AbstractCardiacMechanicsAssembler< DIM > Class Template Reference

#include <AbstractCardiacMechanicsAssembler.hpp>

Inherits NonlinearElasticityAssembler< DIM >.

Inherited by ExplicitCardiacMechanicsAssembler< DIM >, and ImplicitCardiacMechanicsAssembler< DIM >.

Collaboration diagram for AbstractCardiacMechanicsAssembler< DIM >:

Public Member Functions
	AbstractCardiacMechanicsAssembler (QuadraticMesh< DIM > pQuadMesh, std::string outputDirectory, std::vector< unsigned > &rFixedNodes, AbstractIncompressibleMaterialLaw< DIM > pMaterialLaw)
	~AbstractCardiacMechanicsAssembler ()
unsigned	GetTotalNumQuadPoints ()
virtual GaussianQuadratureRule < DIM > *	GetQuadratureRule ()
void	SetConstantFibreSheetDirections (const c_matrix< double, DIM, DIM > &rFibreSheetMatrix)
void	SetVariableFibreSheetDirections (std::string orthoFile)
void	SetCalciumAndVoltage (std::vector< double > &rCalciumConcentrations, std::vector< double > &rVoltages)
virtual void	Solve (double time, double nextTime, double odeTimestep)=0
Protected Member Functions
void	CheckOrthogonality (c_matrix< double, DIM, DIM > &rMatrix)
virtual bool	IsImplicitSolver ()=0
void	AssembleOnElement (Element< DIM, DIM > &rElement, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElem, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElemPrecond, c_vector< double, STENCIL_SIZE > &rBElem, bool assembleResidual, bool assembleJacobian)
virtual void	GetActiveTensionAndTensionDerivs (double currentFibreStretch, unsigned currentQuadPointGlobalIndex, bool assembleJacobian, double &rActiveTension, double &rDerivActiveTensionWrtLambda, double &rDerivActiveTensionWrtDLambdaDt)=0
Protected Attributes
std::vector < AbstractContractionModel * >	mContractionModelSystems
std::vector< double >	mStretches
unsigned	mTotalQuadPoints
bool	mAllocatedMaterialLawMemory
double	mCurrentTime
double	mNextTime
double	mOdeTimestep
c_matrix< double, DIM, DIM >	mConstantFibreSheetDirections
std::vector< c_matrix< double, DIM, DIM > > *	mpVariableFibreSheetDirections
Static Protected Attributes
static const unsigned	STENCIL_SIZE = NonlinearElasticityAssembler<DIM>::STENCIL_SIZE
static const unsigned	NUM_NODES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_NODES_PER_ELEMENT
static const unsigned	NUM_VERTICES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_VERTICES_PER_ELEMENT

Detailed Description

template<unsigned DIM>
class AbstractCardiacMechanicsAssembler< DIM >

AbstractCardiacMechanicsAssembler

Base class to implicit and explicit cardiac mechanics assemblers. Inherits from NonlinearElasticityAssembler Main method is the overloaded AssembleOnElement which does the extra work needed for cardiac problems. The child classes hold the contraction models and need to implement a method for getting the active tension from the model.

Definition at line 47 of file AbstractCardiacMechanicsAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler	(	QuadraticMesh< DIM > *	pQuadMesh,
		std::string	outputDirectory,
		std::vector< unsigned > &	rFixedNodes,
		AbstractIncompressibleMaterialLaw< DIM > *	pMaterialLaw
	)			`[inline]`

Constructor

Parameters:

	pQuadMesh	A pointer to the mesh.
	outputDirectory	The output directory, relative to TEST_OUTPUT
	rFixedNodes	The fixed nodes
	pMaterialLaw	The material law for the tissue. If NULL the default (NashHunterPoleZero) law is used.

Definition at line 177 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), AbstractCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory, AbstractCardiacMechanicsAssembler< DIM >::mConstantFibreSheetDirections, NonlinearElasticityAssembler< DIM >::mpQuadratureRule, AbstractCardiacMechanicsAssembler< DIM >::mpVariableFibreSheetDirections, AbstractCardiacMechanicsAssembler< DIM >::mStretches, and AbstractCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

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

Destructor just deletes memory if it was allocated

Definition at line 214 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory, AbstractNonlinearElasticityAssembler< DIM >::mMaterialLaws, and AbstractCardiacMechanicsAssembler< DIM >::mpVariableFibreSheetDirections.

Member Function Documentation

template<unsigned DIM>

void AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement	(	Element< DIM, DIM > &	rElement,
		c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &	rAElem,
		c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &	rAElemPrecond,
		c_vector< double, STENCIL_SIZE > &	rBElem,
		bool	assembleResidual,
		bool	assembleJacobian
	)			`[inline, protected, virtual]`

Overloaded AssembleOnElement. Apart from a tiny bit of initial set up and the lack of the body force term in the residual, the bits where this is different to the base class AssembleOnElement are restricted to two bits (see code): getting Ta and using it to compute the stress, and (in when Ta is a function of the stretch) the addition of extra term to the Jacobian.

Parameters:

	rElement	The element to assemble on.
	rAElem	The element's contribution to the LHS matrix is returned in this n by n matrix, where n is the no. of nodes in this element. There is no need to zero this matrix before calling.
	rAElemPrecond	The element's contribution to the matrix passed to PetSC in creating a preconditioner
	rBElem	The element's contribution to the RHS vector is returned in this vector of length n, the no. of nodes in this element. There is no need to zero this vector before calling.
	assembleResidual	A bool stating whether to assemble the residual vector.
	assembleJacobian	A bool stating whether to assemble the Jacobian matrix.

Reimplemented from NonlinearElasticityAssembler< DIM >.

Definition at line 312 of file AbstractCardiacMechanicsAssembler.hpp.

template<unsigned DIM>

void AbstractCardiacMechanicsAssembler< DIM >::CheckOrthogonality ( c_matrix< double, DIM, DIM > & rMatrix ) [inline, protected]

Check whether the given matrix is orthogonal, by computing A^T A and verifying whether each component matches the identity matrix, to a given tolerance.

Parameters:

rMatrix

reference to the matrix being tested

Definition at line 94 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::SetConstantFibreSheetDirections(), and AbstractCardiacMechanicsAssembler< DIM >::SetVariableFibreSheetDirections().

template<unsigned DIM>

virtual void AbstractCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs	(	double	currentFibreStretch,
		unsigned	currentQuadPointGlobalIndex,
		bool	assembleJacobian,
		double &	rActiveTension,
		double &	rDerivActiveTensionWrtLambda,
		double &	rDerivActiveTensionWrtDLambdaDt
	)			`[protected, pure virtual]`

Pure method called in AbstractCardiacMechanicsAssembler::AssembleOnElement(), 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 integrand 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 assemblers
	rDerivActiveTensionWrtDLambdaDt	The returned dT_dLamDot, derivative of active tension wrt stretch rate. Only should be set in implicit assemblers

Implemented in ExplicitCardiacMechanicsAssembler< DIM >, and ImplicitCardiacMechanicsAssembler< DIM >.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement().

template<unsigned DIM>

virtual GaussianQuadratureRule<DIM>* AbstractCardiacMechanicsAssembler< DIM >::GetQuadratureRule ( ) [inline, virtual]

Get the quadrature rule used in the elements.

Definition at line 236 of file AbstractCardiacMechanicsAssembler.hpp.

References NonlinearElasticityAssembler< DIM >::mpQuadratureRule.

template<unsigned DIM>

unsigned AbstractCardiacMechanicsAssembler< DIM >::GetTotalNumQuadPoints ( ) [inline]

Get the total number of quad points in the mesh. Pure, implemented in concrete assembler

Definition at line 230 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

virtual bool AbstractCardiacMechanicsAssembler< DIM >::IsImplicitSolver ( ) [protected, pure virtual]

Whether the solver is implicit or not (ie 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 ExplicitCardiacMechanicsAssembler< DIM >, and ImplicitCardiacMechanicsAssembler< DIM >.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement().

template<unsigned DIM>

void AbstractCardiacMechanicsAssembler< DIM >::SetCalciumAndVoltage	(	std::vector< double > &	rCalciumConcentrations,
		std::vector< double > &	rVoltages
	)			`[inline]`

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

Definition at line 292 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractCardiacMechanicsAssembler< DIM >::mContractionModelSystems, and AbstractCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

void AbstractCardiacMechanicsAssembler< DIM >::SetConstantFibreSheetDirections ( const c_matrix< double, DIM, DIM > & rFibreSheetMatrix ) [inline]

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).

Definition at line 248 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractCardiacMechanicsAssembler< DIM >::CheckOrthogonality(), and AbstractCardiacMechanicsAssembler< DIM >::mConstantFibreSheetDirections.

template<unsigned DIM>

void AbstractCardiacMechanicsAssembler< DIM >::SetVariableFibreSheetDirections ( std::string orthoFile ) [inline]

Set a variable fibre-sheet-normal direction (matrices), one for each element, from a file. The file should be a .ortho file (ie each line has the fibre dir, sheet dir, normal dir for that element). The number of elements must match the number in the MECHANICS mesh!

Parameters:

orthoFile

the file containing the fibre/sheet directions

Definition at line 680 of file AbstractCardiacMechanicsAssembler.hpp.

References AbstractCardiacMechanicsAssembler< DIM >::CheckOrthogonality(), NonlinearElasticityAssembler< DIM >::mpQuadMesh, and AbstractCardiacMechanicsAssembler< DIM >::mpVariableFibreSheetDirections.

template<unsigned DIM>

virtual void AbstractCardiacMechanicsAssembler< 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

Implemented in ExplicitCardiacMechanicsAssembler< DIM >, and ImplicitCardiacMechanicsAssembler< DIM >.

Member Data Documentation

template<unsigned DIM>

bool AbstractCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory [protected]

Whether the material law was passed in or the default used

Definition at line 72 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), and AbstractCardiacMechanicsAssembler< DIM >::~AbstractCardiacMechanicsAssembler().

template<unsigned DIM>

c_matrix<double,DIM,DIM> AbstractCardiacMechanicsAssembler< 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 82 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement(), and AbstractCardiacMechanicsAssembler< DIM >::SetConstantFibreSheetDirections().

template<unsigned DIM>

std::vector<AbstractContractionModel*> AbstractCardiacMechanicsAssembler< DIM >::mContractionModelSystems [protected]

Vector of contraction model (pointers). One for each quadrature point. Note the indexing: the i-th entry corresponds to the i-th global quad point, when looping over elements and then quad points

Definition at line 59 of file AbstractCardiacMechanicsAssembler.hpp.

template<unsigned DIM>

double AbstractCardiacMechanicsAssembler< DIM >::mCurrentTime [protected]

Current time

Definition at line 75 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement(), ImplicitCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs(), ImplicitCardiacMechanicsAssembler< DIM >::Solve(), and ExplicitCardiacMechanicsAssembler< DIM >::Solve().

template<unsigned DIM>

double AbstractCardiacMechanicsAssembler< DIM >::mNextTime [protected]

Time to which the solver has been asked to solve to

Definition at line 77 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement(), ImplicitCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs(), ImplicitCardiacMechanicsAssembler< DIM >::Solve(), and ExplicitCardiacMechanicsAssembler< DIM >::Solve().

template<unsigned DIM>

double AbstractCardiacMechanicsAssembler< DIM >::mOdeTimestep [protected]

Time used to integrate the contraction model

Definition at line 79 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement(), ImplicitCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs(), ImplicitCardiacMechanicsAssembler< DIM >::Solve(), and ExplicitCardiacMechanicsAssembler< DIM >::Solve().

template<unsigned DIM>

std::vector<c_matrix<double,DIM,DIM> >* AbstractCardiacMechanicsAssembler< 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 88 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), AbstractCardiacMechanicsAssembler< DIM >::AssembleOnElement(), AbstractCardiacMechanicsAssembler< DIM >::SetVariableFibreSheetDirections(), and AbstractCardiacMechanicsAssembler< DIM >::~AbstractCardiacMechanicsAssembler().

template<unsigned DIM>

std::vector<double> AbstractCardiacMechanicsAssembler< DIM >::mStretches [protected]

Stored stretches (in fibre direction, at each quadrature point). Should be stored when GetActiveTensionAndTensionDerivs() is called, and can be used either in that timestep (implicit solver), or the next timestep (explicit solver)

Definition at line 66 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), ImplicitCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs(), ExplicitCardiacMechanicsAssembler< DIM >::GetActiveTensionAndTensionDerivs(), ImplicitCardiacMechanicsAssembler< DIM >::rGetFibreStretches(), ImplicitCardiacMechanicsAssembler< DIM >::Solve(), and ExplicitCardiacMechanicsAssembler< DIM >::Solve().

template<unsigned DIM>

unsigned AbstractCardiacMechanicsAssembler< DIM >::mTotalQuadPoints [protected]

Total number of quad points in the (mechanics) mesh

Definition at line 69 of file AbstractCardiacMechanicsAssembler.hpp.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), ExplicitCardiacMechanicsAssembler< DIM >::ExplicitCardiacMechanicsAssembler(), AbstractCardiacMechanicsAssembler< DIM >::GetTotalNumQuadPoints(), ImplicitCardiacMechanicsAssembler< DIM >::ImplicitCardiacMechanicsAssembler(), and AbstractCardiacMechanicsAssembler< DIM >::SetCalciumAndVoltage().

template<unsigned DIM>

const unsigned AbstractCardiacMechanicsAssembler< DIM >::NUM_NODES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_NODES_PER_ELEMENT [static, protected]

Number of nodes per element

Reimplemented from NonlinearElasticityAssembler< DIM >.

Definition at line 51 of file AbstractCardiacMechanicsAssembler.hpp.