MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <MonodomainDg0Assembler.hpp>

Inherits AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, 1, false, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >, and AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 1 >.

Inherited by MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >:

[legend]

List of all members.

Public Member Functions
	MonodomainDg0Assembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, MonodomainPde< ELEMENT_DIM, SPACE_DIM > pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBcc, unsigned numQuadPoints=2)
	~MonodomainDg0Assembler ()
Static Public Attributes
static const unsigned	E_DIM = ELEMENT_DIM
static const unsigned	S_DIM = SPACE_DIM
static const unsigned	P_DIM = 1u
Protected Types
typedef MonodomainDg0Assembler < ELEMENT_DIM, SPACE_DIM >	SelfType
typedef AbstractLinearAssembler < ELEMENT_DIM, SPACE_DIM, 1, false, SelfType >	BaseClassType
Protected Member Functions
virtual c_matrix< double, 1 (ELEMENT_DIM+1), 1 (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, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double, 1 *(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, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_vector< double, 1 *ELEMENT_DIM >	ComputeVectorSurfaceTerm (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > &rSurfaceElement, c_vector< double, ELEMENT_DIM > &rPhi, ChastePoint< SPACE_DIM > &rX)
void	ResetInterpolatedQuantities ()
void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)
virtual void	PrepareForAssembleSystem (Vec existingSolutionOrGuess, double time)
void	InitialiseForSolve (Vec initialSolution)
Protected Attributes
HeartConfig *	mpConfig
double	mIionic
double	mIIntracellularStimulus
MonodomainPde< ELEMENT_DIM, SPACE_DIM > *	mpMonodomainPde
Friends
class	AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, 1u, false, SelfType >

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >

MonodomainDg0Assembler

This is essentially the same as the SimpleDg0ParabolicAssembler (which it inherits from), except that the source term (ie ionic current + stimulus) is interpolated from their nodal values, instead of computed at the gauss point, since they are only known at the nodes.

Also, the MonodomainAssembler automatically creates zero neumann boundary conditions when constructed and therefore does not need to take in a BoundaryConditionsContainer.

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

Definition at line 66 of file MonodomainDg0Assembler.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef AbstractLinearAssembler<ELEMENT_DIM, SPACE_DIM, 1, false, SelfType> MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::BaseClassType [protected]

Base class type (to save typing).

Definition at line 91 of file MonodomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef MonodomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SelfType [protected]

This type (to save typing).

Definition at line 90 of file MonodomainDg0Assembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::MonodomainDg0Assembler	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		MonodomainPde< ELEMENT_DIM, SPACE_DIM > *	pPde,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *	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 145 of file MonodomainDg0Assembler.cpp.

References HeartConfig::Instance(), AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpMonodomainPde, AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 1 >::SetMatrixIsConstant(), and AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::SetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::~MonodomainDg0Assembler ( ) [inline]

Destructor.

Definition at line 166 of file MonodomainDg0Assembler.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, 1 (ELEMENT_DIM+1), 1 (ELEMENT_DIM+1)> MonodomainDg0Assembler< 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, 1 > &	rU,
		c_matrix< double, 1, 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

Definition at line 36 of file MonodomainDg0Assembler.cpp.

References HeartConfig::GetCapacitance(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), HeartConfig::GetSurfaceAreaToVolumeRatio(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 1 >::mDt, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig, and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpMonodomainPde.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 1 *ELEMENT_DIM > MonodomainDg0Assembler< 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]`

ComputeVectorSurfaceTerm()

This method is called by AssembleOnSurfaceElement() and tells the assembler what to add to the element stiffness matrix arising from surface element contributions.

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 78 of file MonodomainDg0Assembler.cpp.

References AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditions.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 1 *(ELEMENT_DIM+1)> MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm	(	c_vector< double, ELEMENT_DIM+1 > &	rPhi,
		c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, 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.

Here, the SimpleDg0ParabolicAssembler version of this method is overloaded using the interpolated source term.

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

Definition at line 62 of file MonodomainDg0Assembler.cpp.

References HeartConfig::GetCapacitance(), HeartConfig::GetSurfaceAreaToVolumeRatio(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 1 >::mDtInverse, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainDg0Assembler< 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 100 of file MonodomainDg0Assembler.cpp.

References Node< SPACE_DIM >::GetIndex(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic, and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpMonodomainPde.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainDg0Assembler< 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, 1, false, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >.

Definition at line 119 of file MonodomainDg0Assembler.cpp.

References AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::InitialiseForSolve(), HeartConfig::Instance(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM > >::mpLinearSystem, LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetMatrixIsSymmetric(), LinearSystem::SetPcType(), and LinearSystem::SetRelativeTolerance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::PrepareForAssembleSystem	(	Vec	existingSolutionOrGuess,
		double	time
	)			`[inline, protected, virtual]`

This method is called at the beginning of AssembleSystem() and should be overloaded in the concrete assembler class if there is any work to be done before assembling, for example integrating ODEs such as in the Monodomain assembler.

Parameters:

	existingSolutionOrGuess
	time

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 111 of file MonodomainDg0Assembler.cpp.

References AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, 1 >::mDt, and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpMonodomainPde.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities ( void ) [inline, protected, virtual]

Overridden ResetInterpolatedQuantities() method.

Reimplemented from AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 92 of file MonodomainDg0Assembler.cpp.

References MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus, and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::E_DIM = ELEMENT_DIM [static]

The element dimension (to save typing).

Definition at line 71 of file MonodomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIIntracellularStimulus [protected]

Intracellular stimulus to be interpolated from cache

Definition at line 83 of file MonodomainDg0Assembler.hpp.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mIionic [protected]

Ionic current to be interpolated from cache

Definition at line 81 of file MonodomainDg0Assembler.hpp.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ResetInterpolatedQuantities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected]

Local cache of the configuration singleton instance

Definition at line 78 of file MonodomainDg0Assembler.hpp.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::MonodomainDg0Assembler().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainPde<ELEMENT_DIM,SPACE_DIM>* MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::mpMonodomainPde [protected]

The PDE to be solved.

Definition at line 87 of file MonodomainDg0Assembler.hpp.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::MonodomainDg0Assembler(), and MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::PrepareForAssembleSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::P_DIM = 1u [static]

The problem dimension (to save typing).

Definition at line 73 of file MonodomainDg0Assembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const unsigned MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::S_DIM = SPACE_DIM [static]

The space dimension (to save typing).

Definition at line 72 of file MonodomainDg0Assembler.hpp.

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

/tmp/release_2.0/heart/src/solver/MonodomainDg0Assembler.hpp
/tmp/release_2.0/heart/src/solver/MonodomainDg0Assembler.cpp

MonodomainDg0Assembler< 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 MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >