Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <BidomainAssembler.hpp>
Protected Member Functions | |
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) |
Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL > | |
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) |
Protected Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL > | |
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) |
Assembler, used for assembling the LHS matrix of the linear system that arises when the bidomain equations are discretised, and for assembling the contribution to the RHS vector that comes from a surface integral.
The discretised bidomain equation leads to the linear system (see FEM implementations document)
[ (chi*C/dt) M + K1 K1 ] [ V^{n+1} ] = [ (chi*C/dt) M V^{n} + M F^{n} + c1_surf ] [ K1 K2 ] [ PhiE^{n+1}] [ c2_surf ]
where chi is the surface-area to volume ratio, C the capacitance, dt the timestep M the mass matrix, K1 and K2 stiffness matrices, V^{n} and PhiE^{n} the vector of voltages and phi_e at time n, F^{n} the vector of (chi*Iionic + Istim) at each node, and c1_surf and c2_surf vectors arising from any surface stimuli (usually zero).
This assembler is used to assemble the LHS matrix, ie
[ (chi*C/dt) M + K1 K1 ] [ K1 K2 ]
Hence, this class inherits from AbstractCardiacFeVolumeIntegralAssembler and implements the methods ComputeMatrixTerm()
Definition at line 70 of file BidomainAssembler.hpp.
BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainAssembler | ( | AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, |
BidomainTissue< SPACE_DIM > * | pTissue | ||
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Constructor stores the mesh and pde and sets up boundary conditions.
pMesh | pointer to the mesh |
pTissue | pointer to the tissue |
Definition at line 98 of file BidomainAssembler.cpp.
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inlinevirtual |
Destructor.
Definition at line 109 of file BidomainAssembler.hpp.
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protectedvirtual |
This method is called by AssembleOnElement() and tells the assembler the contribution to add to the element LHS matrix.
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 44 of file BidomainAssembler.cpp.
References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and PdeSimulationTime::GetPdeTimeStepInverse().
Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().