#include <AbstractCardiacMechanicsSolver.hpp>

Inheritance diagram for AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >:

Collaboration diagram for AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >:

Public Member Functions
	AbstractCardiacMechanicsSolver (QuadraticMesh< DIM > &rQuadMesh, ElectroMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory)

virtual	~AbstractCardiacMechanicsSolver ()

void	SetFineCoarseMeshPair (FineCoarseMeshPair< DIM > *pMeshPair)

unsigned	GetTotalNumQuadPoints ()

virtual GaussianQuadratureRule < DIM > *	GetQuadratureRule ()

std::map< unsigned, DataAtQuadraturePoint > &	rGetQuadPointToDataAtQuadPointMap ()

void	SetConstantFibreSheetDirections (const c_matrix< double, DIM, DIM > &rFibreSheetMatrix)

void	SetVariableFibreSheetDirections (const FileFinder &rOrthoFile, bool definedPerQuadraturePoint)

void	SetCalciumAndVoltage (std::vector< double > &rCalciumConcentrations, std::vector< double > &rVoltages)

virtual void	Solve (double time, double nextTime, double odeTimestep)=0

void	ComputeDeformationGradientAndStretchInEachElement (std::vector< c_matrix< double, DIM, DIM > > &rDeformationGradients, std::vector< double > &rStretches)

Public Member Functions inherited from AbstractCardiacMechanicsSolverInterface< DIM >
	AbstractCardiacMechanicsSolverInterface ()

virtual	~AbstractCardiacMechanicsSolverInterface ()

Protected Member Functions
virtual bool	IsImplicitSolver ()=0

void	AddActiveStressAndStressDerivative (c_matrix< double, DIM, DIM > &rC, unsigned elementIndex, unsigned currentQuadPointGlobalIndex, c_matrix< double, DIM, DIM > &rT, FourthOrderTensor< DIM, DIM, DIM, DIM > &rDTdE, bool addToDTdE)

void	SetupChangeOfBasisMatrix (unsigned elementIndex, unsigned currentQuadPointGlobalIndex)

void	Initialise ()

virtual void	GetActiveTensionAndTensionDerivs (double currentFibreStretch, unsigned currentQuadPointGlobalIndex, bool assembleJacobian, double &rActiveTension, double &rDerivActiveTensionWrtLambda, double &rDerivActiveTensionWrtDLambdaDt)=0

Protected Attributes
std::map< unsigned, DataAtQuadraturePoint >	mQuadPointToDataAtQuadPointMap

std::map< unsigned, DataAtQuadraturePoint > ::iterator	mMapIterator

FineCoarseMeshPair< DIM > *	mpMeshPair

unsigned	mTotalQuadPoints

double	mCurrentTime

double	mNextTime

double	mOdeTimestep

c_matrix< double, DIM, DIM >	mConstantFibreSheetDirections

std::vector< c_matrix< double, DIM, DIM > > *	mpVariableFibreSheetDirections

bool	mFibreSheetDirectionsDefinedByQuadraturePoint

c_vector< double, DIM >	mCurrentElementFibreDirection

c_vector< double, DIM >	mCurrentElementSheetDirection

c_vector< double, DIM >	mCurrentElementSheetNormalDirection

ElectroMechanicsProblemDefinition < DIM > &	mrElectroMechanicsProblemDefinition

Static Protected Attributes
static const unsigned	NUM_VERTICES_PER_ELEMENT = ELASTICITY_SOLVER::NUM_VERTICES_PER_ELEMENT

Detailed Description

template<class ELASTICITY_SOLVER, unsigned DIM>
class AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >

AbstractCardiacMechanicsSolver

Base class to implicit and explicit cardiac mechanics solvers. Inherits from IncompressibleNonlinearElasticitySolver or CompressibleNonlinearElasticityAssembler (depending on what the template parameter ELASTICITY_SOLVER is), and also from AbstractCardiacMechanicsSolverInterface which just declares this classes main public methods.

Overloads AddActiveStressAndStressDerivative() which adds on the active tension term to the stress. The child classes hold the contraction models and need to implement a method for getting the active tension from the model.

Definition at line 81 of file AbstractCardiacMechanicsSolver.hpp.

Constructor & Destructor Documentation

template<class ELASTICITY_SOLVER , unsigned DIM>

AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::AbstractCardiacMechanicsSolver	(	QuadraticMesh< DIM > &	rQuadMesh,
		ElectroMechanicsProblemDefinition< DIM > &	rProblemDefinition,
		std::string	outputDirectory
	)

Constructor

Parameters

rQuadMesh	A reference to the mesh.
rProblemDefinition	Object defining body force and boundary conditions
outputDirectory	The output directory, relative to TEST_OUTPUT

Definition at line 41 of file AbstractCardiacMechanicsSolver.cpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::~AbstractCardiacMechanicsSolver ( )

virtual

Destructor

Definition at line 145 of file AbstractCardiacMechanicsSolver.cpp.

Member Function Documentation

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::AddActiveStressAndStressDerivative	(	c_matrix< double, DIM, DIM > &	rC,
		unsigned	elementIndex,
		unsigned	currentQuadPointGlobalIndex,
		c_matrix< double, DIM, DIM > &	rT,
		FourthOrderTensor< DIM, DIM, DIM, DIM > &	rDTdE,
		bool	addToDTdE
	)

protected

Overloaded AddActiveStressAndStressDerivative(), which calls on the contraction model to get the active stress and add it on to the stress tensor

Parameters

rC	The Lagrangian deformation tensor (F^T F)
elementIndex	Index of the current element
currentQuadPointGlobalIndex	The index (assuming an outer loop over elements and an inner loop over quadrature points), of the current quadrature point.
rT	The stress to be added to
rDTdE	the stress derivative to be added to, assuming the final parameter is true
addToDTdE	A boolean flag saying whether the stress derivative is required or not.

Definition at line 212 of file AbstractCardiacMechanicsSolver.cpp.

References Determinant(), and Inverse().

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::ComputeDeformationGradientAndStretchInEachElement	(	std::vector< c_matrix< double, DIM, DIM > > &	rDeformationGradients,
		std::vector< double > &	rStretches
	)

virtual

Compute the deformation gradient, and stretch in the fibre direction, for each element in the mesh. Note: using quadratic interpolation for position, the deformation gradients and stretches actually vary linearly in each element. However, for computational efficiency reasons, when computing deformation gradients and stretches to pass back to the electrophysiology solver, we just assume they are constant in each element (ie ignoring the quadratic correction to the displacement). This means that the (const) deformation gradient and stretch for each element can be computed in advance and stored, and we don't have to worry about interpolation onto the precise location of the cell-model (electrics-mesh) node, just which element it is in, and ditto the electric mesh element centroid.

To compute this (elementwise-)constant F (and from it the constant stretch), we just have to compute F using the deformed positions at the vertices only, with linear bases, rather than all the nodes and quadratic bases.

Parameters

rDeformationGradients	A reference of a std::vector in which the deformation gradient in each element will be returned. Must be allocated prior to being passed in.
rStretches	A reference of a std::vector in which the stretch in each element will be returned. Must be allocated prior to being passed in.

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 422 of file AbstractCardiacMechanicsSolver.cpp.

References LinearBasisFunction< ELEMENT_DIM >::ComputeTransformedBasisFunctionDerivatives(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex().

template<class ELASTICITY_SOLVER , unsigned DIM>

virtual void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::GetActiveTensionAndTensionDerivs	(	double	currentFibreStretch,
		unsigned	currentQuadPointGlobalIndex,
		bool	assembleJacobian,
		double &	rActiveTension,
		double &	rDerivActiveTensionWrtLambda,
		double &	rDerivActiveTensionWrtDLambdaDt
	)

protectedpure virtual

Pure method called in AbstractCardiacMechanicsSolver::AddActiveStressAndStressDerivative(), which needs to provide the active tension (and other info if implicit (if the contraction model depends on stretch or stretch rate)) at a particular quadrature point. Takes in the current fibre stretch.

Parameters

currentFibreStretch	The stretch in the fibre direction
currentQuadPointGlobalIndex	quadrature point the integrand is currently being evaluated at in AssembleOnElement
assembleJacobian	A bool stating whether to assemble the Jacobian matrix.
rActiveTension	The returned active tension
rDerivActiveTensionWrtLambda	The returned dT_dLam, derivative of active tension wrt stretch. Only should be set in implicit solvers
rDerivActiveTensionWrtDLambdaDt	The returned dT_dLamDot, derivative of active tension wrt stretch rate. Only should be set in implicit solver

Implemented in ExplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >, and ImplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >.

template<class ELASTICITY_SOLVER , unsigned DIM>

virtual GaussianQuadratureRule<DIM>* AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::GetQuadratureRule ( )

inlinevirtual

Returns: the quadrature rule used in the elements.

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 247 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

unsigned AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::GetTotalNumQuadPoints ( )

inlinevirtual

Returns: the total number of quad points in the mesh. Pure, implemented in concrete solver

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 241 of file AbstractCardiacMechanicsSolver.hpp.

References AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mTotalQuadPoints.

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::Initialise ( )

protectedvirtual

Sets relevant data at all quadrature points, including whether it is an active region or not.

Calls a contraction cell factory to assign a model to each (quadrature point in each) element.

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 56 of file AbstractCardiacMechanicsSolver.cpp.

References DataAtQuadraturePoint_::ContractionModel, AbstractContractionCellFactory< DIM >::CreateContractionCellForElement(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), HeartRegionCode::GetValidBathId(), DataAtQuadraturePoint_::Stretch, and DataAtQuadraturePoint_::StretchLastTimeStep.

template<class ELASTICITY_SOLVER , unsigned DIM>

virtual bool AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::IsImplicitSolver ( )

protectedpure virtual

Returns: whether the solver is implicit or not (i.e. whether the contraction model depends on lambda (and depends on lambda at the current time)). For whether dTa_dLam dependent terms need to be added to the Jacbobian

Implemented in ExplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >, and ImplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >.

template<class ELASTICITY_SOLVER , unsigned DIM>

std::map<unsigned,DataAtQuadraturePoint>& AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::rGetQuadPointToDataAtQuadPointMap ( )

inline

Returns: access mQuadPointToDataAtQuadPointMap. See doxygen for this variable

Definition at line 255 of file AbstractCardiacMechanicsSolver.hpp.

References AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mQuadPointToDataAtQuadPointMap.

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetCalciumAndVoltage	(	std::vector< double > &	rCalciumConcentrations,
		std::vector< double > &	rVoltages
	)

virtual

Set the intracellular Calcium concentrations and voltages at each quad point. Pure.

Implicit solvers (for contraction models which are functions of stretch (and maybe stretch rate) would integrate the contraction model with this Ca/V/t using the current stretch (ie inside AssembleOnElement, ie inside GetActiveTensionAndTensionDerivs). Explicit solvers (for contraction models which are NOT functions of stretch can immediately integrate the contraction models to get the active tension.

Parameters

rCalciumConcentrations	Reference to a vector of intracellular calcium concentrations at each quadrature point
rVoltages	Reference to a vector of voltages at each quadrature point

Todo:: #1828 / #1211 don't pass in entire vector

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 167 of file AbstractCardiacMechanicsSolver.cpp.

References ContractionModelInputParameters_::intracellularCalciumConcentration.

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetConstantFibreSheetDirections ( const c_matrix< double, DIM, DIM > & rFibreSheetMatrix )

virtual

Set a constant fibre-sheet-normal direction (a matrix) to something other than the default (fibres in X-direction, sheet in the XY plane)

Parameters

rFibreSheetMatrix The fibre-sheet-normal matrix (fibre dir the first column, normal-to-fibre-in sheet in second column, sheet-normal in third column).

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 521 of file AbstractCardiacMechanicsSolver.cpp.

References EXCEPTION.

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetFineCoarseMeshPair ( FineCoarseMeshPair< DIM > * pMeshPair )

virtual

Sets the fine-coarse mesh pair object so that the solver knows about electrics too. It checks that the coarse mesh of the fine-mesh pair has the same number of elements as the quad mesh of this object and throws an exception otherwise.

Parameters

pMeshPair the FineCoarseMeshPair object to be set

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 134 of file AbstractCardiacMechanicsSolver.cpp.

References EXCEPTION, FineCoarseMeshPair< DIM >::GetCoarseMesh(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetupChangeOfBasisMatrix	(	unsigned	elementIndex,
		unsigned	currentQuadPointGlobalIndex
	)

protected

Over-ridden method which sets up an internal variable in the parent class, using the provided fibre-sheet direction information.

Parameters

elementIndex	element global index
currentQuadPointGlobalIndex	quad point global index

Definition at line 192 of file AbstractCardiacMechanicsSolver.cpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetVariableFibreSheetDirections	(	const FileFinder &	rOrthoFile,
		bool	definedPerQuadraturePoint
	)

virtual

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 .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.

Parameters

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

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Definition at line 491 of file AbstractCardiacMechanicsSolver.cpp.

References EXCEPTION, FileFinder::GetAbsolutePath(), FibreReader< DIM >::GetFibreSheetAndNormalMatrix(), and FibreReader< DIM >::GetNumLinesOfData().

template<class ELASTICITY_SOLVER , unsigned DIM>

virtual void AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::Solve	(	double	time,
		double	nextTime,
		double	odeTimestep
	)

pure virtual

Solve for the deformation, integrating the contraction model ODEs.

Parameters

time	the current time
nextTime	the next time
odeTimestep	the ODE timestep

Implements AbstractCardiacMechanicsSolverInterface< DIM >.

Implemented in ExplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >, and ImplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >.

Member Data Documentation

template<class ELASTICITY_SOLVER , unsigned DIM>

c_matrix<double,DIM,DIM> AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mConstantFibreSheetDirections

protected

The fibre-sheet-normal directions (in a matrix), if constant (defaults to the identity, ie fibres in the X-direction, sheet in the XY plane)

Definition at line 122 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

c_vector<double,DIM> AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mCurrentElementFibreDirection

protected

The fibre direction for the current element being assembled on

Definition at line 137 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

c_vector<double,DIM> AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mCurrentElementSheetDirection

protected

The sheet direction for the current element being assembled on

Definition at line 140 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

c_vector<double,DIM> AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mCurrentElementSheetNormalDirection

protected

The sheet normal direction for the current element being assembled on

Definition at line 143 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

double AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mCurrentTime

protected

Current time

Definition at line 110 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

bool AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mFibreSheetDirectionsDefinedByQuadraturePoint

protected

Whether the fibre-sheet directions that where read in where define per element or per quadrature point. Only valid if mpVariableFibreSheetDirections!=NULL

Definition at line 134 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

std::map<unsigned,DataAtQuadraturePoint>::iterator AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mMapIterator

protected

An iterator to the map, used to avoid having to repeatedly search the map.

Definition at line 101 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

double AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mNextTime

protected

Time to which the solver has been asked to solve to

Definition at line 113 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

double AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mOdeTimestep

protected

Time used to integrate the contraction model

Definition at line 116 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

FineCoarseMeshPair<DIM>* AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mpMeshPair

protected

A mesh pair object that can be set by the user to inform the solver about the electrics mesh.

Definition at line 104 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

std::vector<c_matrix<double,DIM,DIM> >* AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mpVariableFibreSheetDirections

protected

The fibre-sheet-normal directions (matrices), one for each element. Only non-NULL if SetVariableFibreSheetDirections() is called, if not mConstantFibreSheetDirections is used instead

Definition at line 128 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

std::map<unsigned,DataAtQuadraturePoint> AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mQuadPointToDataAtQuadPointMap

protected

A map from the index of a quadrature point to the data (contraction model, stretch, stretch at the last time-step) at that quad point. Note that there is no vector of all the quadrature points of the mesh; the quad point index is the index that would be obtained by looping over elements and then looping over quad points.

DISTRIBUTED - only holds data for the quad points within elements owned by this process.

Definition at line 96 of file AbstractCardiacMechanicsSolver.hpp.

Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::rGetQuadPointToDataAtQuadPointMap().

template<class ELASTICITY_SOLVER , unsigned DIM>

ElectroMechanicsProblemDefinition<DIM>& AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mrElectroMechanicsProblemDefinition

protected

This class contains all the information about the electro mechanics problem (except the material law)

Definition at line 149 of file AbstractCardiacMechanicsSolver.hpp.

template<class ELASTICITY_SOLVER , unsigned DIM>

unsigned AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::mTotalQuadPoints

protected

Total number of quad points in the (mechanics) mesh

Definition at line 107 of file AbstractCardiacMechanicsSolver.hpp.

Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::GetTotalNumQuadPoints().

template<class ELASTICITY_SOLVER , unsigned DIM>

const unsigned AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::NUM_VERTICES_PER_ELEMENT = ELASTICITY_SOLVER::NUM_VERTICES_PER_ELEMENT

staticprotected

Useful const from base class

Definition at line 84 of file AbstractCardiacMechanicsSolver.hpp.

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

heart/src/solver/mechanics/AbstractCardiacMechanicsSolver.hpp
heart/src/solver/mechanics/AbstractCardiacMechanicsSolver.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

template<class ELASTICITY_SOLVER, unsigned DIM> class AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class ELASTICITY_SOLVER, unsigned DIM>
class AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >