#include <AbstractFeCableIntegralAssembler.hpp>

Inheritance diagram for AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >:

Collaboration diagram for AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >:

List of all members.

Public Member Functions
	AbstractFeCableIntegralAssembler (MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, unsigned numQuadPoints=2)
virtual	~AbstractFeCableIntegralAssembler ()
Protected Types
typedef LinearBasisFunction< 1 >	CableBasisFunction
Protected Member Functions
void	ComputeTransformedBasisFunctionDerivatives (const ChastePoint< CABLE_ELEMENT_DIM > &rPoint, const c_matrix< double, CABLE_ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rReturnValue)
void	DoAssemble ()
virtual c_matrix< double, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES >	ComputeCableMatrixTerm (c_vector< double, NUM_CABLE_ELEMENT_NODES > &rPhi, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< CABLE_ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES >	ComputeCableVectorTerm (c_vector< double, NUM_CABLE_ELEMENT_NODES > &rPhi, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< CABLE_ELEMENT_DIM, SPACE_DIM > *pElement)
virtual void	AssembleOnCableElement (Element< CABLE_ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES > &rAElem, c_vector< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > &rBElem)
virtual bool	ElementAssemblyCriterion (Element< CABLE_ELEMENT_DIM, SPACE_DIM > &rElement)
Protected Attributes
MixedDimensionMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh
GaussianQuadratureRule< 1 > *	mpCableQuadRule
Static Protected Attributes
static const unsigned	CABLE_ELEMENT_DIM = 1
static const unsigned	NUM_CABLE_ELEMENT_NODES = 2

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
class AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >

The class in similar to AbstractFeVolumeIntegralAssembler (see documentation for this), but is for creating a finite element matrices or vectors that involve integrals over CABLES, ie 1d regions in a 2d/3d mesh. Required for cardiac simulations with a Purkinje network. Uses a MixedDimensionMesh, which is composed of the normal mesh plus cables.

Definition at line 51 of file AbstractFeCableIntegralAssembler.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

typedef LinearBasisFunction<1> AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::CableBasisFunction [protected]

Basis function for use with normal elements.

Definition at line 67 of file AbstractFeCableIntegralAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AbstractFeCableIntegralAssembler	(	MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		unsigned	numQuadPoints = `2`
	)

Constructor.

Parameters:

pMesh	The mesh
numQuadPoints	The number of quadratures points (in each dimension) to use per element. Defaults to 2.

Definition at line 218 of file AbstractFeCableIntegralAssembler.hpp.

References AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpCableQuadRule.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

virtual AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::~AbstractFeCableIntegralAssembler ( ) [inline, virtual]

Destructor.

Definition at line 209 of file AbstractFeCableIntegralAssembler.hpp.

References AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpCableQuadRule.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

void AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AssembleOnCableElement	(	Element< CABLE_ELEMENT_DIM, SPACE_DIM > &	rElement,
		c_matrix< double, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM NUM_CABLE_ELEMENT_NODES > &	rAElem,
		c_vector< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > &	rBElem
	)		`[protected, virtual]`

Calculate the contribution of a single cable element to the linear system.

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.
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.

Called by AssembleSystem(). Calls ComputeCableMatrixTerm() etc.

Todo:: #1320 This assumes that the Jacobian is constant on an element. This is true for linear basis functions, but not for any other type of basis function.

Definition at line 324 of file AbstractFeCableIntegralAssembler.hpp.

References AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateInverseJacobian(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ChastePoint< DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

virtual c_matrix<double,PROBLEM_DIMNUM_CABLE_ELEMENT_NODES,PROBLEM_DIMNUM_CABLE_ELEMENT_NODES> AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableMatrixTerm	(	c_vector< double, NUM_CABLE_ELEMENT_NODES > &	rPhi,
		c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, PROBLEM_DIM > &	rU,
		c_matrix< double, PROBLEM_DIM, SPACE_DIM > &	rGradU,
		Element< CABLE_ELEMENT_DIM, SPACE_DIM > *	pElement
	)		`[inline, protected, virtual]`

This method returns the matrix to be added to element stiffness matrix for a given Gauss point, ie, essentially the INTEGRAND in the integral definition of the matrix (integral over cable region).

The arguments are the bases, bases gradients, x and current solution computed at the Gauss point. The returned matrix will be multiplied by the Gauss weight and Jacobian determinant and added to the element stiffness matrix (see AssembleOnElement()).

** This method has to be implemented in the concrete class if CAN_ASSEMBLE_MATRIX is true. **

NOTE: for linear problems rGradU is NOT set up correctly because it should not be needed.

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.

Definition at line 116 of file AbstractFeCableIntegralAssembler.hpp.

References NEVER_REACHED, and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::NUM_CABLE_ELEMENT_NODES.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

virtual c_vector<double,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES> AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableVectorTerm	(	c_vector< double, NUM_CABLE_ELEMENT_NODES > &	rPhi,
		c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, PROBLEM_DIM > &	rU,
		c_matrix< double, PROBLEM_DIM, SPACE_DIM > &	rGradU,
		Element< CABLE_ELEMENT_DIM, SPACE_DIM > *	pElement
	)		`[inline, protected, virtual]`

This method returns the vector to be added to element stiffness vector for a given Gauss point, ie, essentially the INTEGRAND in the integral definition of the vector. The arguments are the bases, x and current solution computed at the Gauss point. The returned vector will be multiplied by the Gauss weight and Jacobian determinant and added to the element stiffness matrix (see AssembleOnElement()).

** This method has to be implemented in the concrete class if CAN_ASSEMBLE_VECTOR is true. **

NOTE: for linear problems rGradPhi and rGradU are NOT set up correctly because they should not be needed.

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

Definition at line 150 of file AbstractFeCableIntegralAssembler.hpp.

References NEVER_REACHED, and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::NUM_CABLE_ELEMENT_NODES.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

void AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeTransformedBasisFunctionDerivatives	(	const ChastePoint< CABLE_ELEMENT_DIM > &	rPoint,
		const c_matrix< double, CABLE_ELEMENT_DIM, SPACE_DIM > &	rInverseJacobian,
		c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &	rReturnValue
	)		`[protected]`

Compute the derivatives of all basis functions at a point within a cable element. This method will transform the results, for use within Gaussian quadrature for example.

Parameters:

rPoint	The point at which to compute the basis functions. The results are undefined if this is not within the canonical element.
rInverseJacobian	The inverse of the Jacobian matrix mapping the real element into the canonical element.
rReturnValue	A reference to a vector, to be filled in

Returns:: The derivatives of the basis functions, in local index order. Each entry is a vector (c_vector<double, SPACE_DIM> instance) giving the derivative along each axis.

Definition at line 312 of file AbstractFeCableIntegralAssembler.hpp.

References LinearBasisFunction< ELEMENT_DIM >::ComputeBasisFunctionDerivatives().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

void AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble ( ) [protected, virtual]

The main assembly method. Protected, should only be called through Assemble(), AssembleMatrix() or AssembleVector() which set mAssembleMatrix, mAssembleVector accordingly.

Implements AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >.

Definition at line 236 of file AbstractFeCableIntegralAssembler.hpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetStiffnessMatrixGlobalIndices(), PetscMatTools::Zero(), and PetscVecTools::Zero().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

virtual bool AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ElementAssemblyCriterion ( Element< CABLE_ELEMENT_DIM, SPACE_DIM > & rElement ) [inline, protected, virtual]

Whether to include this (cable) element when assembling. Returns true here but can be overridden by the concrete assembler if not all elements should be included.

Parameters:

rElement the element

Definition at line 190 of file AbstractFeCableIntegralAssembler.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

const unsigned AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::CABLE_ELEMENT_DIM = 1 [static, protected]

Cable element dimension.

Definition at line 55 of file AbstractFeCableIntegralAssembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

GaussianQuadratureRule<1>* AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpCableQuadRule [protected]

Quadrature rule for use on cable elements.

Definition at line 64 of file AbstractFeCableIntegralAssembler.hpp.

Referenced by AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AbstractFeCableIntegralAssembler(), and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::~AbstractFeCableIntegralAssembler().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

MixedDimensionMesh<ELEMENT_DIM, SPACE_DIM>* AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpMesh [protected]

Mesh to be solved on.

Definition at line 61 of file AbstractFeCableIntegralAssembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>

const unsigned AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::NUM_CABLE_ELEMENT_NODES = 2 [static, protected]

Number of nodes in a cable element.

Definition at line 58 of file AbstractFeCableIntegralAssembler.hpp.

Referenced by AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableMatrixTerm(), and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableVectorTerm().

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

pde/src/solver/AbstractFeCableIntegralAssembler.hpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation