BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <BidomainDg0Assembler.hpp>

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Collaboration diagram for BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >:

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List of all members.

Public Member Functions

 BidomainDg0Assembler (AbstractMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainPde< SPACE_DIM > *pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc, unsigned numQuadPoints=2)
void SetFixedExtracellularPotentialNodes (std::vector< unsigned > fixedExtracellularPotentialNodes)
void SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)

Static Public Attributes

static const unsigned E_DIM = ELEMENT_DIM
static const unsigned S_DIM = SPACE_DIM
static const unsigned P_DIM = 2u

Protected Types

typedef BidomainDg0Assembler
< ELEMENT_DIM, SPACE_DIM > 		SelfType
typedef
AbstractLinearAssembler
< ELEMENT_DIM, SPACE_DIM,
2, false, SelfType > 		BaseClassType

Protected Member Functions

void ResetInterpolatedQuantities (void)
void InitialiseForSolve (Vec initialSolution)
void IncrementInterpolatedQuantities (double phi_i, const Node< SPACE_DIM > *pNode)
virtual c_matrix< double,
2 *(ELEMENT_DIM+1),
2 *(ELEMENT_DIM+1)> 		ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &u, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double,
2 *(ELEMENT_DIM+1)> 		ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &u, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double,
2 *ELEMENT_DIM > 		ComputeVectorSurfaceTerm (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &rSurfaceElement, c_vector< double, ELEMENT_DIM > &rPhi, ChastePoint< SPACE_DIM > &rX)
virtual void PrepareForAssembleSystem (Vec currentSolution, double time)
virtual void FinaliseAssembleSystem (Vec currentSolution, double currentTime)

Protected Attributes

BidomainPde< SPACE_DIM > * mpBidomainPde
HeartConfig * mpConfig
double mIionic
double mIIntracellularStimulus
double mIExtracellularStimulus
bool mNullSpaceCreated
Vec mExternalVoltageMask
std::vector< unsigned > mFixedExtracellularPotentialNodes
unsigned mRowForAverageOfPhiZeroed

Friends

class AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, SelfType >
 Allow the AbstractStaticAssembler to call our private/protected methods using static polymorphism.

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >

BidomainDg0Assembler

The 2 unknowns are voltage and extracellular potential.

This assembler interpolates quantities such as ionic currents and stimuli from their nodal values (obtained from a BidomainPde) onto a gauss point, and uses the interpolated values in assembly. The assembler also creates boundary conditions, which are zero-Neumann boundary conditions on the surface unless SetFixedExtracellularPotentialNodes() is called.

The user should call Solve() from the superclass AbstractDynamicAssemblerMixin.

NOTE: if any cells have a non-zero extracellular stimulus, phi_e must be fixed at some nodes (using SetFixedExtracellularPotentialNodes() ), else no solution is possible.

Definition at line 68 of file BidomainDg0Assembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh,
BidomainPde< SPACE_DIM > *  pPde,
BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *  pBcc,
unsigned  numQuadPoints = 2 
) [inline]

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

Definition at line 294 of file BidomainDg0Assembler.cpp.

References AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions, and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::SetMesh().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities ( void   )  [inline, protected, virtual]

The concrete subclass can overload this and IncrementInterpolatedQuantities() if there are some quantities which need to be computed at each Gauss point. They are called in AssembleOnElement()

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 37 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve ( Vec  initialSolution  )  [inline, protected, virtual]

Create the linear system object if it hasn't been already.

Can use an initial solution as PETSc template, or base it on the mesh size.

Reimplemented from AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >.

Definition at line 44 of file BidomainDg0Assembler.cpp.

References AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::InitialiseForSolve(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpLinearSystem, LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetPcType(), and LinearSystem::SetRelativeTolerance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities ( double  phi_i,
const Node< SPACE_DIM > *  pNode 
) [inline, protected, virtual]

The concrete subclass can overload this and ResetInterpolatedQuantities() if there are some quantities which need to be computed at each Gauss point. They are called in AssembleOnElement()

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 65 of file BidomainDg0Assembler.cpp.

References Node< SPACE_DIM >::GetIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix< double, 2 *(ELEMENT_DIM+1), 2 *(ELEMENT_DIM+1)> BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm ( c_vector< double, ELEMENT_DIM+1 > &  rPhi,
c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &  rGradPhi,
ChastePoint< SPACE_DIM > &  rX,
c_vector< double, 2 > &  u,
c_matrix< double, 2, SPACE_DIM > &  rGradU,
Element< ELEMENT_DIM, SPACE_DIM > *  pElement 
) [inline, protected, virtual]

ComputeMatrixTerm()

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

Definition at line 75 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, 2 *(ELEMENT_DIM+1)> BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm ( c_vector< double, ELEMENT_DIM+1 > &  rPhi,
c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &  rGradPhi,
ChastePoint< SPACE_DIM > &  rX,
c_vector< double, 2 > &  u,
c_matrix< double, 2, SPACE_DIM > &  rGradU,
Element< ELEMENT_DIM, SPACE_DIM > *  pElement 
) [inline, protected, virtual]

ComputeVectorTerm()

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

Definition at line 131 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, 2 *ELEMENT_DIM > BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorSurfaceTerm ( const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &  rSurfaceElement,
c_vector< double, ELEMENT_DIM > &  rPhi,
ChastePoint< SPACE_DIM > &  rX 
) [inline, protected, virtual]

This method returns the vector to be added to element stiffness vector for a given gauss point in BoundaryElement. 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 determinent and added to the element stiffness matrix (see AssembleOnElement()).

--This method has to be implemented in the concrete class--

Parameters:
rSurfaceElement the element which is being considered.
rPhi The basis functions, rPhi(i) = phi_i, i=1..numBases
rX The point in space

Implements AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 160 of file BidomainDg0Assembler.cpp.

References BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetNeumannBCValue(), and AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::PrepareForAssembleSystem ( Vec  currentSolution,
double  time 
) [inline, protected, virtual]

PrepareForAssembleSystem

Called at the beginning of AbstractLinearAssembler::AssembleSystem() after the system. Here, used to integrate cell odes.

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 182 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem ( Vec  currentSolution,
double  currentTime 
) [inline, protected, virtual]

FinaliseAssembleSystem

Called by AbstractLinearAssmebler::AssembleSystem() after the system has been assembled. Here, used to avoid problems with phi_e drifting by one of 3 methods: pinning nodes, using a null space, or using an "average phi_e = 0" row.

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 188 of file BidomainDg0Assembler.cpp.

References LinearSystem::AssembleFinalLhsMatrix(), LinearSystem::AssembleRhsVector(), DistributedVector::Begin(), DistributedVector::CreateVec(), DistributedVector::End(), LinearSystem::GetSize(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpLinearSystem, DistributedVector::Restore(), LinearSystem::SetMatrixElement(), LinearSystem::SetNullBasis(), LinearSystem::SetRhsVectorElement(), and LinearSystem::ZeroMatrixRow().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned >  fixedExtracellularPotentialNodes  )  [inline]

Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.

Parameters:
the nodes to be fixed.
NOTE: currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.

Definition at line 331 of file BidomainDg0Assembler.cpp.

References BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions, and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpMesh.

Referenced by BidomainProblem< DIM >::CreateAssembler().

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