#include <MicrovesselSolver.hpp>

Collaboration diagram for MicrovesselSolver< DIM >:

Public Member Functions
	MicrovesselSolver ()

virtual	~MicrovesselSolver ()

void	AddDiscreteContinuumSolver (boost::shared_ptr< AbstractDiscreteContinuumSolver< DIM > > pDiscreteContinuumSolver)

std::vector< boost::shared_ptr< AbstractDiscreteContinuumSolver< DIM > > >	GetDiscreteContinuumSolvers ()

void	Increment ()

void	Run ()

void	SetAngiogenesisSolver (boost::shared_ptr< AngiogenesisSolver< DIM > > pAngiogenesisSolver)

void	SetOutputFileHandler (boost::shared_ptr< OutputFileHandler > pFileHandler)

void	SetOutputFrequency (unsigned frequency)

void	SetUpdatePdeEachSolve (bool doUpdate)

void	SetStructuralAdaptationSolver (boost::shared_ptr< StructuralAdaptationSolver< DIM > > pStructuralAdaptationSolver)

void	SetupFromModifier (AbstractCellPopulation< DIM, DIM > &rCellPopulation, units::quantity< unit::length > cellReferenceLength, units::quantity< unit::concentration > cellReferenceConcentration, const std::string &rDirectory)

void	Setup ()

void	SetDiscreteContinuumSolversHaveCompatibleGridIndexing (bool compatibleIndexing)

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

void	SetRegressionSolver (boost::shared_ptr< RegressionSolver< DIM > > pRegressionSolver)

void	UpdateCellData (std::vector< std::string > labels)

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

Private Attributes
boost::shared_ptr< VesselNetwork< DIM > >	mpNetwork

unsigned	mOutputFrequency

boost::shared_ptr< OutputFileHandler >	mpOutputFileHandler

std::vector< boost::shared_ptr< AbstractDiscreteContinuumSolver< DIM > > >	mDiscreteContinuumSolvers

boost::shared_ptr< StructuralAdaptationSolver< DIM > >	mpStructuralAdaptationSolver

boost::shared_ptr< AngiogenesisSolver< DIM > >	mpAngiogenesisSolver

boost::shared_ptr< RegressionSolver< DIM > >	mpRegressionSolver

bool	mDiscreteContinuumSolversHaveCompatibleGridIndexing

bool	mUpdatePdeEachSolve

Detailed Description

template<unsigned DIM>
class MicrovesselSolver< DIM >

This class manages the solution of vascular tumour growth problems. It steps through time, solves a collection of DiscreteContinuum discrete-continuum PDEs and, if required, updates the vessel network. For linking with discrete cell models it can be added to a VascularTumourGrowth simulation modifier.

Definition at line 56 of file MicrovesselSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

MicrovesselSolver< DIM >::MicrovesselSolver ( )

Constructor.

Definition at line 45 of file MicrovesselSolver.cpp.

template<unsigned DIM>

MicrovesselSolver< DIM >::~MicrovesselSolver ( )

virtual

Destructor.

Definition at line 60 of file MicrovesselSolver.cpp.

Member Function Documentation

template<unsigned DIM>

void MicrovesselSolver< DIM >::AddDiscreteContinuumSolver ( boost::shared_ptr< AbstractDiscreteContinuumSolver< DIM > > pDiscreteContinuumSolver )

Add a DiscreteContinuum solver to the collection

Parameters

pDiscreteContinuumSolver a discrete-continuum solver

Definition at line 85 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolvers.

template<unsigned DIM>

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

static

Factory constructor method

Returns: a shared pointer to a new solver

Definition at line 66 of file MicrovesselSolver.cpp.

template<unsigned DIM>

std::vector< boost::shared_ptr< AbstractDiscreteContinuumSolver< DIM > > > MicrovesselSolver< DIM >::GetDiscreteContinuumSolvers ( )

Return the current DiscreteContinuum solvers

Returns: the DiscreteContinuum solvers

Definition at line 91 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolvers.

template<unsigned DIM>

void MicrovesselSolver< DIM >::Increment ( )

Increment one step in time

Definition at line 96 of file MicrovesselSolver.cpp.

Referenced by MicrovesselSolver< DIM >::Run().

template<unsigned DIM>

void MicrovesselSolver< DIM >::Run ( )

Run until the specified end time

Definition at line 184 of file MicrovesselSolver.cpp.

References VesselNetworkWriter< DIM >::Create(), MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::mpNetwork, MicrovesselSolver< DIM >::mpOutputFileHandler, and MicrovesselSolver< DIM >::Setup().

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetAngiogenesisSolver ( boost::shared_ptr< AngiogenesisSolver< DIM > > pAngiogenesisSolver )

Set the angiogenesis solver for the network

Parameters

pAngiogenesisSolver the solver for structural adaptation

Definition at line 205 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mpAngiogenesisSolver.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetDiscreteContinuumSolversHaveCompatibleGridIndexing ( bool compatibleIndexing )

Set to true if we know that our discrete continuum solvers all have the same grid

Parameters

compatibleIndexing doe the grids have compatible indexing

Definition at line 247 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolversHaveCompatibleGridIndexing.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetOutputFileHandler ( boost::shared_ptr< OutputFileHandler > pFileHandler )

Set the output directory for results

Parameters

pFileHandler output file handler containing output directory information

Definition at line 211 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mpOutputFileHandler.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetOutputFrequency ( unsigned frequency )

Set the results output frequency

Parameters

frequency the frequency of simulaiton output

Definition at line 217 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mOutputFrequency.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetRegressionSolver ( boost::shared_ptr< RegressionSolver< DIM > > pRegressionSolver )

Set the regression solver

Parameters

pRegressionSolver the regression solver for the network

Definition at line 309 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mpRegressionSolver.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetStructuralAdaptationSolver ( boost::shared_ptr< StructuralAdaptationSolver< DIM > > pStructuralAdaptationSolver )

Set the structural adaptation solver for the network

Parameters

pStructuralAdaptationSolver the solver for structural adaptation

Definition at line 279 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mpStructuralAdaptationSolver.

template<unsigned DIM>

void MicrovesselSolver< DIM >::Setup ( )

This should be called before running in standalone mode

Definition at line 253 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolvers, MicrovesselSolver< DIM >::mpNetwork, MicrovesselSolver< DIM >::mpOutputFileHandler, MicrovesselSolver< DIM >::mpRegressionSolver, and MicrovesselSolver< DIM >::mpStructuralAdaptationSolver.

Referenced by MicrovesselSolver< DIM >::Run(), and MicrovesselSolver< DIM >::SetupFromModifier().

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetUpdatePdeEachSolve ( bool doUpdate )

Set whether to update the pde at each solve

Parameters

doUpdate update the pde at each solve

Definition at line 79 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mUpdatePdeEachSolve.

template<unsigned DIM>

void MicrovesselSolver< DIM >::SetupFromModifier	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		units::quantity< unit::length >	cellReferenceLength,
		units::quantity< unit::concentration >	cellReferenceConcentration,
		const std::string &	rDirectory
	)

This is called by the MicrovesselSimulationModifier to set up the simulation

Parameters

rCellPopulation	the cell population
cellReferenceLength	the cell length scale
cellReferenceConcentration	the cell concentration scale
rDirectory	the output directory for writing to

Definition at line 223 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolvers, MicrovesselSolver< DIM >::mpNetwork, MicrovesselSolver< DIM >::mpOutputFileHandler, and MicrovesselSolver< DIM >::Setup().

template<unsigned DIM>

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

Set the vessel network

Parameters

pNetwork the vessel network

Definition at line 73 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mpNetwork.

template<unsigned DIM>

void MicrovesselSolver< DIM >::UpdateCellData ( std::vector< std::string > labels )

Update the cell data with any PDE solutions corresponding to the supplied labels

Parameters

labels labels corresponding to cell data that is to be updated

Definition at line 285 of file MicrovesselSolver.cpp.

References MicrovesselSolver< DIM >::mDiscreteContinuumSolvers.

Member Data Documentation

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractDiscreteContinuumSolver<DIM> > > MicrovesselSolver< DIM >::mDiscreteContinuumSolvers

private

The collection of DiscreteContinuum solvers

Definition at line 76 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::AddDiscreteContinuumSolver(), MicrovesselSolver< DIM >::GetDiscreteContinuumSolvers(), MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::Setup(), MicrovesselSolver< DIM >::SetupFromModifier(), and MicrovesselSolver< DIM >::UpdateCellData().

template<unsigned DIM>

bool MicrovesselSolver< DIM >::mDiscreteContinuumSolversHaveCompatibleGridIndexing

private

Can the solution from one DiscreteContinuumSolver be sent directly to another, or is grid sampling needed.

Definition at line 97 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), and MicrovesselSolver< DIM >::SetDiscreteContinuumSolversHaveCompatibleGridIndexing().

template<unsigned DIM>

unsigned MicrovesselSolver< DIM >::mOutputFrequency

private

The frequency of file based output

Definition at line 66 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), and MicrovesselSolver< DIM >::SetOutputFrequency().

template<unsigned DIM>

boost::shared_ptr<AngiogenesisSolver<DIM> > MicrovesselSolver< DIM >::mpAngiogenesisSolver

private

The angiogenesis solver for the vessel network

Definition at line 86 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), and MicrovesselSolver< DIM >::SetAngiogenesisSolver().

template<unsigned DIM>

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

private

The vessel network

Definition at line 61 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::Run(), MicrovesselSolver< DIM >::Setup(), MicrovesselSolver< DIM >::SetupFromModifier(), and MicrovesselSolver< DIM >::SetVesselNetwork().

template<unsigned DIM>

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

private

Filehandler containing output directory information

Definition at line 71 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::Run(), MicrovesselSolver< DIM >::SetOutputFileHandler(), MicrovesselSolver< DIM >::Setup(), and MicrovesselSolver< DIM >::SetupFromModifier().

template<unsigned DIM>

boost::shared_ptr<RegressionSolver<DIM> > MicrovesselSolver< DIM >::mpRegressionSolver

private

The regression solver for the vessel network

Definition at line 91 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::SetRegressionSolver(), and MicrovesselSolver< DIM >::Setup().

template<unsigned DIM>

boost::shared_ptr<StructuralAdaptationSolver<DIM> > MicrovesselSolver< DIM >::mpStructuralAdaptationSolver

private

The structural adaptation solver for the vessel network

Definition at line 81 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), MicrovesselSolver< DIM >::SetStructuralAdaptationSolver(), and MicrovesselSolver< DIM >::Setup().

template<unsigned DIM>

bool MicrovesselSolver< DIM >::mUpdatePdeEachSolve

private

Whether to update the PDE for each solve

Definition at line 102 of file MicrovesselSolver.hpp.

Referenced by MicrovesselSolver< DIM >::Increment(), and MicrovesselSolver< DIM >::SetUpdatePdeEachSolve().

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

projects/MicrovesselChaste/src/simulation/MicrovesselSolver.hpp
projects/MicrovesselChaste/src/simulation/MicrovesselSolver.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

template<unsigned DIM> class MicrovesselSolver< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class MicrovesselSolver< DIM >