#include <AbstractDiscreteContinuumSolver.hpp>

Inheritance diagram for AbstractDiscreteContinuumSolver< DIM >:

Collaboration diagram for AbstractDiscreteContinuumSolver< DIM >:

Public Member Functions
	AbstractDiscreteContinuumSolver ()

virtual	~AbstractDiscreteContinuumSolver ()

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

bool	CellPopulationIsSet ()

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

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< RegularGrid< DIM > > pGrid)=0

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)=0

virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)=0

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 ()

virtual std::vector< double >	GetSolution (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)=0

virtual std::vector< double >	GetSolution (boost::shared_ptr< RegularGrid< DIM > > pGrid)=0

virtual std::vector< double >	GetSolution (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)=0

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)

virtual void	Setup ()=0

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

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

void	SetWriteSolution (bool write=true)

virtual void	Solve ()=0

virtual void	Update ()=0

virtual void	UpdateCellData ()=0

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

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

virtual void	Write ()=0

Protected Attributes
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 AbstractDiscreteContinuumSolver< DIM >

An abstract solver class for continuum-discrete field problems. The class is used by the MicrovesselSolver to provide a concentration or dimensionless field for a single, labelled quantity for cells and/or vessels. It contains methods for sampling on structured and unstructured grids. Derived classes are responsible for updating the values of data fields in cells and vessels on each call and optionally writing the solution to file.

Definition at line 59 of file AbstractDiscreteContinuumSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractDiscreteContinuumSolver< DIM >::AbstractDiscreteContinuumSolver ( )

Constructor

Definition at line 40 of file AbstractDiscreteContinuumSolver.cpp.

template<unsigned DIM>

AbstractDiscreteContinuumSolver< DIM >::~AbstractDiscreteContinuumSolver ( )

virtual

Destructor

Definition at line 63 of file AbstractDiscreteContinuumSolver.cpp.

Member Function Documentation

template<unsigned DIM>

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

Add a DiscreteContinuum boundary condition for the domain

Parameters

pBoundaryCondition the boundary condition

Definition at line 69 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mBoundaryConditions.

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::CellPopulationIsSet ( )

Has a cell population been set?

Returns: whether a cell population been set.

Definition at line 75 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpCellPopulation.

Referenced by FiniteDifferenceSolver< DIM >::Setup(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateCellData(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateCellData().

template<unsigned DIM>

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

virtual

Return the value of the field with ordering determined by child classes

Returns: the value of the field with ordering determined by child classes

Definition at line 81 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mConcentrations.

Referenced by AbstractRegularGridDiscreteContinuumSolver< DIM >::GetConcentrations(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations().

template<unsigned DIM>

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

pure virtual

Return the value of the field at all points on the supplied grid

Parameters

pGrid the sampling grid

Returns: the value of the field ordered according to grid order

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

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

pure virtual

Return the value of the field at the requested points

Parameters

rSamplePoints a vector of sample points

Returns: the value of the field ordered according to input point order

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

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

pure virtual

Return the value of the field on the nodes of the input mesh

Parameters

pMesh the mesh from which nodes are sampled

Returns: the value of the field ordered according to mesh node ordering

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

const std::string & AbstractDiscreteContinuumSolver< DIM >::GetLabel ( )

Return the name of the field being solved for

Returns: a reference to the field name

Definition at line 87 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mLabel.

Referenced by AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateElementSolution(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution().

template<unsigned DIM>

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

Return the nonlinear PDE

Returns: the DiscreteContinuum nonlinear elliptic pde

Definition at line 103 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpNonLinearPde.

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

template<unsigned DIM>

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

Return the PDE

Returns: the DiscreteContinuum linear elliptic pde

Definition at line 93 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpPde.

template<unsigned DIM>

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

Return the reference concentration value.

Returns: the reference concentration value

Definition at line 113 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration.

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

template<unsigned DIM>

std::vector< double > AbstractDiscreteContinuumSolver< DIM >::GetSolution ( )

virtual

Return the value of the field with ordering determined by child classes

Returns: the value of the field with ordering determined by child classes

Definition at line 119 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mSolution.

Referenced by AbstractRegularGridDiscreteContinuumSolver< DIM >::GetSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution().

template<unsigned DIM>

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

pure virtual

Return the value of the field at the requested points

Parameters

rSamplePoints the points for sampling

Returns: the value of the field ordered according to input point order

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

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

pure virtual

Return the value of the field at all points on the supplied grid

Parameters

pGrid the grid to be sampled

Returns: the value of the field ordered according to input point order

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

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

pure virtual

Return the value of the field at all points on the supplied mesh nodes

Parameters

pMesh the mesh for point sampling

Returns: the value of the field ordered according to mesh node order

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::HasRegularGrid ( )

Return true if the solver uses a regular grid to store solutions

Returns: true if the solver uses a regular grid to store solutions

Definition at line 125 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mHasRegularGrid.

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::HasUnstructuredGrid ( )

Return true if the solver uses a unstructured grid to store solutions

Returns: true if the solver uses a unstructured grid to store solutions

Definition at line 131 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mHasUnstructuredGrid.

template<unsigned DIM>

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

Set the cell population

Parameters

rCellPopulation	a reference to the cell population
cellPopulationReferenceLength	the length scale for the cell population
cellPopulationReferenceConcentration	the concentration scale for the cell population

Definition at line 137 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mCellPopulationReferenceConcentration, AbstractDiscreteContinuumSolver< DIM >::mCellPopulationReferenceLength, and AbstractDiscreteContinuumSolver< DIM >::mpCellPopulation.

template<unsigned DIM>

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

Set the file handler containing the working directory

Parameters

pOutputFileHandler the file handler containing the working directory

Definition at line 147 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpOutputFileHandler.

template<unsigned DIM>

void AbstractDiscreteContinuumSolver< DIM >::SetFileName ( const std::string & rFilename )

Set the file name for output

Parameters

rFilename the file name

Definition at line 153 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mFilename.

template<unsigned DIM>

void AbstractDiscreteContinuumSolver< DIM >::SetLabel ( const std::string & rLabel )

Set the name of the field being solved for

Parameters

rLabel a reference to the field name

Definition at line 159 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mLabel.

template<unsigned DIM>

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

Set the nonlinear PDE to be solved

Parameters

pPde	the pde to be solved

Definition at line 171 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpNonLinearPde.

template<unsigned DIM>

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

Set the PDE to be solved

Parameters

pPde	the pde to be solved

Definition at line 165 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpPde.

template<unsigned DIM>

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

Set the reference concentration

Parameters

referenceConcentration the reference concentration

Definition at line 177 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration.

template<unsigned DIM>

virtual void AbstractDiscreteContinuumSolver< DIM >::Setup ( )

pure virtual

Operations to be performed prior to the first solve

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, AbstractRegularGridDiscreteContinuumSolver< DIM >, and FiniteDifferenceSolver< DIM >.

template<unsigned DIM>

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

Set the vessel network

Parameters

pNetwork the vessel network

Definition at line 183 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpNetwork.

template<unsigned DIM>

void AbstractDiscreteContinuumSolver< DIM >::SetWriteSolution ( bool write = true )

Set whether to write the solution to file on next solve

Parameters

write write the solution

Definition at line 189 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mWriteSolution.

template<unsigned DIM>

virtual void AbstractDiscreteContinuumSolver< DIM >::Solve ( )

pure virtual

Do the solve

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, AbstractRegularGridDiscreteContinuumSolver< DIM >, GreensFunctionSolver< DIM >, FiniteDifferenceSolver< DIM >, FiniteElementSolver< DIM >, DistanceMap< DIM >, DensityMap< DIM >, LacunarityCalculator< DIM >, and FunctionMap< DIM >.

template<unsigned DIM>

virtual void AbstractDiscreteContinuumSolver< DIM >::Update ( )

pure virtual

Operations to be performed prior to every solve

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, AbstractRegularGridDiscreteContinuumSolver< DIM >, FiniteElementSolver< DIM >, FiniteDifferenceSolver< DIM >, and LacunarityCalculator< DIM >.

template<unsigned DIM>

virtual void AbstractDiscreteContinuumSolver< DIM >::UpdateCellData ( )

pure virtual

Set the cell data to the values in the field

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, AbstractRegularGridDiscreteContinuumSolver< DIM >, and LacunarityCalculator< DIM >.

template<unsigned DIM>

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

virtual

Update the solution manually

Parameters

rData solution data map

Reimplemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >.

Definition at line 195 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mSolution.

template<unsigned DIM>

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

virtual

Update the solution manually

Parameters

rData solution data map

Reimplemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >.

Definition at line 201 of file AbstractDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mConcentrations.

template<unsigned DIM>

virtual void AbstractDiscreteContinuumSolver< DIM >::Write ( )

pure virtual

Write the solution to file

Implemented in AbstractUnstructuredGridDiscreteContinuumSolver< DIM >, and AbstractRegularGridDiscreteContinuumSolver< DIM >.

Member Data Documentation

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::IsSetupForSolve

protected

Has the Setup function been called.

Definition at line 102 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::Setup(), FiniteElementSolver< DIM >::Solve(), and FiniteDifferenceSolver< DIM >::Solve().

template<unsigned DIM>

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

protected

The DiscreteContinuum boundary conditions, optional

Definition at line 122 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::AddBoundaryCondition(), FiniteDifferenceSolver< DIM >::Setup(), FiniteElementSolver< DIM >::Solve(), and FiniteDifferenceSolver< DIM >::Update().

template<unsigned DIM>

units::quantity<unit::concentration> AbstractDiscreteContinuumSolver< DIM >::mCellPopulationReferenceConcentration

protected

The reference concentration scale for the cellpopulation.

Definition at line 82 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::SetCellPopulation(), and AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateCellData().

template<unsigned DIM>

units::quantity<unit::length> AbstractDiscreteContinuumSolver< DIM >::mCellPopulationReferenceLength

protected

The reference length scale for the cellpopulation.

Definition at line 77 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::SetCellPopulation(), FiniteDifferenceSolver< DIM >::Setup(), and AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateCellData().

template<unsigned DIM>

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

protected

A solution field. Ordering is decided in child classes.

Definition at line 139 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::GetConcentrations(), FiniteElementSolver< DIM >::Solve(), FiniteDifferenceSolver< DIM >::Solve(), GreensFunctionSolver< DIM >::Solve(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateCellData(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractDiscreteContinuumSolver< DIM >::UpdateSolution().

template<unsigned DIM>

std::string AbstractDiscreteContinuumSolver< DIM >::mFilename

protected

The filename for output

Definition at line 92 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::SetFileName(), AbstractRegularGridDiscreteContinuumSolver< DIM >::Write(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Write().

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::mHasRegularGrid

protected

Used to check the type of solver

Definition at line 144 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractRegularGridDiscreteContinuumSolver< DIM >::AbstractRegularGridDiscreteContinuumSolver(), and AbstractDiscreteContinuumSolver< DIM >::HasRegularGrid().

template<unsigned DIM>

bool AbstractDiscreteContinuumSolver< DIM >::mHasUnstructuredGrid

protected

Used to check the type of solver

Definition at line 149 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::AbstractUnstructuredGridDiscreteContinuumSolver(), and AbstractDiscreteContinuumSolver< DIM >::HasUnstructuredGrid().

template<unsigned DIM>

std::string AbstractDiscreteContinuumSolver< DIM >::mLabel

protected

The label for the quantity being solved for

Definition at line 97 of file AbstractDiscreteContinuumSolver.hpp.

template<unsigned DIM>

AbstractCellPopulation<DIM>* AbstractDiscreteContinuumSolver< DIM >::mpCellPopulation

protected

The cell population.

Definition at line 72 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::CellPopulationIsSet(), AbstractDiscreteContinuumSolver< DIM >::SetCellPopulation(), FiniteDifferenceSolver< DIM >::Setup(), and AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateCellData().

template<unsigned DIM>

boost::shared_ptr<VesselNetwork<DIM> > AbstractDiscreteContinuumSolver< DIM >::mpNetwork

protected

The vessel network.

Definition at line 67 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateSubSegments(), FiniteDifferenceSolver< DIM >::Setup(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup(), AbstractDiscreteContinuumSolver< DIM >::SetVesselNetwork(), LacunarityCalculator< DIM >::Solve(), DensityMap< DIM >::Solve(), and DistanceMap< DIM >::Solve().

template<unsigned DIM>

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

protected

The non-linear PDE to be solved

Definition at line 117 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::DoLinearSolve(), AbstractDiscreteContinuumSolver< DIM >::GetNonLinearPde(), AbstractDiscreteContinuumSolver< DIM >::SetNonLinearPde(), FiniteDifferenceSolver< DIM >::Setup(), FiniteElementSolver< DIM >::Solve(), FiniteDifferenceSolver< DIM >::Update(), and FiniteElementSolver< DIM >::Update().

template<unsigned DIM>

boost::shared_ptr<OutputFileHandler> AbstractDiscreteContinuumSolver< DIM >::mpOutputFileHandler

protected

File handler containing the output directory

Definition at line 87 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by AbstractDiscreteContinuumSolver< DIM >::SetFileHandler(), LacunarityCalculator< DIM >::Solve(), AbstractRegularGridDiscreteContinuumSolver< DIM >::Write(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Write(), and GreensFunctionSolver< DIM >::WriteSolution().

template<unsigned DIM>

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

protected

The PDE to be solved

Definition at line 112 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::DoLinearSolve(), AbstractDiscreteContinuumSolver< DIM >::GetPde(), AbstractDiscreteContinuumSolver< DIM >::SetPde(), FiniteDifferenceSolver< DIM >::Setup(), FiniteElementSolver< DIM >::Solve(), FiniteDifferenceSolver< DIM >::Solve(), GreensFunctionSolver< DIM >::Solve(), FiniteDifferenceSolver< DIM >::Update(), and FiniteElementSolver< DIM >::Update().

template<unsigned DIM>

units::quantity<unit::concentration> AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration

protected

This is used internally to scale concentrations before and after linear system solves, reads and writes. Since those functions don't use Boost Units. It should not affect the solution, but can be judiciously chosen to avoid precision problems.

Definition at line 129 of file AbstractDiscreteContinuumSolver.hpp.

Referenced by FiniteDifferenceSolver< DIM >::DoLinearSolve(), AbstractRegularGridDiscreteContinuumSolver< DIM >::GetConcentrations(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrationsAtCentroids(), AbstractDiscreteContinuumSolver< DIM >::GetReferenceConcentration(), AbstractDiscreteContinuumSolver< DIM >::SetReferenceConcentration(), FiniteDifferenceSolver< DIM >::Setup(), FiniteElementSolver< DIM >::Solve(), FiniteDifferenceSolver< DIM >::Solve(), GreensFunctionSolver< DIM >::Solve(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution().