ElectroMechanicsProblemDefinition< DIM > Class Template Reference

#include <ElectroMechanicsProblemDefinition.hpp>

Inherits SolidMechanicsProblemDefinition< DIM >.

Collaboration diagram for ElectroMechanicsProblemDefinition< DIM >:

Public Member Functions
	ElectroMechanicsProblemDefinition (QuadraticMesh< DIM > &rMesh)
	~ElectroMechanicsProblemDefinition ()
void	SetContractionModel (ContractionModelName contractionModel, double timestep)
void	SetUseDefaultCardiacMaterialLaw (CompressibilityType compressibilityType)
void	SetDeformationAffectsElectrophysiology (bool deformationAffectsConductivity, bool deformationAffectsCellModels)
void	SetMechanicsSolveTimestep (double timestep)
void	SetVariableFibreSheetDirectionsFile (std::string fibreSheetDirectionsFile, bool definedPerQuadPoint)
ContractionModelName	GetContractionModel ()
double	GetContractionModelOdeTimestep ()
double	GetMechanicsSolveTimestep ()
bool	GetDeformationAffectsConductivity ()
bool	GetDeformationAffectsCellModels ()
bool	ReadFibreSheetDirectionsFromFile ()
std::string	GetFibreSheetDirectionsFile ()
bool	GetFibreSheetDirectionsDefinedPerQuadraturePoint ()
virtual void	Validate ()
Private Attributes
ContractionModelName	mContractionModel
double	mContractionModelOdeTimeStep
double	mMechanicsSolveTimestep
bool	mDeformationAffectsConductivity
bool	mDeformationAffectsCellModels
AbstractMaterialLaw< DIM > *	mpDefaultMaterialLaw
bool	mReadFibreSheetInformationFromFile
std::string	mFibreSheetDirectionsFile
bool	mFibreSheetDirectionsDefinedPerQuadraturePoint

Detailed Description

template<unsigned DIM>
class ElectroMechanicsProblemDefinition< DIM >

Subclass of SolidMechanicsProblemDefinition with some cardiac-electro-mechanics-specific methods.

Definition at line 44 of file ElectroMechanicsProblemDefinition.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

ElectroMechanicsProblemDefinition< DIM >::ElectroMechanicsProblemDefinition ( QuadraticMesh< DIM > & rMesh ) [inline]

Constructor

Parameters:

rMesh

the mesh

Definition at line 32 of file ElectroMechanicsProblemDefinition.cpp.

template<unsigned DIM>

ElectroMechanicsProblemDefinition< DIM >::~ElectroMechanicsProblemDefinition ( ) [inline]

Destructor

Definition at line 44 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mpDefaultMaterialLaw.

Member Function Documentation

template<unsigned DIM>

ContractionModelName ElectroMechanicsProblemDefinition< DIM >::GetContractionModel ( ) [inline]

Get the contraction model

Definition at line 172 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mContractionModel, and ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep.

template<unsigned DIM>

double ElectroMechanicsProblemDefinition< DIM >::GetContractionModelOdeTimestep ( ) [inline]

Get the contraction model timestep

Definition at line 181 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep.

template<unsigned DIM>

bool ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsCellModels ( ) [inline]

Get whether the deformation affects the cardiac cell models, for example if there are stretch-activated channels in the cell model.

Definition at line 209 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels.

template<unsigned DIM>

bool ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsConductivity ( ) [inline]

Get whether the deformation affects the electrical physiological conductivity (or whether this effect is neglected).

Definition at line 200 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsConductivity.

template<unsigned DIM>

bool ElectroMechanicsProblemDefinition< DIM >::GetFibreSheetDirectionsDefinedPerQuadraturePoint ( ) [inline]

Get whether the fibre-sheet info is defined for each quadrature point in the mesh (if not, if it defined for each element in the mesh). (Should only be called if ReadFibreSheetDirectionsFromFile() returns true).

Definition at line 237 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>

std::string ElectroMechanicsProblemDefinition< DIM >::GetFibreSheetDirectionsFile ( ) [inline]

Get the fibre-sheet file (should only be called if ReadFibreSheetDirectionsFromFile() returns true).

Definition at line 225 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsFile, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>

double ElectroMechanicsProblemDefinition< DIM >::GetMechanicsSolveTimestep ( ) [inline]

Get how often the mechanics is solved

Definition at line 190 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep.

template<unsigned DIM>

bool ElectroMechanicsProblemDefinition< DIM >::ReadFibreSheetDirectionsFromFile ( ) [inline]

Whether the fibre-sheet info should be read from file (if not the defaults should be used).

Definition at line 217 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::SetContractionModel	(	ContractionModelName	contractionModel,
		double	timestep
	)			`[inline]`

Set the contraction model to be used (throughout the tissue).

Note the timestep should be set to a (typical) ODE time-step even if the contraction model is not going to solve ODEs.

Parameters:

	contractionModel	contraction model (from the enumeration ContractionModelName)
	timestep	timestep to be used in solving (ODE-based) contraction models.

Definition at line 53 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mContractionModel, and ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep.

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::SetDeformationAffectsElectrophysiology	(	bool	deformationAffectsConductivity,
		bool	deformationAffectsCellModels
	)			`[inline]`

Set if and how the deformation should affect the electro-physiology.

Parameters:

	deformationAffectsConductivity	Whether the deformation should affect the electrical physiological conductivity (or whether this effect is neglected)
	deformationAffectsCellModels	Whether the deformation should affect the cardiac cell models, for example if there are stretch-activated channels in the cell model.

Several important things to note: (i) this can't be called if fibre-sheet directions have been defined from file for each quadrature point (as opposed to each mechanics element) - this is because if the stretch is to be passed back to the electric mesh nodes, the fibre direction has to be defined at those nodes (ii) currently the set-up stage (computing mechanics mesh elements and weights for electrics mesh nodes) is inefficiently implemented - setup will be very slow for big meshes (iii) if deformationAffectsCellModels is true, the cell model ought to be one for which AbstractCardiacCell::SetStretch() has been implemented to do something (i.e. not generated automatically from CellML). (iv) deformationAffectsConductivity is not currently allowed in the compressible material law case as the effect of the determinant of the deformation gradient on the conductivity has not currently been implemented.

Definition at line 81 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels, and ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsConductivity.

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::SetMechanicsSolveTimestep ( double timestep ) [inline]

Set how often the mechanics is solved for.

Parameters:

timestep

timestep

Definition at line 88 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep.

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::SetUseDefaultCardiacMaterialLaw ( CompressibilityType compressibilityType ) [inline]

Use the default material law (NashHunter in the incompressible case, exponential in the compressible case), throughout the tissue.

Parameters:

compressibilityType

Either INCOMPRESSIBLE or COMPRESSIBLE

Definition at line 61 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mpDefaultMaterialLaw, and SolidMechanicsProblemDefinition< DIM >::SetMaterialLaw().

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::SetVariableFibreSheetDirectionsFile	(	std::string	fibreSheetDirectionsFile,
		bool	definedPerQuadPoint
	)			`[inline]`

Set a variable fibre-sheet-normal direction (matrices), from file. If the second parameter is false, there should be one fibre-sheet definition for each element; otherwise there should be one fibre-sheet definition for each *quadrature point* in the mesh. In the first case, the file should be a standard .ortho file (ie each line has the fibre dir, sheet dir, normal dir for that element), in the second it should have .orthoquad as the format.

If this method is not called, the default fibre-sheet directions are used - ie fibres parallel to X-axis, sheets parallel to Y-axis.

Parameters:

	fibreSheetDirectionsFile	the file containing the fibre/sheet directions
	definedPerQuadPoint	whether the fibre-sheet definitions are for each quadrature point in the mesh (if not, one for each element is assumed).

Definition at line 95 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsFile, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>

void ElectroMechanicsProblemDefinition< DIM >::Validate ( ) [inline, virtual]

Check all variables are set appropriately. Exceptions are thrown if any are not. Derived classes can override but should call this version as well.

Reimplemented from SolidMechanicsProblemDefinition< DIM >.

Definition at line 103 of file ElectroMechanicsProblemDefinition.cpp.

References EXCEPTION, SolidMechanicsProblemDefinition< DIM >::GetCompressibilityType(), ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep, ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels, ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsConductivity, ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.