BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <BidomainDg0Assembler.hpp>

Inheritance diagram for BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >:

List of all members.

Public Member Functions

BidomainDg0Assembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainPde< SPACE_DIM > *pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc, unsigned numQuadPoints=2)

~BidomainDg0Assembler ()

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 InitialiseForSolve (Vec initialSolution)

void IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)

virtual void CheckCompatibilityCondition ()

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 > &rU, 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 existingSolution, double time)

virtual void FinaliseAssembleSystem (Vec existingSolution, double time)

virtual Vec GenerateNullBasis () const

Protected Attributes

BidomainPde< SPACE_DIM > * mpBidomainPde

HeartConfig * mpConfig

double mIionic

double mIIntracellularStimulus

double mIExtracellularStimulus

bool mNullSpaceCreated

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.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SelfType [protected]

This type (to save typing).

Definition at line 79 of file BidomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef AbstractLinearAssembler<ELEMENT_DIM, SPACE_DIM, 2, false, SelfType> BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BaseClassType [protected]

Base class type (to save typing).

Definition at line 80 of file BidomainDg0Assembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler	(	AbstractTetrahedralMesh< 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.

Parameters:

	pMesh	pointer to the mesh
	pPde	pointer to the PDE
	pBcc	pointer to the boundary conditions
	numQuadPoints	number of quadrature points (defaults to 2)

Definition at line 323 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::~BidomainDg0Assembler ( ) [inline]

Destructor.

Definition at line 351 of file BidomainDg0Assembler.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Overridden ResetInterpolatedQuantities() method.

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 37 of file BidomainDg0Assembler.cpp.

References BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic.

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.

Parameters:

initialSolution

an initial guess

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

Definition at line 44 of file BidomainDg0Assembler.cpp.

References HeartConfig::GetAbsoluteTolerance(), HeartConfig::GetRelativeTolerance(), AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::InitialiseForSolve(), HeartConfig::Instance(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig, AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpLinearSystem, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed, LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetMatrixIsSymmetric(), LinearSystem::SetPcType(), and LinearSystem::SetRelativeTolerance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Overridden IncrementInterpolatedQuantities() method.

Parameters:

	phiI
	pNode

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 86 of file BidomainDg0Assembler.cpp.

References Node< SPACE_DIM >::GetIndex(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainPde.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition ( ) [inline, protected, virtual]

Checks whether the linear system will have a solution (if so, infinite solutions) instead of zero solutions. The condition is, if the linear system is Ax=b, that sum b_i over for all the PHI_E components (ie i=1,3,5,..) is zero.

This check is not made if running in parallel, or in debug mode.

The reason why the sum must be zero: the Fredholm alternative states that a singular system Ax=b has a solution if and only if v.b=0 for all v in ker(A) (ie all v such that Av=b). The nullspace ker(A) is one dimensional with basis vector v = (0,1,0,1....,0,1), so v.b = sum_{i=1,3,5..} b_i.

Definition at line 288 of file BidomainDg0Assembler.cpp.

References PetscTools::GetNumProcs(), AbstractBoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryConditions(), AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions, AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpLinearSystem, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed, and LinearSystem::rGetRhsVector().

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

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 > &	rU,
		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.

Parameters:

	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 96 of file BidomainDg0Assembler.cpp.

References HeartConfig::GetCapacitance(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), HeartConfig::GetSurfaceAreaToVolumeRatio(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 2 >::mDt, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainPde, and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().

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.

Parameters:

	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
	u	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 152 of file BidomainDg0Assembler.cpp.

References HeartConfig::GetCapacitance(), HeartConfig::GetSurfaceAreaToVolumeRatio(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 2 >::mDt, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm().

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 181 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	existingSolution,
		double	time
	)			`[inline, protected, virtual]`

PrepareForAssembleSystem

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

Parameters:

	existingSolution	is the voltage to feed into the cell models
	time	the simulation time

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 203 of file BidomainDg0Assembler.cpp.

References AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 2 >::mDt, and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainPde.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem	(	Vec	existingSolution,
		double	time
	)			`[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.

Parameters:

	existingSolution	voltages (phi_e may need shifting)
	time

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 233 of file BidomainDg0Assembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis ( ) const [inline, protected, virtual]

GenerateNullBasis

Called by FinaliseAssembleSystem to get the null basis to use for the particular formulation of the bidomain equations used. Parabolic-Elliptic in BidomainDg0Assembler.

Definition at line 209 of file BidomainDg0Assembler.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpMesh, and DistributedVector::Restore().

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

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:

fixedExtracellularPotentialNodes

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 356 of file BidomainDg0Assembler.cpp.

References BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mFixedExtracellularPotentialNodes, 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().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed ( unsigned rowMeanPhiEZero ) [inline]

Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. It is set from the problem class.

Parameters:

rowMeanPhiEZero

indicates the row of the matrix to be replaced. Ought to be an odd number...

Definition at line 381 of file BidomainDg0Assembler.cpp.

References BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.

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

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::E_DIM = ELEMENT_DIM [static]

The element dimension (to save typing).

Definition at line 73 of file BidomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::S_DIM = SPACE_DIM [static]

The space dimension (to save typing).

Definition at line 74 of file BidomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::P_DIM = 2u [static]

The problem dimension (to save typing).

Definition at line 75 of file BidomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainPde<SPACE_DIM>* BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpBidomainPde [protected]

The PDE to be solved.

Definition at line 86 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainWithBathMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), BidomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::PrepareForAssembleSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected]

Local cache of the configuration singleton instance

Definition at line 89 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem(), BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic [protected]

Ionic current to be interpolated from cache

Definition at line 92 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus [protected]

Intracellular stimulus to be interpolated from cache

Definition at line 94 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIExtracellularStimulus [protected]

Extracellular stimulus to be interpolated from cache

Definition at line 96 of file BidomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated [protected]

Used when intialising null-space solver to resolve singularity

Definition at line 99 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mFixedExtracellularPotentialNodes [protected]

Used when pinning nodes to resolve singularity. This vector indicates the global indices of the nodes to be pinned

Definition at line 104 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed [protected]

Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. This number indicates the row of the matrix to be replaced. This is INT_MAX if unset. It is set from the problem class.

Definition at line 111 of file BidomainDg0Assembler.hpp.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BidomainDg0Assembler(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

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

/tmp/release_1.1/heart/src/solver/BidomainDg0Assembler.hpp
/tmp/release_1.1/heart/src/solver/BidomainDg0Assembler.cpp


Public Member Functions
	BidomainDg0Assembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainPde< SPACE_DIM > pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc, unsigned numQuadPoints=2)
	~BidomainDg0Assembler ()
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	InitialiseForSolve (Vec initialSolution)
void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)
virtual void	CheckCompatibilityCondition ()
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 > &rU, 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 existingSolution, double time)
virtual void	FinaliseAssembleSystem (Vec existingSolution, double time)
virtual Vec	GenerateNullBasis () const
Protected Attributes
BidomainPde< SPACE_DIM > *	mpBidomainPde
HeartConfig *	mpConfig
double	mIionic
double	mIIntracellularStimulus
double	mIExtracellularStimulus
bool	mNullSpaceCreated
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.

BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Static Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Friends

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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