BidomainAssembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <BidomainAssembler.hpp>

Inheritance diagram for BidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for BidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

List of all members.

Public Member Functions

BidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue, double dt, unsigned numQuadPoints=2)

~BidomainAssembler ()

Protected Member Functions

void ResetInterpolatedQuantities ()

void IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)

virtual c_matrix< double,
2 *(ELEMENT_DIM+1),
2 *(ELEMENT_DIM+1)> ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &rU, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double,
2 *(ELEMENT_DIM+1)> ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &u, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double,
2 *ELEMENT_DIM > ComputeVectorSurfaceTerm (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &rSurfaceElement, c_vector< double, ELEMENT_DIM > &rPhi, ChastePoint< SPACE_DIM > &rX)

Protected Attributes

BidomainTissue< SPACE_DIM > * mpBidomainTissue

HeartConfig * mpConfig

double mIionic

double mIIntracellularStimulus

double mIExtracellularStimulus

double mDt

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class BidomainAssembler< ELEMENT_DIM, SPACE_DIM >

Assembler for assembling the LHS matrix and RHS vector of the linear systems solved in bidomain problems

Definition at line 43 of file BidomainAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainAssembler	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BidomainTissue< SPACE_DIM > *	pTissue,
		double	dt,
		unsigned	numQuadPoints = `2`
	)			`[inline]`

Constructor stores the mesh and pde and sets up boundary conditions.

Parameters:

	pMesh	pointer to the mesh
	pTissue	pointer to the tissue
	dt	timestep
	numQuadPoints	number of quadrature points in each dimension

Definition at line 160 of file BidomainAssembler.cpp.

References HeartConfig::Instance(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::~BidomainAssembler ( ) [inline]

Destructor.

Definition at line 149 of file BidomainAssembler.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities ( ) [inline, protected, virtual]

Overridden ResetInterpolatedQuantities() method.

Reimplemented from AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, 2, true, true, CARDIAC >.

Definition at line 35 of file BidomainAssembler.cpp.

References BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIionic.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities	(	double	phiI,
		const Node< SPACE_DIM > *	pNode
	)			`[inline, protected, virtual]`

Overridden IncrementInterpolatedQuantities() method.

Parameters:

	phiI
	pNode

Reimplemented from AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, 2, true, true, CARDIAC >.

Definition at line 43 of file BidomainAssembler.cpp.

References Node< SPACE_DIM >::GetIndex(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, 2 (ELEMENT_DIM+1), 2 (ELEMENT_DIM+1)> BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm	(	c_vector< double, ELEMENT_DIM+1 > &	rPhi,
		c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, 2 > &	rU,
		c_matrix< double, 2, SPACE_DIM > &	rGradU,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)			`[inline, protected, virtual]`

ComputeMatrixTerm()

This method is called by AssembleOnElement() and tells the assembler the contribution to add to the element stiffness matrix.

Parameters:

	rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
	rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
	rX	The point in space
	rU	The unknown as a vector, u(i) = u_i
	rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
	pElement	Pointer to the element

Reimplemented in BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >.

Definition at line 55 of file BidomainAssembler.cpp.

References HeartConfig::GetCapacitance(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), HeartConfig::GetSurfaceAreaToVolumeRatio(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mDt, BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue, and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 2 *(ELEMENT_DIM+1)> BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm	(	c_vector< double, ELEMENT_DIM+1 > &	rPhi,
		c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, 2 > &	u,
		c_matrix< double, 2, SPACE_DIM > &	rGradU,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)			`[inline, protected, virtual]`

ComputeVectorTerm()

This method is called by AssembleOnElement() and tells the assembler the contribution to add to the element stiffness vector.

Parameters:

	rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
	rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
	rX	The point in space
	u	The unknown as a vector, u(i) = u_i
	rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
	pElement	Pointer to the element

Reimplemented in BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >.

Definition at line 111 of file BidomainAssembler.cpp.

References HeartConfig::GetCapacitance(), HeartConfig::GetSurfaceAreaToVolumeRatio(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mDt, BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 2 *ELEMENT_DIM > BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorSurfaceTerm	(	const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &	rSurfaceElement,
		c_vector< double, ELEMENT_DIM > &	rPhi,
		ChastePoint< SPACE_DIM > &	rX
	)			`[inline, protected, virtual]`

ComputeVectorSurfaceTerm()

This method is called by AssembleOnSurfaceElement() and tells the assembler what to add to the element stiffness matrix arising from surface element contributions.

Parameters:

	rSurfaceElement	the element which is being considered.
	rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
	rX	The point in space

Reimplemented from AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, 2, true, true, CARDIAC >.

Definition at line 138 of file BidomainAssembler.cpp.

References AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, 2, true, true, CARDIAC >::mpBoundaryConditions.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainTissue<SPACE_DIM>* BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue [protected]

The PDE to be solved.

Definition at line 47 of file BidomainAssembler.hpp.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected]

Local cache of the configuration singleton instance

Definition at line 49 of file BidomainAssembler.hpp.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainAssembler(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIionic [protected]

Ionic current to be interpolated from cache

Definition at line 51 of file BidomainAssembler.hpp.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus [protected]

Intracellular stimulus to be interpolated from cache

Definition at line 53 of file BidomainAssembler.hpp.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mIExtracellularStimulus [protected]

Extracellular stimulus to be interpolated from cache

Definition at line 55 of file BidomainAssembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mDt [protected]

Timestep (used in LHS matrix creation)

Definition at line 57 of file BidomainAssembler.hpp.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), and BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm().

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

heart/src/solver/electrics/BidomainAssembler.hpp
heart/src/solver/electrics/BidomainAssembler.cpp


Public Member Functions
	BidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue, double dt, unsigned numQuadPoints=2)
	~BidomainAssembler ()
Protected Member Functions
void	ResetInterpolatedQuantities ()
void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)
virtual c_matrix< double, 2 (ELEMENT_DIM+1), 2 (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &rU, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double, 2 *(ELEMENT_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &u, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double, 2 *ELEMENT_DIM >	ComputeVectorSurfaceTerm (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &rSurfaceElement, c_vector< double, ELEMENT_DIM > &rPhi, ChastePoint< SPACE_DIM > &rX)
Protected Attributes
BidomainTissue< SPACE_DIM > *	mpBidomainTissue
HeartConfig *	mpConfig
double	mIionic
double	mIIntracellularStimulus
double	mIExtracellularStimulus
double	mDt

BidomainAssembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class BidomainAssembler< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class BidomainAssembler< ELEMENT_DIM, SPACE_DIM >