Chaste  Release::2018.1
Public Member Functions | Protected Member Functions | List of all members
BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <BidomainWithBathAssembler.hpp>

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

Public Member Functions

 BidomainWithBathAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue)
 
virtual ~BidomainWithBathAssembler ()
 
- Public Member Functions inherited from BidomainAssembler< ELEMENT_DIM, SPACE_DIM >
 BidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue)
 
virtual ~BidomainAssembler ()
 
- Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, true, CARDIAC >
 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,
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)
 

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
 
- Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, true, CARDIAC >
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
 

Detailed Description

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

Assembler for assembling the LHS matrix system solved in bidomain problems with a perfusing bath. See FEM implementations document for the exact definition of this.

Definition at line 50 of file BidomainWithBathAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainWithBathAssembler ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh,
BidomainTissue< SPACE_DIM > *  pTissue 
)
inline

Constructor.

Parameters
pMeshpointer to the mesh
pTissuepointer to the tissue

Definition at line 80 of file BidomainWithBathAssembler.hpp.

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

Destructor.

Definition at line 89 of file BidomainWithBathAssembler.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix< double, 2 *(ELEMENT_DIM+1), 2 *(ELEMENT_DIM+1)> BidomainWithBathAssembler< 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, 2 > &  rU,
c_matrix< double, 2, SPACE_DIM > &  rGradU,
Element< ELEMENT_DIM, SPACE_DIM > *  pElement 
)
protectedvirtual

Overloaded ComputeMatrixTerm() - calls the base class version for tissue elements.

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

Reimplemented from BidomainAssembler< ELEMENT_DIM, SPACE_DIM >.

Definition at line 41 of file BidomainWithBathAssembler.cpp.

References BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), HeartConfig::GetBathConductivity(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetUnsignedAttribute(), HeartConfig::Instance(), and HeartRegionCode::IsRegionBath().

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