#include <PdeAndBoundaryConditions.hpp>

Collaboration diagram for PdeAndBoundaryConditions< DIM >:

Public Member Functions
	PdeAndBoundaryConditions (AbstractLinearEllipticPde< DIM, DIM > pPde=NULL, AbstractBoundaryCondition< DIM > pBoundaryCondition=NULL, bool isNeumannBoundaryCondition=true, Vec solution=NULL, bool deleteMemberPointersInDestructor=false)
	~PdeAndBoundaryConditions ()
AbstractLinearEllipticPde< DIM, DIM > *	GetPde ()
AbstractBoundaryCondition< DIM > *	GetBoundaryCondition () const
Vec	GetSolution ()
Vec	GetSolution () const
void	SetSolution (Vec solution)
bool	IsNeumannBoundaryCondition ()
bool	HasAveragedSourcePde ()
void	DestroySolution ()
void	SetUpSourceTermsForAveragedSourcePde (TetrahedralMesh< DIM, DIM > pMesh, std::map< CellPtr, unsigned > pCellPdeElementMap=NULL)
void	SetDependentVariableName (const std::string &rName)
std::string &	rGetDependentVariableName ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
AbstractLinearEllipticPde< DIM, DIM > *	mpPde
AbstractBoundaryCondition< DIM > *	mpBoundaryCondition
bool	mIsNeumannBoundaryCondition
Vec	mSolution
bool	mDeleteMemberPointersInDestructor
std::string	mDependentVariableName
Friends
class	TestPdeAndBoundaryConditions
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class PdeAndBoundaryConditions< DIM >

A helper class for use in cell-based simulations with PDEs. The class contains a pointer to a linear elliptic PDE, which is to be solved on the domain defined by the cell population. The class also contains information describing the boundary condition that is to be imposed when solving the PDE. Currently we allow Neumann (imposed flux) or Dirichlet (imposed value) boundary conditions. The boundary condition may be constant on the boundary or vary spatially and/or temporally. In cell-based simulations with PDEs, one or more of these objects are accessed via the CellBasedHandler class.

Definition at line 59 of file PdeAndBoundaryConditions.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

PdeAndBoundaryConditions< DIM >::PdeAndBoundaryConditions	(	AbstractLinearEllipticPde< DIM, DIM > *	pPde = `NULL`,
		AbstractBoundaryCondition< DIM > *	pBoundaryCondition = `NULL`,
		bool	isNeumannBoundaryCondition = `true`,
		Vec	solution = `NULL`,
		bool	deleteMemberPointersInDestructor = `false`
	)

Constructor.

Parameters:

pPde	A pointer to a linear elliptic PDE object (defaults to NULL)
pBoundaryCondition	A 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)
solution	A solution vector (defaults to NULL)
deleteMemberPointersInDestructor	whether to delete member pointers in the destructor (defaults to false)

Definition at line 39 of file PdeAndBoundaryConditions.cpp.

References PdeAndBoundaryConditions< DIM >::mSolution.

template<unsigned DIM>

PdeAndBoundaryConditions< DIM >::~PdeAndBoundaryConditions ( )

Destructor.

Definition at line 58 of file PdeAndBoundaryConditions.cpp.

Member Function Documentation

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::DestroySolution ( )

Call PetscTools::Destroy( on mSolution.

Definition at line 113 of file PdeAndBoundaryConditions.cpp.

References PetscTools::Destroy().

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

AbstractBoundaryCondition< DIM > * PdeAndBoundaryConditions< DIM >::GetBoundaryCondition ( ) const

Returns:: mpBoundaryCondition

Definition at line 77 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

AbstractLinearEllipticPde< DIM, DIM > * PdeAndBoundaryConditions< DIM >::GetPde ( )

Returns:: mpPde

Definition at line 71 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

Vec PdeAndBoundaryConditions< DIM >::GetSolution ( )

Returns:: mSolution

Definition at line 83 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), and CellBasedPdeHandler< DIM >::WritePdeSolution().

template<unsigned DIM>

Vec PdeAndBoundaryConditions< DIM >::GetSolution ( ) const

Returns:: mSolution (used in archiving)

Definition at line 89 of file PdeAndBoundaryConditions.cpp.

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::HasAveragedSourcePde ( )

Returns:: whether the PDE is of type AveragedSourcePde

Definition at line 107 of file PdeAndBoundaryConditions.cpp.

template<unsigned DIM>

bool PdeAndBoundaryConditions< DIM >::IsNeumannBoundaryCondition ( )

Returns:: mIsNeumannBoundaryCondition

Definition at line 101 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

std::string & PdeAndBoundaryConditions< DIM >::rGetDependentVariableName ( )

Get the name of the dependent variable.

Returns:: the name

Definition at line 135 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::AddPdeAndBc().

template<unsigned DIM>

template<class Archive >

void PdeAndBoundaryConditions< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Serialize the PDE object.

Parameters:

archive	the archive
version	the current version of this class

Definition at line 74 of file PdeAndBoundaryConditions.hpp.

References PdeAndBoundaryConditions< DIM >::mDependentVariableName, PdeAndBoundaryConditions< DIM >::mIsNeumannBoundaryCondition, PdeAndBoundaryConditions< DIM >::mpBoundaryCondition, and PdeAndBoundaryConditions< DIM >::mpPde.

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetDependentVariableName ( const std::string & rName )

Set the name of the dependent variable.

Parameters:

rName the name.

Definition at line 129 of file PdeAndBoundaryConditions.cpp.

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetSolution ( Vec solution )

Set mSolution.

Parameters:

solution the current solution

Definition at line 95 of file PdeAndBoundaryConditions.cpp.

Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned DIM>

void PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		std::map< CellPtr, unsigned > *	pCellPdeElementMap = `NULL`
	)