CellBasedSimulationWithPdes< DIM > Class Template Reference

#include <CellBasedSimulationWithPdes.hpp>

Inheritance diagram for CellBasedSimulationWithPdes< DIM >:

Collaboration diagram for CellBasedSimulationWithPdes< DIM >:

List of all members.

Public Member Functions

CellBasedSimulationWithPdes (AbstractCellPopulation< DIM > &rCellPopulation, std::vector< PdeAndBoundaryConditions< DIM > * > pdeAndBcCollection=std::vector< PdeAndBoundaryConditions< DIM > * >(), bool deleteCellPopulationAndForceCollection=false, bool initialiseCells=true)

~CellBasedSimulationWithPdes ()

void SetPdeAndBcCollection (std::vector< PdeAndBoundaryConditions< DIM > * > pdeAndBcCollection)

Vec GetCurrentPdeSolution (unsigned pdeIndex)

void SetWriteAverageRadialPdeSolution (unsigned numRadialIntervals=10, bool writeDailyResults=false)

void UseCoarsePdeMesh (double coarseGrainScaleFactor=10.0)

void OutputSimulationParameters (out_stream &rParamsFile)

template<>

void CreateCoarsePdeMesh (double coarseGrainScaleFactor)

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

void SetupSolve ()

void SetupWritePdeSolution ()

void WritePdeSolution (double time)

void WriteAverageRadialPdeSolution (double time, unsigned numIntervals)

void SolvePde ()

void SolvePdeUsingCoarseMesh ()

unsigned FindCoarseElementContainingCell (CellPtr pCell)

void PostSolve ()

void AfterSolve ()

void CreateCoarsePdeMesh (double coarseGrainScaleFactor)

void InitialiseCoarsePdeMesh ()

void WriteVisualizerSetupFile ()

Private Attributes

std::vector
< PdeAndBoundaryConditions
< DIM > * > mPdeAndBcCollection

out_stream mpVizPdeSolutionResultsFile

out_stream mpAverageRadialPdeSolutionResultsFile

bool mWriteAverageRadialPdeSolution

bool mWriteDailyAverageRadialPdeSolution

unsigned mNumRadialIntervals

TetrahedralMesh< DIM, DIM > * mpCoarsePdeMesh

std::map< CellPtr, unsigned > mCellPdeElementMap

Friends

class TestCellBasedSimulationWithPdes

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class CellBasedSimulationWithPdes< DIM >

A cell-based simulation class that includes one or more elliptic PDEs, e.g. describing the transport of nutrients and/or signalling molecules.

Definition at line 48 of file CellBasedSimulationWithPdes.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedSimulationWithPdes< DIM >::CellBasedSimulationWithPdes	(	AbstractCellPopulation< DIM > &	rCellPopulation,
		std::vector< PdeAndBoundaryConditions< DIM > * >	pdeAndBcCollection = `std::vector<PdeAndBoundaryConditions<DIM>*>()`,
		bool	deleteCellPopulationAndForceCollection = `false`,
		bool	initialiseCells = `true`
	)			`[inline]`

Constructor.

Parameters:

	rCellPopulation	A cell population object
	pdeAndBcCollection	A vector of pointers to PdeAndBoundaryConditions objects (defaults to an empty vector0
	deleteCellPopulationAndForceCollection	Whether to delete the cell population on destruction to free up memory
	initialiseCells	Whether to initialise cells (set to false when loading from an archive)

Definition at line 42 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulation< DIM >::mrCellPopulation.

template<unsigned DIM>

CellBasedSimulationWithPdes< DIM >::~CellBasedSimulationWithPdes ( ) [inline]

Destructor.

Free any memory allocated by the constructor. This frees the current PDE solution, if it exists.

Definition at line 63 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

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

Archive the member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 57 of file CellBasedSimulationWithPdes.hpp.

References CellBasedSimulationWithPdes< DIM >::mCellPdeElementMap, CellBasedSimulationWithPdes< DIM >::mNumRadialIntervals, CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution, and CellBasedSimulationWithPdes< DIM >::mWriteDailyAverageRadialPdeSolution.

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SetupSolve ( ) [inline, private, virtual]

Overridden SetupSolve() method.

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 102 of file CellBasedSimulationWithPdes.cpp.

References SimulationTime::GetTime(), CellBasedSimulationWithPdes< DIM >::InitialiseCoarsePdeMesh(), SimulationTime::Instance(), CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh, CellBasedSimulation< DIM >::mrCellPopulation, CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution(), and CellBasedSimulationWithPdes< DIM >::WritePdeSolution().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution ( ) [inline, private]

Set up the PDE solution writer.

Definition at line 118 of file CellBasedSimulationWithPdes.cpp.

References PetscTools::AmMaster(), CellBasedSimulationWithPdes< DIM >::mpAverageRadialPdeSolutionResultsFile, CellBasedSimulationWithPdes< DIM >::mpVizPdeSolutionResultsFile, CellBasedSimulation< DIM >::mpVizSetupFile, CellBasedSimulation< DIM >::mSimulationOutputDirectory, CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution, and OutputFileHandler::OpenOutputFile().

Referenced by CellBasedSimulationWithPdes< DIM >::SetupSolve().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::WritePdeSolution ( double time ) [inline, private]

Write the PDE solution to file at a specified time.

Parameters:

time

The time at which to record the PDE solution

Definition at line 588 of file CellBasedSimulationWithPdes.cpp.

References PetscTools::AmMaster(), CellwiseData< DIM >::GetValue(), CellwiseData< DIM >::Instance(), and CellBasedSimulation< DIM >::mrCellPopulation.

Referenced by CellBasedSimulationWithPdes< DIM >::PostSolve(), and CellBasedSimulationWithPdes< DIM >::SetupSolve().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::WriteAverageRadialPdeSolution	(	double	time,
		unsigned	numIntervals
	)			`[inline, private]`

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

Parameters:

	time	The time at which to record the average radial PDE solution
	numIntervals	The number of radial intervals in which the average PDE solution is calculated

Definition at line 626 of file CellBasedSimulationWithPdes.cpp.

References CellwiseData< DIM >::GetValue(), CellwiseData< DIM >::Instance(), and CellBasedSimulation< DIM >::mrCellPopulation.

Referenced by CellBasedSimulationWithPdes< DIM >::AfterSolve(), and CellBasedSimulationWithPdes< DIM >::PostSolve().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SolvePde ( ) [inline, private]

Solve the PDE.

Definition at line 253 of file CellBasedSimulationWithPdes.cpp.

Referenced by CellBasedSimulationWithPdes< DIM >::PostSolve().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh ( ) [inline, private]

Solve the PDE on a coarse mesh.

Definition at line 354 of file CellBasedSimulationWithPdes.cpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), PdeAndBoundaryConditions< DIM >::DestroySolution(), EXCEPTION, CellBasedSimulationWithPdes< DIM >::FindCoarseElementContainingCell(), PdeAndBoundaryConditions< DIM >::GetBoundaryCondition(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PdeAndBoundaryConditions< DIM >::GetPde(), PdeAndBoundaryConditions< DIM >::GetSolution(), CellwiseData< DIM >::Instance(), PdeAndBoundaryConditions< DIM >::IsNeumannBoundaryCondition(), CellBasedSimulationWithPdes< DIM >::mCellPdeElementMap, CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh, CellBasedSimulationWithPdes< DIM >::mPdeAndBcCollection, CellBasedSimulation< DIM >::mrCellPopulation, CellwiseData< DIM >::ReallocateMemory(), PdeAndBoundaryConditions< DIM >::SetSolution(), PdeAndBoundaryConditions< DIM >::SetUpSourceTermsForAveragedSourcePde(), and CellwiseData< DIM >::SetValue().

Referenced by CellBasedSimulationWithPdes< DIM >::SolvePde().

template<unsigned DIM>

unsigned CellBasedSimulationWithPdes< DIM >::FindCoarseElementContainingCell ( CellPtr pCell ) [inline, private]

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

Parameters:

pCell

the cell

Returns:: the element index.

Definition at line 520 of file CellBasedSimulationWithPdes.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), CellBasedSimulationWithPdes< DIM >::mCellPdeElementMap, CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh, and CellBasedSimulation< DIM >::mrCellPopulation.

Referenced by CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::PostSolve ( ) [inline, private, virtual]

Overridden PostSolve() method.

Todo:: Worry about round-off errors

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 554 of file CellBasedSimulationWithPdes.cpp.

References SimulationTime::GetTime(), SimulationTime::GetTimeStep(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), CellBasedSimulationWithPdes< DIM >::mNumRadialIntervals, CellBasedSimulation< DIM >::mSamplingTimestepMultiple, CellBasedSimulationWithPdes< DIM >::mWriteDailyAverageRadialPdeSolution, CellBasedSimulationWithPdes< DIM >::SolvePde(), CellBasedSimulationWithPdes< DIM >::WriteAverageRadialPdeSolution(), and CellBasedSimulationWithPdes< DIM >::WritePdeSolution().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::AfterSolve ( ) [inline, private, virtual]

Overridden AfterSolve() method.

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 234 of file CellBasedSimulationWithPdes.cpp.

References PetscTools::AmMaster(), SimulationTime::Instance(), CellBasedSimulationWithPdes< DIM >::mNumRadialIntervals, CellBasedSimulationWithPdes< DIM >::mpAverageRadialPdeSolutionResultsFile, CellBasedSimulationWithPdes< DIM >::mpVizPdeSolutionResultsFile, CellBasedSimulation< DIM >::mrCellPopulation, CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution, and CellBasedSimulationWithPdes< DIM >::WriteAverageRadialPdeSolution().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh ( double coarseGrainScaleFactor ) [inline, private]

Create a coarse mesh on which to solve the PDE.

Todo:: currently only works in 2D (see #737)

Parameters:

coarseGrainScaleFactor

the ratio of the width of the coarse PDE mesh to the initial width of the cell population

Definition at line 145 of file CellBasedSimulationWithPdes.cpp.

References EXCEPTION.

Referenced by CellBasedSimulationWithPdes< DIM >::UseCoarsePdeMesh().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::InitialiseCoarsePdeMesh ( ) [inline, private]

Initialise the std::map mCellPdeElementMap.

Definition at line 218 of file CellBasedSimulationWithPdes.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), CellBasedSimulationWithPdes< DIM >::mCellPdeElementMap, CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh, and CellBasedSimulation< DIM >::mrCellPopulation.

Referenced by CellBasedSimulationWithPdes< DIM >::SetupSolve().

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::WriteVisualizerSetupFile ( ) [inline, private, virtual]

Overridden WriteVisualizerSetupFile() method.

Writes out special information about the mesh to the visualizer.

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 89 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulation< DIM >::mForceCollection, and CellBasedSimulation< DIM >::mpVizSetupFile.

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SetPdeAndBcCollection ( std::vector< PdeAndBoundaryConditions< DIM > * > pdeAndBcCollection ) [inline]

A small hack until we fully archive this class - needed to set the PDE after loading a simulation from an archive.

Todo:: Check if archiving has been implemented yet for PDE classes (#1460)

Parameters:

pdeAndBcCollection

A vector of pointers to PdeAndBoundaryConditions objects

Definition at line 72 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::mPdeAndBcCollection.

template<unsigned DIM>

Vec CellBasedSimulationWithPdes< DIM >::GetCurrentPdeSolution ( unsigned pdeIndex ) [inline]

Get the current solution to the PDE problem.

Parameters:

pdeIndex

The index of the PDE in the vector mPdeAndBcCollection

Definition at line 78 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::mPdeAndBcCollection.

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::SetWriteAverageRadialPdeSolution	(	unsigned	numRadialIntervals = `10`,
		bool	writeDailyResults = `false`
	)			`[inline]`

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

Parameters:

	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 618 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::mNumRadialIntervals, CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution, and CellBasedSimulationWithPdes< DIM >::mWriteDailyAverageRadialPdeSolution.

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::UseCoarsePdeMesh ( double coarseGrainScaleFactor = 10.0 ) [inline]

Solve the PDE problem on a coarse mesh.

Parameters:

coarseGrainScaleFactor

the ratio of the width of the coarse PDE mesh to the initial width of the cell population (defaults to 10.0)

Definition at line 133 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh(), and CellBasedSimulationWithPdes< DIM >::mPdeAndBcCollection.

template<unsigned DIM>

void CellBasedSimulationWithPdes< DIM >::OutputSimulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs simulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 694 of file CellBasedSimulationWithPdes.cpp.

References CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution, CellBasedSimulationWithPdes< DIM >::mWriteDailyAverageRadialPdeSolution, and CellBasedSimulation< DIM >::OutputSimulationParameters().

template<>

void CellBasedSimulationWithPdes< 2 >::CreateCoarsePdeMesh ( double coarseGrainScaleFactor ) [inline]

The CreateCoarsePdeMesh method is currently only implemented in 2D, hence there are two definitions to this method (one templated and one not).

Parameters:

coarseGrainScaleFactor

the ratio of the width of the coarse PDE mesh to the initial width of the cell population

Definition at line 157 of file CellBasedSimulationWithPdes.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh, CellBasedSimulation< DIM >::mrCellPopulation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from CellBasedSimulation< DIM >.

Definition at line 55 of file CellBasedSimulationWithPdes.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<PdeAndBoundaryConditions<DIM>*> CellBasedSimulationWithPdes< DIM >::mPdeAndBcCollection [private]

Vector of pointers to linear elliptic PDE objects with additional boundary condition information.

Definition at line 72 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::GetCurrentPdeSolution(), CellBasedSimulationWithPdes< DIM >::SetPdeAndBcCollection(), CellBasedSimulationWithPdes< DIM >::SolvePde(), CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh(), and CellBasedSimulationWithPdes< DIM >::UseCoarsePdeMesh().

template<unsigned DIM>

out_stream CellBasedSimulationWithPdes< DIM >::mpVizPdeSolutionResultsFile [private]

File that the values of the PDE solution are written out to.

Definition at line 77 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::AfterSolve(), and CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution().

template<unsigned DIM>

out_stream CellBasedSimulationWithPdes< DIM >::mpAverageRadialPdeSolutionResultsFile [private]

File that the average radial PDE solution is written out to.

Definition at line 82 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::AfterSolve(), and CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution().

template<unsigned DIM>

bool CellBasedSimulationWithPdes< DIM >::mWriteAverageRadialPdeSolution [private]

Whether to write to file the average radial PDE solution.

Definition at line 87 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::AfterSolve(), CellBasedSimulationWithPdes< DIM >::OutputSimulationParameters(), CellBasedSimulationWithPdes< DIM >::serialize(), CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution(), and CellBasedSimulationWithPdes< DIM >::SetWriteAverageRadialPdeSolution().

template<unsigned DIM>

bool CellBasedSimulationWithPdes< DIM >::mWriteDailyAverageRadialPdeSolution [private]

Whether to write the average radial PDE solution DAILY.

Definition at line 92 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::OutputSimulationParameters(), CellBasedSimulationWithPdes< DIM >::PostSolve(), CellBasedSimulationWithPdes< DIM >::serialize(), and CellBasedSimulationWithPdes< DIM >::SetWriteAverageRadialPdeSolution().

template<unsigned DIM>

unsigned CellBasedSimulationWithPdes< DIM >::mNumRadialIntervals [private]

Number of radial 'bins' used to calculate the average radial PDE solution.

Definition at line 98 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::AfterSolve(), CellBasedSimulationWithPdes< DIM >::PostSolve(), CellBasedSimulationWithPdes< DIM >::serialize(), and CellBasedSimulationWithPdes< DIM >::SetWriteAverageRadialPdeSolution().

template<unsigned DIM>

TetrahedralMesh<DIM,DIM>* CellBasedSimulationWithPdes< DIM >::mpCoarsePdeMesh [private]

Coarse mesh on which to solve the PDE.

Definition at line 103 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh(), CellBasedSimulationWithPdes< DIM >::FindCoarseElementContainingCell(), CellBasedSimulationWithPdes< DIM >::InitialiseCoarsePdeMesh(), CellBasedSimulationWithPdes< DIM >::SetupSolve(), CellBasedSimulationWithPdes< DIM >::SolvePde(), CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh(), and CellBasedSimulationWithPdes< DIM >::~CellBasedSimulationWithPdes().

template<unsigned DIM>

std::map<CellPtr, unsigned> CellBasedSimulationWithPdes< DIM >::mCellPdeElementMap [private]

Map between cells and the elements of the coarse PDE mesh containing them.

Definition at line 108 of file CellBasedSimulationWithPdes.hpp.

Referenced by CellBasedSimulationWithPdes< DIM >::FindCoarseElementContainingCell(), CellBasedSimulationWithPdes< DIM >::InitialiseCoarsePdeMesh(), CellBasedSimulationWithPdes< DIM >::serialize(), and CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh().

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

cell_based/src/simulation/CellBasedSimulationWithPdes.hpp
cell_based/src/simulation/CellBasedSimulationWithPdes.cpp


Public Member Functions
	CellBasedSimulationWithPdes (AbstractCellPopulation< DIM > &rCellPopulation, std::vector< PdeAndBoundaryConditions< DIM > * > pdeAndBcCollection=std::vector< PdeAndBoundaryConditions< DIM > * >(), bool deleteCellPopulationAndForceCollection=false, bool initialiseCells=true)
	~CellBasedSimulationWithPdes ()
void	SetPdeAndBcCollection (std::vector< PdeAndBoundaryConditions< DIM > * > pdeAndBcCollection)
Vec	GetCurrentPdeSolution (unsigned pdeIndex)
void	SetWriteAverageRadialPdeSolution (unsigned numRadialIntervals=10, bool writeDailyResults=false)
void	UseCoarsePdeMesh (double coarseGrainScaleFactor=10.0)
void	OutputSimulationParameters (out_stream &rParamsFile)
template<>
void	CreateCoarsePdeMesh (double coarseGrainScaleFactor)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	SetupSolve ()
void	SetupWritePdeSolution ()
void	WritePdeSolution (double time)
void	WriteAverageRadialPdeSolution (double time, unsigned numIntervals)
void	SolvePde ()
void	SolvePdeUsingCoarseMesh ()
unsigned	FindCoarseElementContainingCell (CellPtr pCell)
void	PostSolve ()
void	AfterSolve ()
void	CreateCoarsePdeMesh (double coarseGrainScaleFactor)
void	InitialiseCoarsePdeMesh ()
void	WriteVisualizerSetupFile ()
Private Attributes
std::vector < PdeAndBoundaryConditions < DIM > * >	mPdeAndBcCollection
out_stream	mpVizPdeSolutionResultsFile
out_stream	mpAverageRadialPdeSolutionResultsFile
bool	mWriteAverageRadialPdeSolution
bool	mWriteDailyAverageRadialPdeSolution
unsigned	mNumRadialIntervals
TetrahedralMesh< DIM, DIM > *	mpCoarsePdeMesh
std::map< CellPtr, unsigned >	mCellPdeElementMap
Friends
class	TestCellBasedSimulationWithPdes
class	boost::serialization::access

CellBasedSimulationWithPdes< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class CellBasedSimulationWithPdes< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class CellBasedSimulationWithPdes< DIM >