ImmersedBoundarySvgWriter< DIM > Class Template Reference

#include <ImmersedBoundarySvgWriter.hpp>

Inheritance diagram for ImmersedBoundarySvgWriter< DIM >:

Collaboration diagram for ImmersedBoundarySvgWriter< DIM >:

Public Member Functions
	ImmersedBoundarySvgWriter ()
virtual	~ImmersedBoundarySvgWriter ()
virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void	AddPointToSvgFile (out_stream &rSvgFile, c_vector< double, DIM > location, unsigned region, double rad)
void	OutputSimulationModifierParameters (out_stream &rParamsFile)
unsigned	GetSamplingMultiple () const
void	SetSamplingMultiple (unsigned samplingMultiple)
double	GetSvgSize () const
void	SetSvgSize (double svgSize)
Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
	AbstractCellBasedSimulationModifier ()
virtual	~AbstractCellBasedSimulationModifier ()
virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0
virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0
virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
void	OutputSimulationModifierInfo (out_stream &rParamsFile)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

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

Private Attributes
unsigned	mSamplingMultiple
double	mSvgSize
std::string	mOutputDirectory
std::string	mSvgHeader
std::string	mSvgFooter

Friends
class	TestImmersedBoundarySvgWriter
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class ImmersedBoundarySvgWriter< DIM >

A modifier class which after each simulation time step exports the simulation geometry to a scalable vector graphic (SVG) file.

Definition at line 50 of file ImmersedBoundarySvgWriter.hpp.

Constructor & Destructor Documentation

ImmersedBoundarySvgWriter()

template<unsigned DIM>

ImmersedBoundarySvgWriter< DIM >::ImmersedBoundarySvgWriter

(

)

Default constructor.

Definition at line 40 of file ImmersedBoundarySvgWriter.cpp.

~ImmersedBoundarySvgWriter()

template<unsigned DIM>

ImmersedBoundarySvgWriter< DIM >::~ImmersedBoundarySvgWriter ( )

virtual

Destructor.

Definition at line 51 of file ImmersedBoundarySvgWriter.cpp.

Member Function Documentation

AddPointToSvgFile()

template<unsigned DIM>

void ImmersedBoundarySvgWriter< DIM >::AddPointToSvgFile	(	out_stream &	rSvgFile,
		c_vector< double, DIM >	location,
		unsigned	region,
		double	rad
	)

Helper method for UpdateAtEndOfTimeStep().

Add a circle representing a point location to the svg file.

Parameters

rSvgFile	the svg file stream to add to
location	the location of the point
region	metadata to allow different colouring for points
rad	the radius of circle representing the point

Definition at line 147 of file ImmersedBoundarySvgWriter.cpp.

GetSamplingMultiple()

template<unsigned DIM>

unsigned ImmersedBoundarySvgWriter< DIM >::GetSamplingMultiple

(

)

const

Returns

mSamplingMultiple

Definition at line 203 of file ImmersedBoundarySvgWriter.cpp.

GetSvgSize()

template<unsigned DIM>

double ImmersedBoundarySvgWriter< DIM >::GetSvgSize

(

)

const

Returns

mSvgSize

Definition at line 216 of file ImmersedBoundarySvgWriter.cpp.

OutputSimulationModifierParameters()

template<unsigned DIM>

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

virtual

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

Parameters

rParamsFile

the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Definition at line 195 of file ImmersedBoundarySvgWriter.cpp.

References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

serialize()

template<unsigned DIM>

template<class Archive >

void ImmersedBoundarySvgWriter< 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 79 of file ImmersedBoundarySvgWriter.hpp.

References ImmersedBoundarySvgWriter< DIM >::mOutputDirectory, ImmersedBoundarySvgWriter< DIM >::mSamplingMultiple, ImmersedBoundarySvgWriter< DIM >::mSvgFooter, ImmersedBoundarySvgWriter< DIM >::mSvgHeader, and ImmersedBoundarySvgWriter< DIM >::mSvgSize.

SetSamplingMultiple()

template<unsigned DIM>

void ImmersedBoundarySvgWriter< DIM >::SetSamplingMultiple

(

unsigned

samplingMultiple

)

Parameters

samplingMultiple

the new value of mSamplingMultiple

Definition at line 209 of file ImmersedBoundarySvgWriter.cpp.

SetSvgSize()

template<unsigned DIM>

void ImmersedBoundarySvgWriter< DIM >::SetSvgSize

(

double

svgSize

)

Parameters

svgSize

the new value of mSvgSize

Definition at line 222 of file ImmersedBoundarySvgWriter.cpp.

SetupSolve()

template<unsigned DIM>

void ImmersedBoundarySvgWriter< 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 90 of file ImmersedBoundarySvgWriter.cpp.

UpdateAtEndOfTimeStep()

template<unsigned DIM>

void ImmersedBoundarySvgWriter< 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 56 of file ImmersedBoundarySvgWriter.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetAverageNodeSpacingOfElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), OutputFileHandler::OpenOutputFile(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh().

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file ImmersedBoundarySvgWriter.hpp.

TestImmersedBoundarySvgWriter

template<unsigned DIM>

friend class TestImmersedBoundarySvgWriter

friend

Definition at line 67 of file ImmersedBoundarySvgWriter.hpp.

Member Data Documentation

mOutputDirectory

template<unsigned DIM>

std::string ImmersedBoundarySvgWriter< DIM >::mOutputDirectory

private

Set to the output directory during SetupSolve()

Definition at line 59 of file ImmersedBoundarySvgWriter.hpp.

Referenced by ImmersedBoundarySvgWriter< DIM >::serialize().

mSamplingMultiple

template<unsigned DIM>

unsigned ImmersedBoundarySvgWriter< DIM >::mSamplingMultiple

private

The sampling frequency for exporting svg frames

Definition at line 53 of file ImmersedBoundarySvgWriter.hpp.

Referenced by ImmersedBoundarySvgWriter< DIM >::serialize().

mSvgFooter

template<unsigned DIM>

std::string ImmersedBoundarySvgWriter< DIM >::mSvgFooter

private

The svg file footer, which will be constant for a given simulation

Definition at line 65 of file ImmersedBoundarySvgWriter.hpp.

Referenced by ImmersedBoundarySvgWriter< DIM >::serialize().

mSvgHeader

template<unsigned DIM>

std::string ImmersedBoundarySvgWriter< DIM >::mSvgHeader

private

The svg file header, which will be constant for a given simulation

Definition at line 62 of file ImmersedBoundarySvgWriter.hpp.

Referenced by ImmersedBoundarySvgWriter< DIM >::serialize().

mSvgSize

template<unsigned DIM>

double ImmersedBoundarySvgWriter< DIM >::mSvgSize

private

The width and height in pixels of the svg file

Definition at line 56 of file ImmersedBoundarySvgWriter.hpp.

Referenced by ImmersedBoundarySvgWriter< DIM >::serialize().

---

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

• cell_based/src/simulation/modifiers/ImmersedBoundarySvgWriter.hpp
• cell_based/src/simulation/modifiers/ImmersedBoundarySvgWriter.cpp