GreensFunctionSolver< DIM > Class Template Reference

#include <GreensFunctionSolver.hpp>

Inheritance diagram for GreensFunctionSolver< DIM >:

Collaboration diagram for GreensFunctionSolver< DIM >:

Public Member Functions
	GreensFunctionSolver ()
	~GreensFunctionSolver ()
void	SetSubSegmentCutoff (units::quantity< unit::length > value)
void	Solve ()
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	Setup ()
virtual void	UpdateCellData ()
virtual void	UpdateSolution (std::vector< double > &rData)
virtual void	UpdateSolution (std::vector< units::quantity< unit::concentration > > &rData)
virtual void	Update ()
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)

Private Member Functions
void	GenerateSubSegments ()
void	GenerateTissuePoints ()
void	UpdateGreensFunctionMatrices (bool updateGtt=0, bool updateGvv=0, bool updateGtv=0, bool updateGvt=0)
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	GetVesselVesselInteractionMatrix ()
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	GetTissueTissueInteractionMatrix ()
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	GetTissueVesselInteractionMatrix ()
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	GetVesselTissueInteractionMatrix ()
void	WriteSolution (std::map< std::string, std::vector< units::quantity< unit::concentration > > > &segmentPointData)

Private Attributes
boost::shared_ptr< Part< DIM > >	mpDomain
std::vector< DimensionalChastePoint< DIM > >	mSinkCoordinates
std::vector< unsigned >	mSinkPointMap
std::vector< DimensionalChastePoint< DIM > >	mSubSegmentCoordinates
std::vector< units::quantity< unit::length > >	mSubSegmentLengths
std::vector< units::quantity< unit::molar_flow_rate > >	mSinkRates
std::vector< units::quantity< unit::molar_flow_rate > >	mSourceRates
std::vector< units::quantity< unit::concentration > >	mSegmentConcentration
std::map< unsigned, boost::shared_ptr< VesselSegment< DIM > > >	mSegmentPointMap
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	mGtt
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	mGvv
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	mGvt
boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > >	mGtv
units::quantity< unit::length >	mSubsegmentCutoff

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 GreensFunctionSolver< DIM >

A class for solving diffusion-reaction PDEs based on the Greens Function method of Secomb and co-workers.

The method is described here: Secomb, T.W., Hsu, R., Park, E.Y.H. and Dewhirst, M.W. Green's function methods for analysis of oxygen delivery to tissue by microvascular networks. Annals of Biomedical Engineering, 32: 1519-1529 (2004).

The present code is based on a C++ implementation available here (without license): http://physiology.arizona.edu/people/secomb/greens_c3 however it has been re-written from scratch following Chaste style and using PETSc linear solvers.

Definition at line 62 of file GreensFunctionSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

GreensFunctionSolver< DIM >::GreensFunctionSolver

(

)

Constructor

Definition at line 53 of file GreensFunctionSolver.cpp.

template<unsigned DIM>

GreensFunctionSolver< DIM >::~GreensFunctionSolver

(

)

Destructor

Definition at line 74 of file GreensFunctionSolver.cpp.

Member Function Documentation

template<unsigned DIM>

void GreensFunctionSolver< DIM >::GenerateSubSegments ( )

private

Generate vessel subsegments

Definition at line 219 of file GreensFunctionSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpNetwork, GreensFunctionSolver< DIM >::mSegmentPointMap, GreensFunctionSolver< DIM >::mSubSegmentCoordinates, GreensFunctionSolver< DIM >::mSubsegmentCutoff, and GreensFunctionSolver< DIM >::mSubSegmentLengths.

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

template<unsigned DIM>

void GreensFunctionSolver< DIM >::GenerateTissuePoints ( )

private

Generate tissue points

Definition at line 267 of file GreensFunctionSolver.cpp.

References AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, GreensFunctionSolver< DIM >::mSinkCoordinates, and GreensFunctionSolver< DIM >::mSinkPointMap.

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

template<unsigned DIM>

boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > > GreensFunctionSolver< DIM >::GetTissueTissueInteractionMatrix ( )

private

Update Gtt

Returns

Gtt

Definition at line 342 of file GreensFunctionSolver.cpp.

References AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, and GreensFunctionSolver< DIM >::mSinkCoordinates.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > > GreensFunctionSolver< DIM >::GetTissueVesselInteractionMatrix ( )

private

Update Gtv

Returns

Gtv

Definition at line 370 of file GreensFunctionSolver.cpp.

References AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, GreensFunctionSolver< DIM >::mSinkCoordinates, and GreensFunctionSolver< DIM >::mSubSegmentCoordinates.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > > GreensFunctionSolver< DIM >::GetVesselTissueInteractionMatrix ( )

private

Update Gvt

Returns

Gvt

Definition at line 402 of file GreensFunctionSolver.cpp.

References AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, GreensFunctionSolver< DIM >::mSinkCoordinates, and GreensFunctionSolver< DIM >::mSubSegmentCoordinates.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr< boost::multi_array< units::quantity< unit::per_length >, 2 > > GreensFunctionSolver< DIM >::GetVesselVesselInteractionMatrix ( )

private

Update Gvv

Returns

Gvv

Definition at line 303 of file GreensFunctionSolver.cpp.

References GreensFunctionSolver< DIM >::mSegmentPointMap, GreensFunctionSolver< DIM >::mSubSegmentCoordinates, and GreensFunctionSolver< DIM >::mSubSegmentLengths.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

void GreensFunctionSolver< DIM >::SetSubSegmentCutoff

(

units::quantity< unit::length >

value

)

Set the minimum subsegment length

Parameters

value

the minimum subsegment length

Definition at line 80 of file GreensFunctionSolver.cpp.

References GreensFunctionSolver< DIM >::mSubsegmentCutoff.

template<unsigned DIM>

void GreensFunctionSolver< DIM >::Solve ( )

virtual

Do the solve

Implements AbstractRegularGridDiscreteContinuumSolver< DIM >.

Definition at line 86 of file GreensFunctionSolver.cpp.

References GreensFunctionSolver< DIM >::GenerateSubSegments(), GreensFunctionSolver< DIM >::GenerateTissuePoints(), BaseUnits::GetReferenceTimeScale(), BaseUnits::Instance(), AbstractDiscreteContinuumSolver< DIM >::mConcentrations, GreensFunctionSolver< DIM >::mGvv, AbstractDiscreteContinuumSolver< DIM >::mLabel, AbstractDiscreteContinuumSolver< DIM >::mpPde, AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration, GreensFunctionSolver< DIM >::mSegmentConcentration, GreensFunctionSolver< DIM >::mSinkCoordinates, GreensFunctionSolver< DIM >::mSinkRates, GreensFunctionSolver< DIM >::mSourceRates, GreensFunctionSolver< DIM >::mSubSegmentCoordinates, AbstractDiscreteContinuumSolver< DIM >::mWriteSolution, GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices(), AbstractRegularGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and GreensFunctionSolver< DIM >::WriteSolution().

template<unsigned DIM>

void GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices ( bool  updateGtt = 0, bool  updateGvv = 0, bool  updateGtv = 0, bool  updateGvt = 0  )

private

Update the greens function matrices

Parameters

updateGtt	Update Gtt
updateGvv	Update Gvv
updateGtv	Update Gtv
updateGvt	Update Gvt

Definition at line 280 of file GreensFunctionSolver.cpp.

References GreensFunctionSolver< DIM >::GetTissueTissueInteractionMatrix(), GreensFunctionSolver< DIM >::GetTissueVesselInteractionMatrix(), GreensFunctionSolver< DIM >::GetVesselTissueInteractionMatrix(), GreensFunctionSolver< DIM >::GetVesselVesselInteractionMatrix(), GreensFunctionSolver< DIM >::mGtt, GreensFunctionSolver< DIM >::mGtv, GreensFunctionSolver< DIM >::mGvt, and GreensFunctionSolver< DIM >::mGvv.

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

template<unsigned DIM>

void GreensFunctionSolver< DIM >::WriteSolution ( std::map< std::string, std::vector< units::quantity< unit::concentration > > > &  segmentPointData )

private

Over-ridden method for writing solution to file

Parameters

segmentPointData

the concentrations in each segment

Definition at line 434 of file GreensFunctionSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mpOutputFileHandler, AbstractRegularGridDiscreteContinuumSolver< DIM >::mpRegularGrid, AbstractRegularGridDiscreteContinuumSolver< DIM >::mpVtkSolution, GreensFunctionSolver< DIM >::mSubSegmentCoordinates, RegularGridWriter::SetFilename(), GeometryWriter::SetFileName(), RegularGridWriter::SetImage(), GeometryWriter::SetInput(), RegularGridWriter::Write(), and GeometryWriter::Write().

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

Member Data Documentation

template<unsigned DIM>

boost::shared_ptr<boost::multi_array<units::quantity<unit::per_length> , 2> > GreensFunctionSolver< DIM >::mGtt

private

Greens function matrix for tissue-tissue case

Definition at line 112 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr<boost::multi_array<units::quantity<unit::per_length> , 2> > GreensFunctionSolver< DIM >::mGtv

private

Greens function matrix for tissue-vessel case

Definition at line 127 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr<boost::multi_array<units::quantity<unit::per_length> , 2> > GreensFunctionSolver< DIM >::mGvt

private

Greens function matrix for vessel-tissue case

Definition at line 122 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr<boost::multi_array<units::quantity<unit::per_length> , 2> > GreensFunctionSolver< DIM >::mGvv

private

Greens function matrix for vessel-vessel case

Definition at line 117 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::Solve(), and GreensFunctionSolver< DIM >::UpdateGreensFunctionMatrices().

template<unsigned DIM>

boost::shared_ptr<Part<DIM> > GreensFunctionSolver< DIM >::mpDomain

private

A cuboidal tissue domain

Definition at line 67 of file GreensFunctionSolver.hpp.

template<unsigned DIM>

std::vector<units::quantity<unit::concentration> > GreensFunctionSolver< DIM >::mSegmentConcentration

private

Species concentration in vessels

Definition at line 102 of file GreensFunctionSolver.hpp.

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

template<unsigned DIM>

std::map<unsigned, boost::shared_ptr<VesselSegment<DIM> > > GreensFunctionSolver< DIM >::mSegmentPointMap

private

Map between vessel segments and point locations

Definition at line 107 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateSubSegments(), and GreensFunctionSolver< DIM >::GetVesselVesselInteractionMatrix().

template<unsigned DIM>

std::vector<DimensionalChastePoint<DIM> > GreensFunctionSolver< DIM >::mSinkCoordinates

private

The positions of point sinks

Definition at line 72 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateTissuePoints(), GreensFunctionSolver< DIM >::GetTissueTissueInteractionMatrix(), GreensFunctionSolver< DIM >::GetTissueVesselInteractionMatrix(), GreensFunctionSolver< DIM >::GetVesselTissueInteractionMatrix(), and GreensFunctionSolver< DIM >::Solve().

template<unsigned DIM>

std::vector<unsigned> GreensFunctionSolver< DIM >::mSinkPointMap

private

Map between point sinks and segments

Definition at line 77 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateTissuePoints().

template<unsigned DIM>

std::vector<units::quantity<unit::molar_flow_rate> > GreensFunctionSolver< DIM >::mSinkRates

private

Sink rate ordered by point index

Definition at line 92 of file GreensFunctionSolver.hpp.

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

template<unsigned DIM>

std::vector<units::quantity<unit::molar_flow_rate> > GreensFunctionSolver< DIM >::mSourceRates

private

Source rate ordered by point index

Definition at line 97 of file GreensFunctionSolver.hpp.

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

template<unsigned DIM>

std::vector<DimensionalChastePoint<DIM> > GreensFunctionSolver< DIM >::mSubSegmentCoordinates

private

Coorindates of subsegments

Definition at line 82 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateSubSegments(), GreensFunctionSolver< DIM >::GetTissueVesselInteractionMatrix(), GreensFunctionSolver< DIM >::GetVesselTissueInteractionMatrix(), GreensFunctionSolver< DIM >::GetVesselVesselInteractionMatrix(), GreensFunctionSolver< DIM >::Solve(), and GreensFunctionSolver< DIM >::WriteSolution().

template<unsigned DIM>

units::quantity<unit::length> GreensFunctionSolver< DIM >::mSubsegmentCutoff

private

Minimum subsegment length

Definition at line 132 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateSubSegments(), and GreensFunctionSolver< DIM >::SetSubSegmentCutoff().

template<unsigned DIM>

std::vector<units::quantity<unit::length> > GreensFunctionSolver< DIM >::mSubSegmentLengths

private

Subsegment lengths

Definition at line 87 of file GreensFunctionSolver.hpp.

Referenced by GreensFunctionSolver< DIM >::GenerateSubSegments(), and GreensFunctionSolver< DIM >::GetVesselVesselInteractionMatrix().

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

• projects/MicrovesselChaste/src/pde/solvers/GreensFunctionSolver.hpp
• projects/MicrovesselChaste/src/pde/solvers/GreensFunctionSolver.cpp