#include <AveragedSourceEllipticPde.hpp>

Inheritance diagram for AveragedSourceEllipticPde< DIM >:

Collaboration diagram for AveragedSourceEllipticPde< DIM >:

Public Member Functions
	AveragedSourceEllipticPde (AbstractCellPopulation< DIM > &rCellPopulation, double sourceCoefficient=0.0, double diffusionCoefficient=1.0)

const AbstractCellPopulation< DIM > &	rGetCellPopulation () const

double	GetCoefficient () const

virtual void	SetupSourceTerms (TetrahedralMesh< DIM, DIM > &rCoarseMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)

double	ComputeConstantInUSourceTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement)

double	ComputeLinearInUCoeffInSourceTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement)

c_matrix< double, DIM, DIM >	ComputeDiffusionTerm (const ChastePoint< DIM > &rX)

double	GetUptakeRateForElement (unsigned elementIndex)

Public Member Functions inherited from AbstractLinearEllipticPde< DIM, DIM >
	AbstractLinearEllipticPde ()

virtual	~AbstractLinearEllipticPde ()

virtual double	ComputeConstantInUSourceTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement)=0

virtual double	ComputeLinearInUCoeffInSourceTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement)=0

virtual c_matrix< double, SPACE_DIM, SPACE_DIM >	ComputeDiffusionTerm (const ChastePoint< SPACE_DIM > &rX)=0

virtual double	ComputeConstantInUSourceTermAtNode (const Node< SPACE_DIM > &rNode)

virtual double	ComputeLinearInUCoeffInSourceTermAtNode (const Node< SPACE_DIM > &rNode)

Public Member Functions inherited from AbstractLinearPde< ELEMENT_DIM, SPACE_DIM >
	AbstractLinearPde ()

virtual	~AbstractLinearPde ()

Protected Attributes
AbstractCellPopulation< DIM > &	mrCellPopulation

double	mSourceCoefficient

double	mDiffusionCoefficient

std::vector< double >	mCellDensityOnCoarseElements

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	TestCellBasedEllipticPdes

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AveragedSourceEllipticPde< DIM >

An elliptic PDE to be solved numerically using the finite element method, for coupling to a cell-based simulation.

The PDE takes the form

Grad.(D*Grad(u)) + k*u*rho(x) = 0,

where the scalars D and k are specified by the members mDiffusionCoefficient and mSourceCoefficient, respectively. Their values must be set in the constructor.

The function rho(x) denotes the local density of non-apoptotic cells. This quantity is computed for each element of a 'coarse' finite element mesh that is passed to the method SetupSourceTerms() and stored in the member mCellDensityOnCoarseElements. For a point x, rho(x) is defined to be the number of non-apoptotic cells whose centres lie in each finite element containing that point, scaled by the area of that element.

Todo:: make member names and methods consistent with those of AveragedSourceParabolicPde (#2876)

Definition at line 68 of file AveragedSourceEllipticPde.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AveragedSourceEllipticPde< DIM >::AveragedSourceEllipticPde	(	AbstractCellPopulation< DIM > &	rCellPopulation,
		double	sourceCoefficient = `0.0`,
		double	diffusionCoefficient = `1.0`
	)

Constructor.

Parameters

rCellPopulation	reference to the cell population
sourceCoefficient	the source term coefficient (defaults to 0.0)
diffusionCoefficient	the rate of diffusion (defaults to 1.0)

Definition at line 40 of file AveragedSourceEllipticPde.cpp.

Member Function Documentation

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::ComputeConstantInUSourceTerm	(	const ChastePoint< DIM > &	rX,
		Element< DIM, DIM > *	pElement
	)

Overridden ComputeConstantInUSourceTerm() method.

Parameters

rX	The point in space
pElement	the element

Returns: the constant in u part of the source term, i.e g(x) in Div(D Grad u) + f(x)u + g(x) = 0.

Definition at line 108 of file AveragedSourceEllipticPde.cpp.

template<unsigned DIM>

c_matrix< double, DIM, DIM > AveragedSourceEllipticPde< DIM >::ComputeDiffusionTerm ( const ChastePoint< DIM > & rX )

Overridden ComputeDiffusionTerm() method.

Parameters

rX	The point in space at which the diffusion term is computed

Returns: a matrix.

Definition at line 121 of file AveragedSourceEllipticPde.cpp.

References AveragedSourceEllipticPde< DIM >::mDiffusionCoefficient.

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::ComputeLinearInUCoeffInSourceTerm	(	const ChastePoint< DIM > &	rX,
		Element< DIM, DIM > *	pElement
	)

Overridden ComputeLinearInUCoeffInSourceTerm() method.

Parameters

rX	The point in space
pElement	the element

Returns: the coefficient of u in the linear part of the source term, i.e f(x) in Div(D Grad u) + f(x)u + g(x) = 0.

Definition at line 114 of file AveragedSourceEllipticPde.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AveragedSourceEllipticPde< DIM >::mCellDensityOnCoarseElements, and AveragedSourceEllipticPde< DIM >::mSourceCoefficient.

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::GetCoefficient ( ) const

Returns: mSourceCoefficient

Definition at line 56 of file AveragedSourceEllipticPde.cpp.

References AveragedSourceEllipticPde< DIM >::mSourceCoefficient.

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::GetUptakeRateForElement ( unsigned elementIndex )

Returns: the uptake rate.

Parameters

elementIndex the element we wish to return the uptake rate for

Definition at line 127 of file AveragedSourceEllipticPde.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, and AveragedSourceEllipticPde< DIM >::mCellDensityOnCoarseElements.

template<unsigned DIM>

const AbstractCellPopulation< DIM > & AveragedSourceEllipticPde< DIM >::rGetCellPopulation ( ) const

Returns: const reference to the cell population (used in archiving).

Definition at line 50 of file AveragedSourceEllipticPde.cpp.

References AveragedSourceEllipticPde< DIM >::mrCellPopulation.

template<unsigned DIM>

template<class Archive >

void AveragedSourceEllipticPde< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the PDE and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 83 of file AveragedSourceEllipticPde.hpp.

References AveragedSourceEllipticPde< DIM >::mCellDensityOnCoarseElements, AveragedSourceEllipticPde< DIM >::mDiffusionCoefficient, and AveragedSourceEllipticPde< DIM >::mSourceCoefficient.

template<unsigned DIM>

void AveragedSourceEllipticPde< DIM >::SetupSourceTerms	(	TetrahedralMesh< DIM, DIM > &	rCoarseMesh,
		std::map< CellPtr, unsigned > *	pCellPdeElementMap = `nullptr`
	)