AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL > Class Template Reference
#include <AbstractFeCableIntegralAssembler.hpp>
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 44 of file AbstractFeCableIntegralAssembler.hpp.
Member Typedef Documentation
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 60 of file AbstractFeCableIntegralAssembler.hpp.
Constructor & Destructor Documentation
| 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 | |||
| ) | [inline] |
Constructor.
- Parameters:
-
pMesh The mesh numQuadPoints The number of quadratures points (in each dimension) to use per element. Defaults to 2.
Definition at line 211 of file AbstractFeCableIntegralAssembler.hpp.
| virtual AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::~AbstractFeCableIntegralAssembler | ( | ) | [inline, virtual] |
Destructor.
Definition at line 202 of file AbstractFeCableIntegralAssembler.hpp.
Member Function Documentation
| 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 | |||
| ) | [inline, 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 317 of file AbstractFeCableIntegralAssembler.hpp.
References AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateInverseJacobian(), LinearBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableMatrixTerm(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableVectorTerm(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeTransformedBasisFunctionDerivatives(), AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::GetCurrentSolutionOrGuessValue(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), ReplicatableVector::GetSize(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::IncrementInterpolatedQuantities(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mAssembleMatrix, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mAssembleVector, AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mCurrentSolutionOrGuessReplicated, AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpCableQuadRule, AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ResetInterpolatedQuantities(), ChastePoint< DIM >::rGetLocation(), Node< SPACE_DIM >::rGetLocation(), and GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint().
| virtual c_matrix<double,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES,PROBLEM_DIM*NUM_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 109 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.
| 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 143 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.
| 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 | |||
| ) | [inline, 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 305 of file AbstractFeCableIntegralAssembler.hpp.
| void AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble | ( | ) | [inline, 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 229 of file AbstractFeCableIntegralAssembler.hpp.
References AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AssembleOnCableElement(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ElementAssemblyCriterion(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetStiffnessMatrixGlobalIndices(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mAssembleMatrix, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mAssembleVector, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mMatrixToAssemble, AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::mpMesh, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mVectorToAssemble, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mZeroMatrixBeforeAssembly, AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::mZeroVectorBeforeAssembly, AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::NUM_CABLE_ELEMENT_NODES, PetscMatTools::Zero(), and PetscVecTools::Zero().
| 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 183 of file AbstractFeCableIntegralAssembler.hpp.
Member Data Documentation
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 48 of file AbstractFeCableIntegralAssembler.hpp.
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 57 of file AbstractFeCableIntegralAssembler.hpp.
Referenced by AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AbstractFeCableIntegralAssembler(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AssembleOnCableElement(), and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::~AbstractFeCableIntegralAssembler().
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 54 of file AbstractFeCableIntegralAssembler.hpp.
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 51 of file AbstractFeCableIntegralAssembler.hpp.
Referenced by AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableMatrixTerm(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableVectorTerm(), and AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble().
The documentation for this class was generated from the following file:
- pde/src/solver/AbstractFeCableIntegralAssembler.hpp
