#include <FiniteDifferenceSolver.hpp>

Inheritance diagram for FiniteDifferenceSolver< DIM >:

Collaboration diagram for FiniteDifferenceSolver< DIM >:

Public Member Functions
	FiniteDifferenceSolver ()

virtual	~FiniteDifferenceSolver ()

boost::shared_ptr< std::vector< std::pair< bool, units::quantity< unit::concentration > > > >	GetRGBoundaryConditions ()

virtual void	Solve ()

void	Setup ()

void	Update ()

void	UpdateBoundaryConditionsEachSolve (bool doUpdate)

Public Member Functions inherited from AbstractRegularGridDiscreteContinuumSolver< DIM >
	AbstractRegularGridDiscreteContinuumSolver ()

virtual	~AbstractRegularGridDiscreteContinuumSolver ()

boost::shared_ptr< RegularGrid< DIM > >	GetGrid ()

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< RegularGrid< DIM > > pGrid)

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)

virtual std::vector< double >	GetSolution (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)

virtual std::vector< double >	GetSolution (boost::shared_ptr< RegularGrid< DIM > > pGrid)

virtual std::vector< double >	GetSolution (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)

virtual vtkSmartPointer< vtkImageData >	GetVtkSolution ()

void	SetGrid (boost::shared_ptr< RegularGrid< DIM > > pRegularGrid)

virtual void	UpdateCellData ()

virtual void	UpdateSolution (std::vector< double > &rData)

virtual void	UpdateSolution (std::vector< units::quantity< unit::concentration > > &rData)

virtual void	Write ()

Public Member Functions inherited from AbstractDiscreteContinuumSolver< DIM >
	AbstractDiscreteContinuumSolver ()

virtual	~AbstractDiscreteContinuumSolver ()

void	AddBoundaryCondition (boost::shared_ptr< DiscreteContinuumBoundaryCondition< DIM > > pBoundaryCondition)

bool	CellPopulationIsSet ()

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations ()

const std::string &	GetLabel ()

boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > >	GetNonLinearPde ()

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

units::quantity< unit::concentration >	GetReferenceConcentration ()

virtual std::vector< double >	GetSolution ()

bool	HasRegularGrid ()

bool	HasUnstructuredGrid ()

void	SetCellPopulation (AbstractCellPopulation< DIM > &rCellPopulation, units::quantity< unit::length > cellPopulationReferenceLength, units::quantity< unit::concentration > cellPopulationReferenceConcentration)

void	SetFileHandler (boost::shared_ptr< OutputFileHandler > pOutputFileHandler)

void	SetFileName (const std::string &rFilename)

void	SetLabel (const std::string &rLabel)

void	SetPde (boost::shared_ptr< AbstractDiscreteContinuumLinearEllipticPde< DIM, DIM > > pPde)

void	SetNonLinearPde (boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > > pPde)

void	SetReferenceConcentration (units::quantity< unit::concentration > referenceConcentration)

void	SetVesselNetwork (boost::shared_ptr< VesselNetwork< DIM > > pNetwork)

void	SetWriteSolution (bool write=true)

virtual void	UpdateSolution (const std::vector< double > &rData)

virtual void	UpdateSolution (const std::vector< units::quantity< unit::concentration > > &rData)

Static Public Member Functions
static boost::shared_ptr< FiniteDifferenceSolver< DIM > >	Create ()

Private Member Functions
void	DoLinearSolve ()

Private Attributes
boost::shared_ptr< std::vector< std::pair< bool, units::quantity< unit::concentration > > > >	mpBoundaryConditions

bool	mUpdateBoundaryConditionsEachSolve

bool	mBoundaryConditionsSet

Additional Inherited Members
Protected Attributes inherited from AbstractRegularGridDiscreteContinuumSolver< DIM >
vtkSmartPointer< vtkImageData >	mpVtkSolution

boost::shared_ptr< RegularGrid< DIM > >	mpRegularGrid

Protected Attributes inherited from AbstractDiscreteContinuumSolver< DIM >
boost::shared_ptr< VesselNetwork< DIM > >	mpNetwork

AbstractCellPopulation< DIM > *	mpCellPopulation

units::quantity< unit::length >	mCellPopulationReferenceLength

units::quantity< unit::concentration >	mCellPopulationReferenceConcentration

boost::shared_ptr< OutputFileHandler >	mpOutputFileHandler

std::string	mFilename

std::string	mLabel

bool	IsSetupForSolve

bool	mWriteSolution

boost::shared_ptr< AbstractDiscreteContinuumLinearEllipticPde< DIM, DIM > >	mpPde

boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > >	mpNonLinearPde

std::vector< boost::shared_ptr< DiscreteContinuumBoundaryCondition< DIM > > >	mBoundaryConditions

units::quantity< unit::concentration >	mReferenceConcentration

std::vector< double >	mSolution

std::vector< units::quantity< unit::concentration > >	mConcentrations

bool	mHasRegularGrid

bool	mHasUnstructuredGrid

Detailed Description

template<unsigned DIM>
class FiniteDifferenceSolver< DIM >

Finite difference solver for concentration based reaction diffusion PDEs. It can include discrete representations of cells and vessels.

Definition at line 48 of file FiniteDifferenceSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

FiniteDifferenceSolver< DIM >::FiniteDifferenceSolver ( )

Constructor

Definition at line 56 of file FiniteDifferenceSolver.cpp.

template<unsigned DIM>

FiniteDifferenceSolver< DIM >::~FiniteDifferenceSolver ( )

virtual

Destructor

Definition at line 73 of file FiniteDifferenceSolver.cpp.

Member Function Documentation

template<unsigned DIM>

boost::shared_ptr< FiniteDifferenceSolver< DIM > > FiniteDifferenceSolver< DIM >::Create ( )

static

Factory constructor method

Returns: a shared pointer to a new solver

Definition at line 66 of file FiniteDifferenceSolver.cpp.

template<unsigned DIM>

void FiniteDifferenceSolver< DIM >::DoLinearSolve ( )

private

Do a linear PDE solve

Definition at line 168 of file FiniteDifferenceSolver.cpp.

References BaseUnits::GetReferenceTimeScale(), BaseUnits::Instance(), FiniteDifferenceSolver< DIM >::mpBoundaryConditions, AbstractDiscreteContinuumSolver< DIM >::mpNonLinearPde, AbstractDiscreteContinuumSolver< DIM >::mpPde, AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration, AbstractDiscreteContinuumSolver< DIM >::mWriteSolution, AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractRegularGridDiscreteContinuumSolver< DIM >::Write().

Referenced by FiniteDifferenceSolver< DIM >::Solve().

template<unsigned DIM>

boost::shared_ptr< std::vector< std::pair< bool, units::quantity< unit::concentration > > > > FiniteDifferenceSolver< DIM >::GetRGBoundaryConditions ( )

Get the boundary conditions in the finite difference representation

Returns: pointer to the vector of boundary conditions, which is pairs of whether to apply-concentration values ordered by grid index.

Definition at line 79 of file FiniteDifferenceSolver.cpp.

References FiniteDifferenceSolver< DIM >::mpBoundaryConditions.

Referenced by FiniteDifferenceSolver< DIM >::Solve().

template<unsigned DIM>

void FiniteDifferenceSolver< DIM >::Setup ( )

virtual

Overridden setup method

Reimplemented from AbstractRegularGridDiscreteContinuumSolver< DIM >.

Definition at line 91 of file FiniteDifferenceSolver.cpp.

Referenced by FiniteDifferenceSolver< DIM >::Solve().

template<unsigned DIM>

void FiniteDifferenceSolver< DIM >::Solve ( )

virtual

Overridden solve method

Implements AbstractRegularGridDiscreteContinuumSolver< DIM >.

Definition at line 298 of file FiniteDifferenceSolver.cpp.

template<unsigned DIM>

void FiniteDifferenceSolver< DIM >::Update ( )

virtual

Overridden update method

Reimplemented from AbstractRegularGridDiscreteContinuumSolver< DIM >.

Definition at line 144 of file FiniteDifferenceSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mBoundaryConditions, FiniteDifferenceSolver< DIM >::mBoundaryConditionsSet, FiniteDifferenceSolver< DIM >::mpBoundaryConditions, AbstractDiscreteContinuumSolver< DIM >::mpNonLinearPde, AbstractDiscreteContinuumSolver< DIM >::mpPde, and FiniteDifferenceSolver< DIM >::mUpdateBoundaryConditionsEachSolve.

Referenced by FiniteDifferenceSolver< DIM >::Setup().

template<unsigned DIM>

void FiniteDifferenceSolver< DIM >::UpdateBoundaryConditionsEachSolve ( bool doUpdate )

Whether to update the boundary conditions on each solve

Parameters

doUpdate update the boundary conditions on each solve

Definition at line 85 of file FiniteDifferenceSolver.cpp.

References FiniteDifferenceSolver< DIM >::mUpdateBoundaryConditionsEachSolve.

Member Data Documentation

template<unsigned DIM>

bool FiniteDifferenceSolver< DIM >::mBoundaryConditionsSet

private

Do the boundary conditions need to be udpated each solve.

Definition at line 64 of file FiniteDifferenceSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::Update().

template<unsigned DIM>

boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > > FiniteDifferenceSolver< DIM >::mpBoundaryConditions

private

Solver specific copy of boundary condition information, used for efficiency. It is a vector of pairs of whether to apply-concentration values ordered by grid index.

Definition at line 54 of file FiniteDifferenceSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::DoLinearSolve(), FiniteDifferenceSolver< DIM >::GetRGBoundaryConditions(), FiniteDifferenceSolver< DIM >::Setup(), and FiniteDifferenceSolver< DIM >::Update().

template<unsigned DIM>

bool FiniteDifferenceSolver< DIM >::mUpdateBoundaryConditionsEachSolve

private

Do the boundary conditions need to be udpated each solve.

Definition at line 59 of file FiniteDifferenceSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::Update(), and FiniteDifferenceSolver< DIM >::UpdateBoundaryConditionsEachSolve().

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

projects/MicrovesselChaste/src/pde/solvers/FiniteDifferenceSolver.hpp
projects/MicrovesselChaste/src/pde/solvers/FiniteDifferenceSolver.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<unsigned DIM> class FiniteDifferenceSolver< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class FiniteDifferenceSolver< DIM >