ImplicitCardiacMechanicsAssembler< DIM > Class Template Reference

#include <ImplicitCardiacMechanicsAssembler.hpp>

Inheritance diagram for ImplicitCardiacMechanicsAssembler< DIM >:

Collaboration diagram for ImplicitCardiacMechanicsAssembler< DIM >:

List of all members.

Public Member Functions

ImplicitCardiacMechanicsAssembler (QuadraticMesh< DIM > *pQuadMesh, std::string outputDirectory, std::vector< unsigned > &rFixedNodes, AbstractIncompressibleMaterialLaw< DIM > *pMaterialLaw=NULL)

~ImplicitCardiacMechanicsAssembler ()

unsigned GetTotalNumQuadPoints ()

GaussianQuadratureRule< DIM > * GetQuadratureRule ()

void SetIntracellularCalciumConcentrations (std::vector< double > &caI)

std::vector< double > & rGetLambda ()

void Solve (double time, double nextTime, double odeTimestep)

Private Member Functions

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)

Private Attributes

std::vector
< NhsSystemWithImplicitSolver > mCellMechSystems

std::vector< double > mLambdaLastTimeStep

std::vector< double > mLambda

double mCurrentTime

double mNextTime

double mOdeTimestep

bool mAllocatedMaterialLawMemory

unsigned mTotalQuadPoints

Static Private 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

Friends

class TestImplicitCardiacMechanicsAssembler

Detailed Description

template<unsigned DIM>
class ImplicitCardiacMechanicsAssembler< DIM >

Implicit Cardiac Mechanics Assembler

Solves cardiac mechanics implicitly (together with the NHS cell models for determining the active tension), taking in the intracellular Calcium concentration. See CardiacElectroMechanicsProblem documentation for more detail.

Definition at line 51 of file ImplicitCardiacMechanicsAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

ImplicitCardiacMechanicsAssembler< DIM >::ImplicitCardiacMechanicsAssembler	(	QuadraticMesh< DIM > *	pQuadMesh,
		std::string	outputDirectory,
		std::vector< unsigned > &	rFixedNodes,
		AbstractIncompressibleMaterialLaw< DIM > *	pMaterialLaw = `NULL`
	)			`[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. Defaults to NULL, in which case a default material law is used.

Definition at line 32 of file ImplicitCardiacMechanicsAssembler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), GaussianQuadratureRule< ELEM_DIM >::GetNumQuadPoints(), ImplicitCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory, ImplicitCardiacMechanicsAssembler< DIM >::mCellMechSystems, ImplicitCardiacMechanicsAssembler< DIM >::mLambda, ImplicitCardiacMechanicsAssembler< DIM >::mLambdaLastTimeStep, NonlinearElasticityAssembler< DIM >::mpQuadratureRule, and ImplicitCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

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

Destructor just deletes memory if it was allocated

Definition at line 61 of file ImplicitCardiacMechanicsAssembler.cpp.

References ImplicitCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory, and AbstractNonlinearElasticityAssembler< DIM >::mMaterialLaws.

Member Function Documentation

template<unsigned DIM>

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

Get the total number of quad points in the mesh

Definition at line 71 of file ImplicitCardiacMechanicsAssembler.cpp.

References ImplicitCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

GaussianQuadratureRule< DIM > * ImplicitCardiacMechanicsAssembler< DIM >::GetQuadratureRule ( ) [inline]

Get the quadrature rule used in the elements

Definition at line 77 of file ImplicitCardiacMechanicsAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::mpQuadratureRule.

template<unsigned DIM>

void ImplicitCardiacMechanicsAssembler< DIM >::SetIntracellularCalciumConcentrations ( std::vector< double > & caI ) [inline]

Set the intracellular Calcium concentrations (note: in an explicit algorithm we would set the active tension as the forcing quantity; the implicit algorithm takes in the Calcium concentration and solves for the active tension implicitly together with the mechanics).

Parameters:

caI

the intracellular calcium concentrations

Definition at line 83 of file ImplicitCardiacMechanicsAssembler.cpp.

References ImplicitCardiacMechanicsAssembler< DIM >::mCellMechSystems, and ImplicitCardiacMechanicsAssembler< DIM >::mTotalQuadPoints.

template<unsigned DIM>

std::vector< double > & ImplicitCardiacMechanicsAssembler< DIM >::rGetLambda ( ) [inline]

Get lambda (the stretch ratio). NOTE: the i-th entry of this vector is assumed to be the i-th quad point obtained by looping over cells in the obvious way and then looping over quad points. These quad points, in the same order, can be obtained by using the QuadraturePointsGroup class.

Definition at line 93 of file ImplicitCardiacMechanicsAssembler.cpp.

References ImplicitCardiacMechanicsAssembler< DIM >::mLambda.

template<unsigned DIM>

void ImplicitCardiacMechanicsAssembler< DIM >::Solve	(	double	time,
		double	nextTime,
		double	odeTimestep
	)			`[inline]`

Solve for the deformation using quasi-static nonlinear elasticity. (not dynamic nonlinear elasticity, despite the times taken in - just ONE deformation is solved for. The cell models are integrated implicitly over the time range using the ODE timestep provided, as part of the solve, and updated at the end once the solution has been found, as is lambda.

Parameters:

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

Definition at line 100 of file ImplicitCardiacMechanicsAssembler.cpp.

References NonlinearElasticityAssembler< DIM >::AssembleSystem(), ImplicitCardiacMechanicsAssembler< DIM >::mCellMechSystems, ImplicitCardiacMechanicsAssembler< DIM >::mCurrentTime, ImplicitCardiacMechanicsAssembler< DIM >::mLambdaLastTimeStep, ImplicitCardiacMechanicsAssembler< DIM >::mNextTime, ImplicitCardiacMechanicsAssembler< DIM >::mOdeTimestep, and AbstractNonlinearElasticityAssembler< DIM >::Solve().

template<unsigned DIM>

void ImplicitCardiacMechanicsAssembler< 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, private, 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): calculating Ta implicitly and using it to compute the stress, and the addition of a corresponding 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 128 of file ImplicitCardiacMechanicsAssembler.cpp.

Member Data Documentation

template<unsigned DIM>

const unsigned ImplicitCardiacMechanicsAssembler< DIM >::STENCIL_SIZE = NonlinearElasticityAssembler<DIM>::STENCIL_SIZE [static, private]

Stencil size

Reimplemented from NonlinearElasticityAssembler< DIM >.

Definition at line 56 of file ImplicitCardiacMechanicsAssembler.hpp.

template<unsigned DIM>

const unsigned ImplicitCardiacMechanicsAssembler< DIM >::NUM_NODES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_NODES_PER_ELEMENT [static, private]

Number of nodes per element

Reimplemented from NonlinearElasticityAssembler< DIM >.

Definition at line 57 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

const unsigned ImplicitCardiacMechanicsAssembler< DIM >::NUM_VERTICES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_VERTICES_PER_ELEMENT [static, private]

Number of vertices per element

Reimplemented from NonlinearElasticityAssembler< DIM >.

Definition at line 58 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

std::vector<NhsSystemWithImplicitSolver> ImplicitCardiacMechanicsAssembler< DIM >::mCellMechSystems [private]

The NHS cell systems (with their own implicit solvers, which take in [Ca]_i and return Ta. 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 64 of file ImplicitCardiacMechanicsAssembler.hpp.

Referenced by ImplicitCardiacMechanicsAssembler< DIM >::AssembleOnElement(), ImplicitCardiacMechanicsAssembler< DIM >::ImplicitCardiacMechanicsAssembler(), ImplicitCardiacMechanicsAssembler< DIM >::SetIntracellularCalciumConcentrations(), and ImplicitCardiacMechanicsAssembler< DIM >::Solve().

template<unsigned DIM>

std::vector<double> ImplicitCardiacMechanicsAssembler< DIM >::mLambdaLastTimeStep [private]

The stretch ratio (in the fibre direction) at the last timestep. 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 70 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

std::vector<double> ImplicitCardiacMechanicsAssembler< DIM >::mLambda [private]

The current stretch ratio (in the fibre direction). 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 76 of file ImplicitCardiacMechanicsAssembler.hpp.

Referenced by ImplicitCardiacMechanicsAssembler< DIM >::AssembleOnElement(), ImplicitCardiacMechanicsAssembler< DIM >::ImplicitCardiacMechanicsAssembler(), and ImplicitCardiacMechanicsAssembler< DIM >::rGetLambda().

template<unsigned DIM>

double ImplicitCardiacMechanicsAssembler< DIM >::mCurrentTime [private]

Current time

Definition at line 79 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

double ImplicitCardiacMechanicsAssembler< DIM >::mNextTime [private]

Time to which the solver has been asked to solve to

Definition at line 81 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

double ImplicitCardiacMechanicsAssembler< DIM >::mOdeTimestep [private]

Time used to integrate the NHS model

Definition at line 83 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

bool ImplicitCardiacMechanicsAssembler< DIM >::mAllocatedMaterialLawMemory [private]

Whether the material law was passed in or the default used

Definition at line 86 of file ImplicitCardiacMechanicsAssembler.hpp.

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

template<unsigned DIM>

unsigned ImplicitCardiacMechanicsAssembler< DIM >::mTotalQuadPoints [private]

Total number of quad points in the (mechanics) mesh

Definition at line 89 of file ImplicitCardiacMechanicsAssembler.hpp.

Referenced by ImplicitCardiacMechanicsAssembler< DIM >::GetTotalNumQuadPoints(), ImplicitCardiacMechanicsAssembler< DIM >::ImplicitCardiacMechanicsAssembler(), and ImplicitCardiacMechanicsAssembler< DIM >::SetIntracellularCalciumConcentrations().

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

/tmp/release_1.1/heart/src/solver/ImplicitCardiacMechanicsAssembler.hpp
/tmp/release_1.1/heart/src/solver/ImplicitCardiacMechanicsAssembler.cpp


Public Member Functions
	ImplicitCardiacMechanicsAssembler (QuadraticMesh< DIM > pQuadMesh, std::string outputDirectory, std::vector< unsigned > &rFixedNodes, AbstractIncompressibleMaterialLaw< DIM > pMaterialLaw=NULL)
	~ImplicitCardiacMechanicsAssembler ()
unsigned	GetTotalNumQuadPoints ()
GaussianQuadratureRule< DIM > *	GetQuadratureRule ()
void	SetIntracellularCalciumConcentrations (std::vector< double > &caI)
std::vector< double > &	rGetLambda ()
void	Solve (double time, double nextTime, double odeTimestep)
Private Member Functions
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)
Private Attributes
std::vector < NhsSystemWithImplicitSolver >	mCellMechSystems
std::vector< double >	mLambdaLastTimeStep
std::vector< double >	mLambda
double	mCurrentTime
double	mNextTime
double	mOdeTimestep
bool	mAllocatedMaterialLawMemory
unsigned	mTotalQuadPoints
Static Private 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
Friends
class	TestImplicitCardiacMechanicsAssembler

ImplicitCardiacMechanicsAssembler< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description

template<unsigned DIM> class ImplicitCardiacMechanicsAssembler< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class ImplicitCardiacMechanicsAssembler< DIM >