< DIM >::SwitchOn().

template<unsigned DIM>

bool Electrodes< DIM >::mGroundSecondElectrode [private]

Whether the second electrode is grounded

Definition at line 65 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::Electrodes(), Electrodes< DIM >::HasGroundedElectrode(), Electrodes< DIM >::load(), and Electrodes< DIM >::save().

template<unsigned DIM>

double Electrodes< DIM >::mLeftElectrodeArea [private]

Left electrode area

Definition at line 82 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), and Electrodes< DIM >::Electrodes().

template<unsigned DIM>

boost::shared_ptr<BoundaryConditionsContainer<DIM,DIM,2> > Electrodes< DIM >::mpBoundaryConditionsContainer [private]

The created bcc, which BidomainProblem will use

Definition at line 67 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::Electrodes(), Electrodes< DIM >::GetBoundaryConditionsContainer(), Electrodes< DIM >::load(), and Electrodes< DIM >::save().

template<unsigned DIM>

AbstractTetrahedralMesh<DIM,DIM>* Electrodes< DIM >::mpMesh [private]

This is needed for archiving: the boundary conditions refer to nodes and/or elements, so need the mesh to be archived, but don't have a pointer to the mesh itself.

Definition at line 79 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), Electrodes< DIM >::Electrodes(), Electrodes< DIM >::load(), and Electrodes< DIM >::save().

template<unsigned DIM>

double Electrodes< DIM >::mRightElectrodeArea [private]

Right electrode area

Definition at line 85 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), and Electrodes< DIM >::Electrodes().

template<unsigned DIM>

double Electrodes< DIM >::mStartTime [private]

The time the electrodes are switched on

Definition at line 69 of file Electrodes.hpp.

Referenced by Electrodes< DIM >::Electrodes(), Electrodes< DIM >::GetSwitchOnTime(), Electrodes< DIM >::load(), Electrodes< DIM >::save(), and Electrodes< DIM >::SwitchOn().