#include <VolumeDependentAveragedSourceEllipticPde.hpp>

Inheritance diagram for VolumeDependentAveragedSourceEllipticPde< DIM >:

Collaboration diagram for VolumeDependentAveragedSourceEllipticPde< DIM >:

Public Member Functions
	VolumeDependentAveragedSourceEllipticPde (AbstractCellPopulation< DIM > &rCellPopulation, double coefficient=0.0)

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

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

const AbstractCellPopulation< DIM > &	rGetCellPopulation () const

double	GetCoefficient () const

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 ()

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

Private Attributes
NodeBasedCellPopulation< DIM > *	mpStaticCastCellPopulation

Friends
class	TestCellBasedEllipticPdes

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AveragedSourceEllipticPde< DIM >
AbstractCellPopulation< DIM > &	mrCellPopulation

double	mSourceCoefficient

double	mDiffusionCoefficient

std::vector< double >	mCellDensityOnCoarseElements

Detailed Description

template<unsigned DIM>
class VolumeDependentAveragedSourceEllipticPde< DIM >

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

This class inherits from AveragedSourceEllipticPde and may only be used with a NodeBasedCellPopulation, since it assumes that each cell is associated with a Node object.

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 a weighted sum of the non-apoptotic cells whose centres lie in each finite element containing that point, scaled by the area of that element. The weighting assigned to each cell is given by the square of the radius of the associated node, which is accessed using the GetRadius() method.

Todo:: Consider creating a VolumeDependentAveragedSourceParabolicPde class

Definition at line 74 of file VolumeDependentAveragedSourceEllipticPde.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VolumeDependentAveragedSourceEllipticPde< DIM >::VolumeDependentAveragedSourceEllipticPde	(	AbstractCellPopulation< DIM > &	rCellPopulation,
		double	coefficient = `0.0`
	)

Constructor.

Parameters

rCellPopulation	reference to the cell population
coefficient	the coefficient of consumption of nutrient by cells (defaults to 0.0)

Definition at line 40 of file VolumeDependentAveragedSourceEllipticPde.cpp.

References VolumeDependentAveragedSourceEllipticPde< DIM >::mpStaticCastCellPopulation, and AveragedSourceEllipticPde< DIM >::mrCellPopulation.

Member Function Documentation

template<unsigned DIM>

template<class Archive >

void VolumeDependentAveragedSourceEllipticPde< 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 89 of file VolumeDependentAveragedSourceEllipticPde.hpp.

template<unsigned DIM>

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