#include <MicrovesselSimulationModifier.hpp>

Inheritance diagram for MicrovesselSimulationModifier< DIM >:

Collaboration diagram for MicrovesselSimulationModifier< DIM >:

Public Member Functions
	MicrovesselSimulationModifier ()

virtual	~MicrovesselSimulationModifier ()

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

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

void	SetMicrovesselSolver (boost::shared_ptr< MicrovesselSolver< DIM > > pSolver)

virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)

void	SetCellPopulationLengthScale (units::quantity< unit::length > cellLengthScale)

void	SetCellPopulationConcentrationScale (units::quantity< unit::concentration > cellConcentrationScale)

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

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

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Private Attributes
boost::shared_ptr< MicrovesselSolver< DIM > >	mpSolver

std::vector< std::string >	mUpdateLabels

units::quantity< unit::length >	mCellPopulationReferenceLength

units::quantity< unit::concentration >	mCellPopulationReferenceConcentration

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class MicrovesselSimulationModifier< DIM >

A modifier class which at each simulation time step in a cell based simulation increments a MicrovesselSolver. This solver updates a collection of PDEs and the state of a vessel network. It also updates the cell data for use in the next time step of the cell based simulation.

Definition at line 51 of file MicrovesselSimulationModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

MicrovesselSimulationModifier< DIM >::MicrovesselSimulationModifier ( )

Default constructor.

Definition at line 42 of file MicrovesselSimulationModifier.cpp.

template<unsigned DIM>

MicrovesselSimulationModifier< DIM >::~MicrovesselSimulationModifier ( )

virtual

Destructor.

Definition at line 52 of file MicrovesselSimulationModifier.cpp.

Member Function Documentation

template<unsigned DIM>

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

static

Construct a new instance of the class and return a shared pointer to it.

Returns: a shared pointer to the class instance

Definition at line 57 of file MicrovesselSimulationModifier.cpp.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Definition at line 138 of file MicrovesselSimulationModifier.cpp.

template<unsigned DIM>

template<class Archive >

void MicrovesselSimulationModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 63 of file MicrovesselSimulationModifier.hpp.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::SetCellDataUpdateLabels ( std::vector< std::string > labels )

Set the labels which will be used to update cell data

Parameters

labels the labels which will be used to update cell data

Definition at line 94 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mUpdateLabels.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::SetCellPopulationConcentrationScale ( units::quantity< unit::concentration > cellConcentrationScale )

Set the concentration scale for the cell population

Parameters

cellConcentrationScale the concentration scale for the cell population

Definition at line 112 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mCellPopulationReferenceConcentration.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::SetCellPopulationLengthScale ( units::quantity< unit::length > cellLengthScale )

Set the length scale for the cell population

Parameters

cellLengthScale the length scale for the cell population

Definition at line 106 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mCellPopulationReferenceLength.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::SetMicrovesselSolver ( boost::shared_ptr< MicrovesselSolver< DIM > > pSolver )

Set the vascular tumour solver

Parameters

pSolver pointer to the vascular tumour solver

Definition at line 100 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mpSolver.

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)

virtual

Overridden SetupSolve() method. Specify what to do in the simulation before the start of the time loop.

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Definition at line 64 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mCellPopulationReferenceConcentration, MicrovesselSimulationModifier< DIM >::mCellPopulationReferenceLength, MicrovesselSimulationModifier< DIM >::mpSolver, and MicrovesselSimulationModifier< DIM >::UpdateCellData().

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

virtual

Overridden UpdateAtEndOfTimeStep() method. Specify what to do in the simulation at the end of each time step.

Parameters

rCellPopulation reference to the cell population

Definition at line 118 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mpSolver, and MicrovesselSimulationModifier< DIM >::UpdateCellData().

template<unsigned DIM>

void MicrovesselSimulationModifier< DIM >::UpdateCellData ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

Helper method to compute the volume of each cell in the population and store these in the CellData.

Parameters

rCellPopulation reference to the cell population

Definition at line 128 of file MicrovesselSimulationModifier.cpp.

References MicrovesselSimulationModifier< DIM >::mpSolver, and MicrovesselSimulationModifier< DIM >::mUpdateLabels.

Referenced by MicrovesselSimulationModifier< DIM >::SetupSolve(), and MicrovesselSimulationModifier< DIM >::UpdateAtEndOfTimeStep().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 54 of file MicrovesselSimulationModifier.hpp.

Member Data Documentation

template<unsigned DIM>

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

private

The reference concentration scale for the cellpopulation.

Definition at line 88 of file MicrovesselSimulationModifier.hpp.

Referenced by MicrovesselSimulationModifier< DIM >::SetCellPopulationConcentrationScale(), and MicrovesselSimulationModifier< DIM >::SetupSolve().

template<unsigned DIM>

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

private

The reference length scale for the cellpopulation.

Definition at line 83 of file MicrovesselSimulationModifier.hpp.

Referenced by MicrovesselSimulationModifier< DIM >::SetCellPopulationLengthScale(), and MicrovesselSimulationModifier< DIM >::SetupSolve().

template<unsigned DIM>

boost::shared_ptr<MicrovesselSolver<DIM> > MicrovesselSimulationModifier< DIM >::mpSolver

private

The vascular tumour solver

Definition at line 73 of file MicrovesselSimulationModifier.hpp.

Referenced by MicrovesselSimulationModifier< DIM >::SetMicrovesselSolver(), MicrovesselSimulationModifier< DIM >::SetupSolve(), MicrovesselSimulationModifier< DIM >::UpdateAtEndOfTimeStep(), and MicrovesselSimulationModifier< DIM >::UpdateCellData().

template<unsigned DIM>

std::vector<std::string> MicrovesselSimulationModifier< DIM >::mUpdateLabels

private

The species labels for cell data updates

Definition at line 78 of file MicrovesselSimulationModifier.hpp.

Referenced by MicrovesselSimulationModifier< DIM >::SetCellDataUpdateLabels(), and MicrovesselSimulationModifier< DIM >::UpdateCellData().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class MicrovesselSimulationModifier< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class MicrovesselSimulationModifier< DIM >