Chaste  Release::2017.1
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <ExtendedBidomainAssembler.hpp>

+ Inheritance diagram for ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >:
+ Collaboration diagram for ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions

 ExtendedBidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, ExtendedBidomainTissue< SPACE_DIM > *pTissue)
 
virtual ~ExtendedBidomainAssembler ()
 
- Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 3, true, true, NORMAL >
 AbstractCardiacFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > *pTissue)
 
- Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
 AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
 
virtual ~AbstractFeVolumeIntegralAssembler ()
 
- Public Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
 AbstractFeAssemblerCommon ()
 
void SetCurrentSolution (Vec currentSolution)
 
virtual ~AbstractFeAssemblerCommon ()
 
- Public Member Functions inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
 AbstractFeAssemblerInterface ()
 
void SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)
 
void SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly)
 
void Assemble ()
 
void AssembleMatrix ()
 
void AssembleVector ()
 
virtual ~AbstractFeAssemblerInterface ()
 

Protected Member Functions

virtual c_matrix< double, 3 *(ELEMENT_DIM+1), 3 *(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, 3 > &rU, c_matrix< double, 3, 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)
 

Protected Attributes

ExtendedBidomainTissue< SPACE_DIM > * mpExtendedBidomainTissue
 
- Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 3, true, true, NORMAL >
AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * mpCardiacTissue
 
HeartConfig * mpConfig
 
- Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
 
GaussianQuadratureRule< ELEMENT_DIM > * mpQuadRule
 
- Protected Attributes inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
ReplicatableVector mCurrentSolutionOrGuessReplicated
 
- Protected Attributes inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
Vec mVectorToAssemble
 
Mat mMatrixToAssemble
 
bool mAssembleMatrix
 
bool mAssembleVector
 
bool mZeroMatrixBeforeAssembly
 
bool mZeroVectorBeforeAssembly
 
PetscInt mOwnershipRangeLo
 
PetscInt mOwnershipRangeHi
 

Additional Inherited Members

- Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
typedef LinearBasisFunction< ELEMENT_DIM > BasisFunction
 

Detailed Description

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

This is a derived class of AbstractCardiacFeVolumeIntegralAssembler and takes care of assembling LHS for solution of the extended bidomain euqations

See Buist ML, Poh YC. An Extended Bidomain Framework Incorporating Multiple Cell Types. Biophysical Journal, Volume 99, Issue 1, 13-18, 7 July 2010.

Major differences with bidomain assembler:

  • there are two cells (instead of one)
  • extracellular stimulus is present

Definition at line 70 of file ExtendedBidomainAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ExtendedBidomainAssembler ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh,
ExtendedBidomainTissue< SPACE_DIM > *  pTissue 
)

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

Parameters
pMeshpointer to the mesh
pTissuepointer to the tissue

Definition at line 132 of file ExtendedBidomainAssembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::~ExtendedBidomainAssembler ( )
virtual

Destructor.

Definition at line 142 of file ExtendedBidomainAssembler.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix< double, 3 *(ELEMENT_DIM+1), 3 *(ELEMENT_DIM+1)> ExtendedBidomainAssembler< 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, 3 > &  rU,
c_matrix< double, 3, SPACE_DIM > &  rGradU,
Element< ELEMENT_DIM, SPACE_DIM > *  pElement 
)
protectedvirtual

ComputeMatrixTerm()

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

Parameters
rPhiThe basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhiBasis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rXThe point in space
rUThe unknown as a vector, u(i) = u_i
rGradUThe gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElementPointer to the element
Returns
stencil matrix

Definition at line 45 of file ExtendedBidomainAssembler.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and PdeSimulationTime::GetPdeTimeStep().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainTissue<SPACE_DIM>* ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainTissue
protected

The tissue for which we assemble the matrix

Definition at line 77 of file ExtendedBidomainAssembler.hpp.

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