AveragedSourceEllipticPde< DIM > Class Template Reference

#include <AveragedSourceEllipticPde.hpp>

Inheritance diagram for AveragedSourceEllipticPde< DIM >:

Collaboration diagram for AveragedSourceEllipticPde< DIM >:

Public Member Functions
	AveragedSourceEllipticPde (AbstractCellPopulation< DIM > &rCellPopulation, double constantSourceCoefficient=0.0, double linearSourceCoefficient=0.0, double diffusionCoefficient=1.0, bool scaleByCellVolume=false)
const AbstractCellPopulation< DIM > &	rGetCellPopulation () const
double	GetConstantCoefficient () const
double	GetLinearCoefficient () const
double	GetDiffusionCoefficient () const
bool	GetScaleByCellVolume () const
virtual void	SetupSourceTerms (TetrahedralMesh< DIM, DIM > &rCoarseMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)
double	ComputeConstantInUSourceTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement) override
double	ComputeLinearInUCoeffInSourceTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement) override
c_matrix< double, DIM, DIM >	ComputeDiffusionTerm (const ChastePoint< DIM > &rX) override
double	GetUptakeRateForElement (unsigned elementIndex)
Public Member Functions inherited from AbstractLinearEllipticPde< DIM, DIM >
	AbstractLinearEllipticPde ()
	~AbstractLinearEllipticPde () override=default
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	mConstantSourceCoefficient
double	mLinearSourceCoefficient
double	mDiffusionCoefficient
bool	mScaleByCellVolume
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

AveragedSourceEllipticPde()

template<unsigned DIM>

AveragedSourceEllipticPde< DIM >::AveragedSourceEllipticPde	(	AbstractCellPopulation< DIM > &	rCellPopulation,
		double	constantSourceCoefficient = 0.0,
		double	linearSourceCoefficient = 0.0,
		double	diffusionCoefficient = 1.0,
		bool	scaleByCellVolume = false
	)

Constructor.

Parameters

rCellPopulation	reference to the cell population
constantSourceCoefficient	the constant source term coefficient (defaults to 0.0)
linearSourceCoefficient	the linear source term coefficient (defaults to 0.0)
diffusionCoefficient	the rate of diffusion (defaults to 1.0)
scaleByCellVolume	whether to scale by cell volume (defaults to)

Definition at line 40 of file AveragedSourceEllipticPde.cpp.

Member Function Documentation

ComputeConstantInUSourceTerm()

template<unsigned DIM>

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

override

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 145 of file AveragedSourceEllipticPde.cpp.

References EXCEPT_IF, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex().

ComputeDiffusionTerm()

template<unsigned DIM>

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

override

Overridden ComputeDiffusionTerm() method.

Parameters

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

Returns

a matrix.

Definition at line 161 of file AveragedSourceEllipticPde.cpp.

ComputeLinearInUCoeffInSourceTerm()

template<unsigned DIM>

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

override

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 153 of file AveragedSourceEllipticPde.cpp.

References EXCEPT_IF, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex().

GetConstantCoefficient()

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::GetConstantCoefficient

(

)

const

Returns

mConstantSourceCoefficient

Definition at line 60 of file AveragedSourceEllipticPde.cpp.

GetDiffusionCoefficient()

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::GetDiffusionCoefficient

(

)

const

Returns

mDiffusionCoefficient

Definition at line 72 of file AveragedSourceEllipticPde.cpp.

GetLinearCoefficient()

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::GetLinearCoefficient

(

)

const

Returns

mLinearSourceCoefficient

Definition at line 66 of file AveragedSourceEllipticPde.cpp.

GetScaleByCellVolume()

template<unsigned DIM>

bool AveragedSourceEllipticPde< DIM >::GetScaleByCellVolume

(

)

const

Returns

mScaleByCellVolume

Definition at line 78 of file AveragedSourceEllipticPde.cpp.

GetUptakeRateForElement()

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 167 of file AveragedSourceEllipticPde.cpp.

rGetCellPopulation()

template<unsigned DIM>

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

(

)

const

Returns

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

Definition at line 54 of file AveragedSourceEllipticPde.cpp.

serialize()

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 >::mConstantSourceCoefficient, AveragedSourceEllipticPde< DIM >::mDiffusionCoefficient, AveragedSourceEllipticPde< DIM >::mLinearSourceCoefficient, and AveragedSourceEllipticPde< DIM >::mScaleByCellVolume.

SetupSourceTerms()

template<unsigned DIM>

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

virtual

Set up the source terms.

Parameters

rCoarseMesh	reference to the coarse mesh
pCellPdeElementMap	optional pointer to the map from cells to coarse elements

Definition at line 84 of file AveragedSourceEllipticPde.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 75 of file AveragedSourceEllipticPde.hpp.

TestCellBasedEllipticPdes

template<unsigned DIM>

friend class TestCellBasedEllipticPdes

friend

Definition at line 70 of file AveragedSourceEllipticPde.hpp.

Member Data Documentation

mCellDensityOnCoarseElements

template<unsigned DIM>

std::vector<double> AveragedSourceEllipticPde< DIM >::mCellDensityOnCoarseElements

protected

Vector of averaged cell densities on elements of the coarse mesh.

Definition at line 111 of file AveragedSourceEllipticPde.hpp.

Referenced by AveragedSourceEllipticPde< DIM >::serialize().

mConstantSourceCoefficient

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::mConstantSourceCoefficient

protected

Coefficient of constant source term.

Definition at line 99 of file AveragedSourceEllipticPde.hpp.

Referenced by AveragedSourceEllipticPde< DIM >::serialize().

mDiffusionCoefficient

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::mDiffusionCoefficient

protected

Diffusion coefficient.

Definition at line 105 of file AveragedSourceEllipticPde.hpp.

Referenced by AveragedSourceEllipticPde< DIM >::serialize().

mLinearSourceCoefficient

template<unsigned DIM>

double AveragedSourceEllipticPde< DIM >::mLinearSourceCoefficient

protected

Coefficient of linear source term.

Definition at line 102 of file AveragedSourceEllipticPde.hpp.

Referenced by AveragedSourceEllipticPde< DIM >::serialize().

mrCellPopulation

template<unsigned DIM>

AbstractCellPopulation<DIM>& AveragedSourceEllipticPde< DIM >::mrCellPopulation

protected

The cell population member.

Definition at line 96 of file AveragedSourceEllipticPde.hpp.

mScaleByCellVolume

template<unsigned DIM>

bool AveragedSourceEllipticPde< DIM >::mScaleByCellVolume

protected

Whether to scale terms by cell volume.

Definition at line 108 of file AveragedSourceEllipticPde.hpp.

Referenced by AveragedSourceEllipticPde< DIM >::serialize().

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

• cell_based/src/cell_based_pde/pdes/AveragedSourceEllipticPde.hpp
• cell_based/src/cell_based_pde/pdes/AveragedSourceEllipticPde.cpp