#include <AbstractBoxDomainPdeModifier.hpp>

Inheritance diagram for AbstractBoxDomainPdeModifier< DIM >:

Collaboration diagram for AbstractBoxDomainPdeModifier< DIM >:

Public Member Functions
	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)

virtual	~AbstractBoxDomainPdeModifier ()

double	GetStepSize ()

void	SetBcsOnBoxBoundary (bool setBcsOnBoxBoundary)

bool	AreBcsSetOnBoxBoundary ()

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

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

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

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

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

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

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)

virtual	~AbstractPdeModifier ()

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

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

bool	IsNeumannBoundaryCondition ()

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

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

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

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

bool	GetOutputGradient ()

void	SetOutputGradient (bool outputGradient)

void	SetOutputSolutionAtPdeNodes (bool outputSolutionAtPdeNodes)

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

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

Protected Attributes
std::map< CellPtr, unsigned >	mCellPdeElementMap

boost::shared_ptr < ChasteCuboid< DIM > >	mpMeshCuboid

double	mStepSize

bool	mSetBcsOnBoxBoundary

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

TetrahedralMesh< DIM, DIM > *	mpFeMesh

std::string	mOutputDirectory

bool	mOutputGradient

bool	mOutputSolutionAtPdeNodes

out_stream	mpVizPdeSolutionResultsFile

bool	mDeleteFeMesh

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

Friends
class	TestEllipticBoxDomainPdeModifier

class	TestParabolicBoxDomainPdeModifier

class	TestOffLatticeSimulationWithPdes

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractBoxDomainPdeModifier< DIM >

An abstract modifier class containing functionality common to EllipticBoxDomainPdeModifier and ParabolicBoxDomainPdeModifier, which both solve a linear elliptic or parabolic PDE coupled to a cell-based simulation on a coarse domain.

Definition at line 50 of file AbstractBoxDomainPdeModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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`
	)

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 41 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractBoxDomainPdeModifier< DIM >::GenerateFeMesh(), AbstractPdeModifier< DIM >::mDeleteFeMesh, AbstractBoxDomainPdeModifier< DIM >::mpMeshCuboid, and AbstractBoxDomainPdeModifier< DIM >::mStepSize.

template<unsigned DIM>

AbstractBoxDomainPdeModifier< DIM >::~AbstractBoxDomainPdeModifier ( )

virtual

Destructor.

Definition at line 64 of file AbstractBoxDomainPdeModifier.cpp.

Member Function Documentation

template<unsigned DIM>

bool AbstractBoxDomainPdeModifier< DIM >::AreBcsSetOnBoxBoundary ( )

Returns: mSetBcsOnCoarseBoundary.

Definition at line 81 of file AbstractBoxDomainPdeModifier.cpp.

template<unsigned DIM>

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

Helper method to generate the mesh.

Parameters

pMeshCuboid	the outer boundary for the FE mesh.
stepSize	the step size to be used in the FE mesh.

Definition at line 95 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh(), NEVER_REACHED, and ChastePoint< DIM >::rGetLocation().

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier().

template<unsigned DIM>

double AbstractBoxDomainPdeModifier< DIM >::GetStepSize ( )

Returns: mStepSize.

Definition at line 69 of file AbstractBoxDomainPdeModifier.cpp.

template<unsigned DIM>

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

Initialise mCellPdeElementMap.

Parameters

rCellPopulation reference to the cell population

Definition at line 205 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre().

template<unsigned DIM>

void AbstractBoxDomainPdeModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Reimplemented in ParabolicBoxDomainPdeModifier< DIM >, and EllipticBoxDomainPdeModifier< DIM >.

Definition at line 235 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractPdeModifier< DIM >::OutputSimulationModifierParameters().

Referenced by EllipticBoxDomainPdeModifier< DIM >::OutputSimulationModifierParameters(), and ParabolicBoxDomainPdeModifier< DIM >::OutputSimulationModifierParameters().

template<unsigned DIM>

template<class Archive >

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

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 68 of file AbstractBoxDomainPdeModifier.hpp.

References AbstractBoxDomainPdeModifier< DIM >::mpMeshCuboid, AbstractBoxDomainPdeModifier< DIM >::mSetBcsOnBoxBoundary, and AbstractBoxDomainPdeModifier< DIM >::mStepSize.

template<unsigned DIM>

void AbstractBoxDomainPdeModifier< DIM >::SetBcsOnBoxBoundary ( bool setBcsOnBoxBoundary )

Set mSetBcsOnCoarseBoundary.

Parameters

setBcsOnBoxBoundary whether to set the boundary condition on the edge of the box domain rather than the cell population

Definition at line 75 of file AbstractBoxDomainPdeModifier.cpp.

template<unsigned DIM>

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

virtual

Overridden SetupSolve() method.

Specifies what to do in the simulation before the start of the time loop.

Here we just initialize the Cell PDE element map

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Reimplemented from AbstractPdeModifier< DIM >.

Reimplemented in EllipticBoxDomainPdeModifier< DIM >, and ParabolicBoxDomainPdeModifier< DIM >.

Definition at line 87 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractPdeModifier< DIM >::SetupSolve().

Referenced by ParabolicBoxDomainPdeModifier< DIM >::SetupSolve(), and EllipticBoxDomainPdeModifier< DIM >::SetupSolve().

template<unsigned DIM>

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

Helper method to copy the PDE solution to CellData

Here we need to interpolate from the FE mesh onto the cells.

Parameters

rCellPopulation reference to the cell population

Definition at line 132 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), LinearBasisFunction< ELEMENT_DIM >::ComputeTransformedBasisFunctionDerivatives(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), and NEVER_REACHED.

template<unsigned DIM>

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

Update the mCellPdeElementMap

This method should be called before sending the element map to a PDE class to ensure map is up to date.

Parameters

rCellPopulation reference to the cell population

Definition at line 221 of file AbstractBoxDomainPdeModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 59 of file AbstractBoxDomainPdeModifier.hpp.

Member Data Documentation

template<unsigned DIM>

std::map<CellPtr, unsigned> AbstractBoxDomainPdeModifier< DIM >::mCellPdeElementMap

protected

Map between cells and the elements of the FE mesh containing them.

Definition at line 79 of file AbstractBoxDomainPdeModifier.hpp.

template<unsigned DIM>

boost::shared_ptr<ChasteCuboid<DIM> > AbstractBoxDomainPdeModifier< DIM >::mpMeshCuboid

protected

Pointer to a ChasteCuboid storing the outer boundary for the FE mesh. Stored as a member to facilitate archiving.

Definition at line 85 of file AbstractBoxDomainPdeModifier.hpp.

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier(), and AbstractBoxDomainPdeModifier< DIM >::serialize().

template<unsigned DIM>

bool AbstractBoxDomainPdeModifier< DIM >::mSetBcsOnBoxBoundary

protected

Whether to set the boundary condition on the edge of the box domain rather than the cell population. Default to true.

Definition at line 97 of file AbstractBoxDomainPdeModifier.hpp.

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

template<unsigned DIM>

double AbstractBoxDomainPdeModifier< DIM >::mStepSize

protected

The step size to be used in the FE mesh. Stored as a member to facilitate archiving.

Definition at line 91 of file AbstractBoxDomainPdeModifier.hpp.

Referenced by AbstractBoxDomainPdeModifier< DIM >::AbstractBoxDomainPdeModifier(), and AbstractBoxDomainPdeModifier< DIM >::serialize().

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

cell_based/src/cell_based_pde/AbstractBoxDomainPdeModifier.hpp
cell_based/src/cell_based_pde/AbstractBoxDomainPdeModifier.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractBoxDomainPdeModifier< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractBoxDomainPdeModifier< DIM >