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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractFeVolumeIntegralAssembler.hpp>
Public Member Functions | |
AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh) | |
virtual | ~AbstractFeVolumeIntegralAssembler () |
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AbstractFeAssemblerCommon () | |
void | SetCurrentSolution (Vec currentSolution) |
virtual | ~AbstractFeAssemblerCommon () |
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AbstractFeAssemblerInterface () | |
void | SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true) |
void | SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly) |
void | Assemble () |
void | AssembleMatrix () |
void | AssembleVector () |
virtual | ~AbstractFeAssemblerInterface () |
Protected Types | |
typedef LinearBasisFunction< ELEMENT_DIM > | BasisFunction |
Protected Member Functions | |
void | ComputeTransformedBasisFunctionDerivatives (const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rReturnValue) |
void | DoAssemble () |
virtual c_matrix< double, PROBLEM_DIM *(ELEMENT_DIM+1), PROBLEM_DIM *(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, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement) |
virtual c_vector< double, PROBLEM_DIM *(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, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement) |
virtual void | AssembleOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM *(ELEMENT_DIM+1), PROBLEM_DIM *(ELEMENT_DIM+1) > &rAElem, c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> &rBElem) |
virtual bool | ElementAssemblyCriterion (Element< ELEMENT_DIM, SPACE_DIM > &rElement) |
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virtual double | GetCurrentSolutionOrGuessValue (unsigned nodeIndex, unsigned indexOfUnknown) |
virtual void | ResetInterpolatedQuantities () |
virtual void | IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode) |
virtual void | IncrementInterpolatedGradientQuantities (const c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, unsigned phiIndex, const Node< SPACE_DIM > *pNode) |
Protected Attributes | |
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | mpMesh |
GaussianQuadratureRule< ELEMENT_DIM > * | mpQuadRule |
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ReplicatableVector | mCurrentSolutionOrGuessReplicated |
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Vec | mVectorToAssemble |
Mat | mMatrixToAssemble |
bool | mAssembleMatrix |
bool | mAssembleVector |
bool | mZeroMatrixBeforeAssembly |
bool | mZeroVectorBeforeAssembly |
PetscInt | mOwnershipRangeLo |
PetscInt | mOwnershipRangeHi |
An abstract class for creating finite element vectors or matrices that are defined by integrals over the computational domain of functions of basis functions (for example, stiffness or mass matrices), that require assembly by looping over each element in the mesh and computing the element-wise integrals and adding it to the full matrix or vector.
This class is used for VOLUME integrals. For surface integrals there is a similar class, AbstractFeSurfaceIntegralAssembler.
This class can be used to assemble a matrix OR a vector OR one of each. The template booleans CAN_ASSEMBLE_VECTOR and CAN_ASSEMBLE_MATRIX should be chosen accordingly.
The class provides the functionality to loop over elements, perform element-wise integration (using Gaussian quadrature and linear basis functions), and add the results to the final matrix or vector. The concrete class which inherits from this must implement either COMPUTE_MATRIX_TERM or COMPUTE_VECTOR_TERM or both, which should return the INTEGRAND, as a function of the basis functions.
The final template parameter defines how much interpolation (onto quadrature points) is required by the concrete class.
CARDIAC: only interpolates the first component of the unknown (ie the voltage) NORMAL: interpolates the position X and all components of the unknown u NONLINEAR: interpolates X, u and grad(u). Also computes the gradient of the basis functions when assembling vectors.
This class inherits from AbstractFeAssemblerCommon which is where some member variables (the matrix/vector to be created, for example) are defined.
Definition at line 78 of file AbstractFeVolumeIntegralAssembler.hpp.
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protected |
Basis function for use with normal elements.
Definition at line 89 of file AbstractFeVolumeIntegralAssembler.hpp.
AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AbstractFeVolumeIntegralAssembler | ( | AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh | ) |
Constructor.
pMesh | The mesh |
Definition at line 244 of file AbstractFeVolumeIntegralAssembler.hpp.
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inlinevirtual |
Destructor.
Definition at line 237 of file AbstractFeVolumeIntegralAssembler.hpp.
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protectedvirtual |
Calculate the contribution of a single element to the linear system.
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 ComputeMatrixTerm() etc.
Definition at line 345 of file AbstractFeVolumeIntegralAssembler.hpp.
References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), Node< SPACE_DIM >::rGetLocation(), and GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint().
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inlineprotectedvirtual |
** This method has to be implemented in the concrete class if CAN_ASSEMBLE_MATRIX is true. **
NOTE: When INTERPOLATION_LEVEL==NORMAL, rGradU does not get set up and should not be used.
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 LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 143 of file AbstractFeVolumeIntegralAssembler.hpp.
References NEVER_REACHED.
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protected |
Compute the derivatives of all basis functions at a point within an element. This method will transform the results, for use within Gaussian quadrature for example.
This is almost identical to LinearBasisFunction::ComputeTransformedBasisFunctionDerivatives, except that it is also templated over SPACE_DIM and can handle cases such as 1d in 3d space.
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 (returned) Returns (via rReturnValue) 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 332 of file AbstractFeVolumeIntegralAssembler.hpp.
References LinearBasisFunction< ELEMENT_DIM >::ComputeBasisFunctionDerivatives().
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inlineprotectedvirtual |
** This method has to be implemented in the concrete class if CAN_ASSEMBLE_VECTOR is true. **
NOTE: When INTERPOLATION_LEVEL==NORMAL, rGradPhi and rGradU do not get set up and should not be used.
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 LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 178 of file AbstractFeVolumeIntegralAssembler.hpp.
References NEVER_REACHED.
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protectedvirtual |
The main assembly method. 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 257 of file AbstractFeVolumeIntegralAssembler.hpp.
References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetStiffnessMatrixGlobalIndices(), PetscMatTools::Zero(), and PetscVecTools::Zero().
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inlineprotectedvirtual |
rElement | the element |
Definition at line 219 of file AbstractFeVolumeIntegralAssembler.hpp.
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protected |
Mesh to be solved on.
Definition at line 83 of file AbstractFeVolumeIntegralAssembler.hpp.
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Quadrature rule for use on normal elements.
Definition at line 86 of file AbstractFeVolumeIntegralAssembler.hpp.
Referenced by AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AbstractFeVolumeIntegralAssembler(), and AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::~AbstractFeVolumeIntegralAssembler().