#include <ParabolicBoxDomainPdeModifier.hpp>

Inheritance diagram for ParabolicBoxDomainPdeModifier< DIM >:

Collaboration diagram for ParabolicBoxDomainPdeModifier< DIM >:

Public Member Functions
	ParabolicBoxDomainPdeModifier (boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=boost::shared_ptr< AbstractLinearPde< DIM, DIM > >(), boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid=boost::shared_ptr< ChasteCuboid< DIM > >(), double stepSize=1.0, Vec solution=nullptr)

	~ParabolicBoxDomainPdeModifier () override=default

void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override

void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) override

virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > >	ConstructBoundaryConditionsContainer (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	SetupInitialSolutionVector (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

Vec	InterpolateSolutionFromCellMovement (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	SetMoveSolutionWithCells (bool moveSolutionWithCells)

bool	GetMoveSolutionWithCells () const

void	OutputSimulationModifierParameters (out_stream &rParamsFile) override

Public Member Functions inherited from AbstractBoxDomainPdeModifier< DIM >
	AbstractBoxDomainPdeModifier (boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=boost::shared_ptr< AbstractLinearPde< DIM, DIM > >(), boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid=boost::shared_ptr< ChasteCuboid< DIM > >(), double stepSize=1.0, Vec solution=nullptr)

	~AbstractBoxDomainPdeModifier () override=default

double	GetStepSize () const

void	SetBcsOnBoxBoundary (bool setBcsOnBoxBoundary)

bool	AreBcsSetOnBoxBoundary () const

void	SetBcsOnBoundingSphere (bool setBcsOnBoundingSphere)

bool	AreBcsSetOnBoundingSphere () const

void	SetUseVoronoiCellsForInterpolation (bool useVoronoiCellsForInterpolation)

bool	GetUseVoronoiCellsForInterpolation () const

void	SetTypicalCellRadius (double typicalCellRadius)

double	GetTypicalCellRadius () const

void	ConstructBoundaryConditionsContainerHelper (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > pBcc)

void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) override

void	GenerateFeMesh (boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid, double stepSize)

void	GenerateAndReturnFeMesh (boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid, double stepSize, TetrahedralMesh< DIM, DIM > *pMesh)

void	UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	InitialiseCellPdeElementMap (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	UpdateCellPdeElementMap (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

Public Member Functions inherited from AbstractPdeModifier< DIM >
	AbstractPdeModifier (boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=NULL, boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, Vec solution=nullptr)

	~AbstractPdeModifier () override

boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	GetPde ()

boost::shared_ptr< AbstractBoundaryCondition< DIM > >	GetBoundaryCondition ()

bool	IsNeumannBoundaryCondition () const

void	SetDependentVariableName (const std::string &rName)

std::string &	rGetDependentVariableName ()

bool	HasAveragedSourcePde ()

void	SetUpSourceTermsForAveragedSourcePde (TetrahedralMesh< DIM, DIM > pMesh, std::map< CellPtr, unsigned > pCellPdeElementMap=nullptr)

Vec	GetSolution ()

Vec	GetSolution () const

TetrahedralMesh< DIM, DIM > *	GetFeMesh () const

void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) override

void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override

void	UpdateAtEndOfSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation) override

bool	GetOutputGradient () const

void	SetOutputGradient (bool outputGradient)

void	SetOutputSolutionAtPdeNodes (bool outputSolutionAtPdeNodes)

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

virtual	~AbstractCellBasedSimulationModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

void	OutputSimulationModifierInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

Private Attributes
bool	mMoveSolutionWithCells

std::map< CellPtr, c_vector< double, DIM > >	mOldCellLocations

Friends
class	TestParabolicBoxDomainPdeModifier

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractBoxDomainPdeModifier< DIM >
std::map< CellPtr, unsigned >	mCellPdeElementMap

boost::shared_ptr< ChasteCuboid< DIM > >	mpMeshCuboid

double	mStepSize

bool	mSetBcsOnBoxBoundary

bool	mSetBcsOnBoundingSphere

bool	mUseVoronoiCellsForInterpolation

double	mTypicalCellRadius

Protected Attributes inherited from AbstractPdeModifier< DIM >
boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	mpPde

boost::shared_ptr< AbstractBoundaryCondition< DIM > >	mpBoundaryCondition

bool	mIsNeumannBoundaryCondition

std::string	mDependentVariableName

Vec	mSolution = nullptr

TetrahedralMesh< DIM, DIM > *	mpFeMesh = nullptr

std::string	mOutputDirectory {}

bool	mOutputGradient = false

bool	mOutputSolutionAtPdeNodes = false

out_stream	mpVizPdeSolutionResultsFile

bool	mDeleteFeMesh = false

std::vector< double >	mIsDirichletBoundaryNode

Detailed Description

template<unsigned DIM>
class ParabolicBoxDomainPdeModifier< DIM >

A modifier class in which a linear parabolic PDE coupled to a cell-based simulation is solved on a coarse domain.

The finite element mesh used to solve the PDE numerically is a fixed tessellation of a cuboid (box), which must be supplied to the constructor. The value of the dependent variable is interpolated between coarse mesh nodes to obtain a value at each cell, which is stored and updated in a CellData item.

At each time step the boundary condition supplied to the constructor may be imposed either on the boundary of the box domain, or on the boundary of the cell population (which is assumed to lie within the box domain). This choice can be made using the AbstractBoxDomainPdeModifier method SetBcsOnBoxBoundary(), which is inherited by this class.

Examples of PDEs in the source folder that can be solved using this class are AveragedSourceParabolicPde and UniformSourceParabolicPde.

Definition at line 64 of file ParabolicBoxDomainPdeModifier.hpp.

Constructor & Destructor Documentation

◆ ParabolicBoxDomainPdeModifier()

template<unsigned DIM>

ParabolicBoxDomainPdeModifier< DIM >::ParabolicBoxDomainPdeModifier	(	boost::shared_ptr< AbstractLinearPde< DIM, DIM > >	pPde = `boost::shared_ptr<AbstractLinearPde<DIM,DIM> >()`,
		boost::shared_ptr< AbstractBoundaryCondition< DIM > >	pBoundaryCondition = `boost::shared_ptr<AbstractBoundaryCondition<DIM> >()`,
		bool	isNeumannBoundaryCondition = `true`,
		boost::shared_ptr< ChasteCuboid< DIM > >	pMeshCuboid = `boost::shared_ptr<ChasteCuboid<DIM> >()`,
		double	stepSize = `1.0`,
		Vec	solution = `nullptr`
	)

Constructor.

Parameters

pPde	A shared pointer to a linear PDE object (defaults to NULL)
pBoundaryCondition	A shared pointer to an abstract boundary condition (defaults to NULL, corresponding to a constant boundary condition with value zero)
isNeumannBoundaryCondition	Whether the boundary condition is Neumann (defaults to true)
pMeshCuboid	A shared pointer to a ChasteCuboid specifying the outer boundary for the FE mesh (defaults to NULL)
stepSize	step size to be used in the FE mesh (defaults to 1.0, i.e. the default cell size)
solution	solution vector (defaults to NULL)

Definition at line 42 of file ParabolicBoxDomainPdeModifier.cpp.

◆ ~ParabolicBoxDomainPdeModifier()

template<unsigned DIM>

ParabolicBoxDomainPdeModifier< DIM >::~ParabolicBoxDomainPdeModifier ( )

overridedefault

Destructor.

Member Function Documentation

◆ ConstructBoundaryConditionsContainer()

template<unsigned DIM>

std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ParabolicBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

virtual

Helper method to construct the boundary conditions container for the PDE.

Parameters

rCellPopulation reference to the cell population

Returns: the full boundary conditions container

Definition at line 152 of file ParabolicBoxDomainPdeModifier.cpp.

◆ GetMoveSolutionWithCells()

template<unsigned DIM>

bool ParabolicBoxDomainPdeModifier< DIM >::GetMoveSolutionWithCells ( ) const

Returns: mMoveSolutionWithCells.

Definition at line 337 of file ParabolicBoxDomainPdeModifier.cpp.

◆ InterpolateSolutionFromCellMovement()

template<unsigned DIM>

Vec ParabolicBoxDomainPdeModifier< DIM >::InterpolateSolutionFromCellMovement ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

Helper method to interpolate the PDE solution from cells using the CellData. Use the cells voronoi region as all fe nodes in a cell centre voronoi region are given the value from cell data.

Parameters

rCellPopulation reference to the cell population