CellBasedPdeHandler< DIM > Class Template Reference

#include <CellBasedPdeHandler.hpp>

Inherited by CellBasedPdeHandlerOnCuboid< DIM >.

Collaboration diagram for CellBasedPdeHandler< DIM >:

Public Member Functions
	CellBasedPdeHandler (AbstractCellPopulation< DIM > *pCellPopulation, bool deleteMemberPointersInDestructor=false)
virtual	~CellBasedPdeHandler ()
const AbstractCellPopulation < DIM > *	GetCellPopulation () const
TetrahedralMesh< DIM, DIM > *	GetCoarsePdeMesh ()
void	OpenResultsFiles (std::string outputDirectory)
void	CloseResultsFiles ()
bool	GetWriteAverageRadialPdeSolution ()
bool	GetWriteDailyAverageRadialPdeSolution ()
void	UpdateCellPdeElementMap ()
bool	GetImposeBcsOnCoarseBoundary ()
unsigned	GetNumRadialIntervals ()
virtual void	SolvePdeAndWriteResultsToFile (unsigned samplingTimestepMultiple)
virtual std::auto_ptr < BoundaryConditionsContainer < DIM, DIM, 1 > >	ConstructBoundaryConditionsContainer (PdeAndBoundaryConditions< DIM > pPdeAndBc, TetrahedralMesh< DIM, DIM > pMesh)
double	GetPdeSolutionAtPoint (const c_vector< double, DIM > &rPoint, const std::string &rVariable)
unsigned	FindCoarseElementContainingCell (CellPtr pCell)
virtual Vec	GetPdeSolution (const std::string &rName="")
void	SetWriteAverageRadialPdeSolution (const std::string &rName, unsigned numRadialIntervals=10, bool writeDailyResults=false)
void	SetImposeBcsOnCoarseBoundary (bool setBcsOnCoarseBoundary)
virtual void	UseCoarsePdeMesh (double stepSize, ChasteCuboid< DIM > meshCuboid, bool centreOnCellPopulation=false)
void	AddPdeAndBc (PdeAndBoundaryConditions< DIM > *pPdeAndBc)
virtual void	OutputParameters (out_stream &rParamsFile)
Protected Member Functions
void	InitialiseCellPdeElementMap ()
virtual void	WritePdeSolution (double time)
void	WriteAverageRadialPdeSolution (double time)
bool	PdeSolveNeedsCoarseMesh ()
Protected Attributes
AbstractCellPopulation< DIM > *	mpCellPopulation
std::vector < PdeAndBoundaryConditions < DIM > * >	mPdeAndBcCollection
std::string	mDirPath
out_stream	mpVizPdeSolutionResultsFile
out_stream	mpAverageRadialPdeSolutionResultsFile
bool	mWriteAverageRadialPdeSolution
bool	mWriteDailyAverageRadialPdeSolution
std::string	mAverageRadialSolutionVariableName
bool	mSetBcsOnCoarseBoundary
unsigned	mNumRadialIntervals
TetrahedralMesh< DIM, DIM > *	mpCoarsePdeMesh
std::map< CellPtr, unsigned >	mCellPdeElementMap
bool	mDeleteMemberPointersInDestructor
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestCellBasedPdeHandler
class	TestOffLatticeSimulationWithPdes
class	TestOnLatticeSimulationWithPdes
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class CellBasedPdeHandler< DIM >

A helper class, containing code for handling the numerical solution of one or more PDEs (using the finite element method) associated with a cell-based simulation object.

By letting AbstractCellBasedSimulation have a pointer to an object of this type as a member variable, we separate out all PDE-related functionality into this class, and thus obviate the need for specialized cell-based simulation subclasses.

Definition at line 60 of file CellBasedPdeHandler.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedPdeHandler< DIM >::CellBasedPdeHandler	(	AbstractCellPopulation< DIM > *	pCellPopulation,
		bool	deleteMemberPointersInDestructor = `false`
	)			`[inline]`

Constructor.

Parameters:

	pCellPopulation	pointer to a cell population
	deleteMemberPointersInDestructor	whether to delete member pointers in the destructor (defaults to false)

Todo:: change to exceptions (#1891)

Definition at line 48 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), and CellBasedPdeHandler< DIM >::mpCellPopulation.

template<unsigned DIM>

CellBasedPdeHandler< DIM >::~CellBasedPdeHandler ( ) [inline, virtual]

Destructor.

Definition at line 65 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mDeleteMemberPointersInDestructor, CellBasedPdeHandler< DIM >::mpCoarsePdeMesh, and CellBasedPdeHandler< DIM >::mPdeAndBcCollection.

Member Function Documentation

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::AddPdeAndBc ( PdeAndBoundaryConditions< DIM > * pPdeAndBc ) [inline]

Pass a PDE and associated boundary conditions to the simulation.

Parameters:

pPdeAndBc

a pointer to a PdeAndBoundaryConditions object

Definition at line 99 of file CellBasedPdeHandler.cpp.

References EXCEPTION, CellBasedPdeHandler< DIM >::mPdeAndBcCollection, and PdeAndBoundaryConditions< DIM >::rGetDependentVariableName().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::CloseResultsFiles ( ) [inline]

Close results files. Called by AbstractCellBasedSimulation::Solve().

Definition at line 227 of file CellBasedPdeHandler.cpp.

References PetscTools::AmMaster(), SimulationTime::Instance(), CellBasedPdeHandler< DIM >::mpAverageRadialPdeSolutionResultsFile, CellBasedPdeHandler< DIM >::mpVizPdeSolutionResultsFile, CellBasedPdeHandler< DIM >::mWriteAverageRadialPdeSolution, and CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution().

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

template<unsigned DIM>

std::auto_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer	(	PdeAndBoundaryConditions< DIM > *	pPdeAndBc,
		TetrahedralMesh< DIM, DIM > *	pMesh
	)			`[inline, virtual]`

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

Parameters:

	pPdeAndBc	a pointer to the PDE and BCs
	pMesh	the mesh on which to solve the PDE

Returns:: the full boundary conditions container

Reimplemented in CellBasedPdeHandlerOnCuboid< DIM >.

Definition at line 473 of file CellBasedPdeHandler.cpp.

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

template<unsigned DIM>

unsigned CellBasedPdeHandler< DIM >::FindCoarseElementContainingCell ( CellPtr pCell ) [inline]

Find the index of the coarse mesh element containing a given cell.

Parameters:

pCell

the cell

Returns:: the element index.

Definition at line 544 of file CellBasedPdeHandler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), CellBasedPdeHandler< DIM >::mCellPdeElementMap, CellBasedPdeHandler< DIM >::mpCellPopulation, and CellBasedPdeHandler< DIM >::mpCoarsePdeMesh.

template<unsigned DIM>

const AbstractCellPopulation< DIM > * CellBasedPdeHandler< DIM >::GetCellPopulation ( ) const [inline]

Get a pointer to the cell population.

Returns:: a const pointer to mpCellPopulation

Definition at line 87 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mpCellPopulation.

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * CellBasedPdeHandler< DIM >::GetCoarsePdeMesh ( ) [inline]

Returns:: mpCoarsePdeMesh

Definition at line 93 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mpCoarsePdeMesh.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetImposeBcsOnCoarseBoundary ( ) [inline]

Returns:: mSetBcsOnCoarseBoundary

Definition at line 815 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mSetBcsOnCoarseBoundary.

template<unsigned DIM>

unsigned CellBasedPdeHandler< DIM >::GetNumRadialIntervals ( ) [inline]

Returns:: mNumRadialIntervals

Definition at line 821 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mNumRadialIntervals.

template<unsigned DIM>

Vec CellBasedPdeHandler< DIM >::GetPdeSolution ( const std::string & rName = "" ) [inline, virtual]

Returns:: the solution to the PDE at this time step.

Parameters:

rName

The name of the dependent variable for the PDE in the vector mPdeAndBcCollection. This defaults to an empty string in the case there is only one PDE.

Definition at line 116 of file CellBasedPdeHandler.cpp.

References EXCEPTION, and CellBasedPdeHandler< DIM >::mPdeAndBcCollection.

template<unsigned DIM>

double CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint	(	const c_vector< double, DIM > &	rPoint,
		const std::string &	rVariable
	)			`[inline]`

Find the solution of one of the PDEs at a point in space

Parameters:

	rPoint	the position in space
	rVariable	the dependent variable of the PDE whose solution you want to find

Returns:: the solution of the required PDE at the given point.

Definition at line 744 of file CellBasedPdeHandler.cpp.

References Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), PdeAndBoundaryConditions< DIM >::GetSolution(), CellBasedPdeHandler< DIM >::mpCellPopulation, CellBasedPdeHandler< DIM >::mpCoarsePdeMesh, CellBasedPdeHandler< DIM >::mPdeAndBcCollection, and NEVER_REACHED.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetWriteAverageRadialPdeSolution ( ) [inline]

Returns:: mWriteAverageRadialPdeSolution

Definition at line 803 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mWriteAverageRadialPdeSolution.

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::GetWriteDailyAverageRadialPdeSolution ( ) [inline]

Returns:: mWriteDailyAverageRadialPdeSolution

Definition at line 809 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mWriteDailyAverageRadialPdeSolution.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap ( ) [inline, protected]

Initialise mCellPdeElementMap.

This method is only called Solve(), but is written as a separate method for testing purposes.

Definition at line 138 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), CellBasedPdeHandler< DIM >::mCellPdeElementMap, CellBasedPdeHandler< DIM >::mpCellPopulation, and CellBasedPdeHandler< DIM >::mpCoarsePdeMesh.

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

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::OpenResultsFiles ( std::string outputDirectory ) [inline]

Open results files and write initial conditions to file. Called by AbstractCellBasedSimulation::Solve().

Parameters:

outputDirectory

the output directory, relative to where Chaste output is stored

Definition at line 173 of file CellBasedPdeHandler.cpp.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::OutputParameters ( out_stream & rParamsFile ) [inline, virtual]

Output parameters to file.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented in CellBasedPdeHandlerOnCuboid< DIM >.

Definition at line 827 of file CellBasedPdeHandler.cpp.

References Identifiable::GetIdentifier(), CellBasedPdeHandler< DIM >::mNumRadialIntervals, CellBasedPdeHandler< DIM >::mSetBcsOnCoarseBoundary, CellBasedPdeHandler< DIM >::mWriteAverageRadialPdeSolution, and CellBasedPdeHandler< DIM >::mWriteDailyAverageRadialPdeSolution.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().

template<unsigned DIM>

bool CellBasedPdeHandler< DIM >::PdeSolveNeedsCoarseMesh ( ) [inline, protected]

Returns:: Whether the population being used requires the use of separate `coarse` mesh to solve PDEs

Definition at line 840 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mpCellPopulation.

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

template<unsigned DIM>

template<class Archive >

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

Archive the member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented in CellBasedPdeHandlerOnCuboid< DIM >.

Definition at line 78 of file CellBasedPdeHandler.hpp.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SetImposeBcsOnCoarseBoundary ( bool setBcsOnCoarseBoundary ) [inline]

Impose the PDE boundary conditions on the edge of the cell population when using the coarse mesh. The default option is to impose the condition on the boundary of the coarse mesh.

Parameters:

setBcsOnCoarseBoundary

whether to impose the BCs on the edge of the cell population

Definition at line 679 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mSetBcsOnCoarseBoundary.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SetWriteAverageRadialPdeSolution	(	const std::string &	rName,
		unsigned	numRadialIntervals = `10`,
		bool	writeDailyResults = `false`
	)			`[inline]`

Write the final (and optionally also the daily) average radial PDE solution to file.

Parameters:

	rName	The name of the quantity that we are averaging.
	numRadialIntervals	The number of radial intervals in which the average PDE solution is calculated (defaults to 10)
	writeDailyResults	Whether to record the average radial PDE solution at the end of each day of the simulation (defaults to false)

Definition at line 670 of file CellBasedPdeHandler.cpp.

References CellBasedPdeHandler< DIM >::mAverageRadialSolutionVariableName, CellBasedPdeHandler< DIM >::mNumRadialIntervals, CellBasedPdeHandler< DIM >::mWriteAverageRadialPdeSolution, and CellBasedPdeHandler< DIM >::mWriteDailyAverageRadialPdeSolution.

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile ( unsigned samplingTimestepMultiple ) [inline, virtual]

Solve the PDE and write the solution to file.

Parameters:

samplingTimestepMultiple

the ratio of the number of actual timesteps to the number of timesteps at which results are written to file.

Todo:: enable the coarse PDE mesh to change size, e.g. for a growing domain (#630/#1891)

Todo:: enable this in the case where a coarse PDE mesh is used

Todo:: Worry about round-off errors (#1891)

Definition at line 308 of file CellBasedPdeHandler.cpp.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap ( ) [inline]

Update the mCellPdeElementMap

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

Definition at line 159 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), CellBasedPdeHandler< DIM >::mCellPdeElementMap, CellBasedPdeHandler< DIM >::mpCellPopulation, and CellBasedPdeHandler< DIM >::mpCoarsePdeMesh.

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

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::UseCoarsePdeMesh	(	double	stepSize,
		ChasteCuboid< DIM >	meshCuboid,
		bool	centreOnCellPopulation = `false`
	)			`[inline, virtual]`

Solve the PDE problem on a coarse mesh.

Parameters:

	stepSize	horizontal and vertical distance between mesh points
	meshCuboid	the cuboid defining the size and location of the mesh.
	centreOnCellPopulation	whether to centre the coarse mesh on the centre of the cell population.

Definition at line 242 of file CellBasedPdeHandler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh(), EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ChasteCuboid< SPACE_DIM >::GetWidth(), CellBasedPdeHandler< DIM >::mpCellPopulation, CellBasedPdeHandler< DIM >::mpCoarsePdeMesh, CellBasedPdeHandler< DIM >::mPdeAndBcCollection, NEVER_REACHED, ChastePoint< DIM >::rGetLocation(), ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), ChasteCuboid< SPACE_DIM >::rGetUpperCorner(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

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

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution ( double time ) [inline, protected]

Write the average radial PDE solution to file at a specified time.

Outputs a line of space-separated values of the form: [time] [radius interval 0] [average solution 0] [radius interval 1] [average solution 1] ...

Parameters:

time

The time at which to record the average radial PDE solution

Definition at line 685 of file CellBasedPdeHandler.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), CellBasedPdeHandler< DIM >::mAverageRadialSolutionVariableName, CellBasedPdeHandler< DIM >::mNumRadialIntervals, and CellBasedPdeHandler< DIM >::mpCellPopulation.

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

template<unsigned DIM>

void CellBasedPdeHandler< DIM >::WritePdeSolution ( double time ) [inline, protected, virtual]

Write the PDE solution to file at a specified time.

Outputs a line of space-separated values of the form: [time] [node 0 index] [node 0 x-pos] [node 0 y-pos] [node 0 z-pos] [node 0 solution] ...

where [node 0 index] is equal to 0 if mpCoarsePdeMesh exists, otherwise [node 0 index] is the location index corresponding to the cell first encountered by the cell population Iterator, and so on.

Parameters:

time

The time at which to record the PDE solution

Definition at line 576 of file CellBasedPdeHandler.cpp.