#include <ImmersedBoundarySimulationModifier.hpp>

Inheritance diagram for ImmersedBoundarySimulationModifier< DIM >:

Collaboration diagram for ImmersedBoundarySimulationModifier< DIM >:

Public Member Functions
	ImmersedBoundarySimulationModifier ()

virtual	~ImmersedBoundarySimulationModifier ()=default

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

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

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

void	SetNodeNeighbourUpdateFrequency (unsigned newFrequency)

unsigned	GetNodeNeighbourUpdateFrequency ()

void	AddImmersedBoundaryForce (boost::shared_ptr< AbstractImmersedBoundaryForce< DIM > > pForce)

void	AddNormalNoise () const

bool	GetZeroFieldSums () const

void	SetZeroFieldSums (bool zeroFieldSums)

void	SetReynoldsNumber (double reynoldsNumber)

double	GetReynoldsNumber ()

bool	GetAdditiveNormalNoise () const

void	SetAdditiveNormalNoise (bool additiveNormalNoise)

double	GetNoiseStrength () const

void	SetNoiseStrength (double noiseStrength)

unsigned	GetNoiseSkip () const

void	SetNoiseSkip (unsigned noiseSkip)

double	GetNoiseLengthScale () const

void	SetNoiseLengthScale (double noiseLengthScale)

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)

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

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

void	ClearForcesAndSources ()

void	RecalculateAverageNodeSpacings ()

void	AddImmersedBoundaryForceContributions ()

void	PropagateForcesToFluidGrid ()

void	PropagateFluidSourcesToGrid ()

void	SolveNavierStokesSpectral ()

double	Delta1D (double dist, double spacing)

void	Upwind2d (const multi_array< double, 3 > &rInput, multi_array< double, 3 > &rOutput)

void	CalculateSourceGradients (const multi_array< double, 3 > &rRhs, multi_array< double, 3 > &rGradients)

void	ZeroFieldSums (multi_array< double, 3 > &rField)

Private Attributes
ImmersedBoundaryMesh< DIM, DIM > *	mpMesh

ImmersedBoundaryCellPopulation< DIM > *	mpCellPopulation

unsigned	mNodeNeighbourUpdateFrequency

double	mGridSpacingX

double	mGridSpacingY

double	mFftNorm

bool	mAdditiveNormalNoise

double	mNoiseStrength

unsigned	mNoiseSkip

double	mNoiseLengthScale

bool	mZeroFieldSums

std::unique_ptr< ObsoleteBoxCollection< DIM > >	mpBoxCollection

std::vector< std::pair< Node< DIM > , Node< DIM > > >	mNodePairs

std::map< unsigned, std::set< unsigned > >	mNodeNeighbours

double	mReynoldsNumber

std::complex< double >	mI

std::vector< boost::shared_ptr< AbstractImmersedBoundaryForce< DIM > > >	mForceCollection

std::unique_ptr< ImmersedBoundary2dArrays< DIM > >	mpArrays

std::unique_ptr< ImmersedBoundaryFftInterface< DIM > >	mpFftInterface

std::unique_ptr< UniformGridRandomFieldGenerator< DIM > >	mpRandomField

Friends
class	TestImmersedBoundarySimulationModifier

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class ImmersedBoundarySimulationModifier< DIM >

A modifier class which at each simulation time step implements the immersed boundary algorithm similar to Rejniak et al (2004). A computational model of the mechanics of growth of the villous trophoblast bilayer. Bull. Math. Biol. 66:199–232. doi:10.1016/j.bulm.2003.06.001.

Definition at line 64 of file ImmersedBoundarySimulationModifier.hpp.

Constructor & Destructor Documentation

◆ ImmersedBoundarySimulationModifier()

template<unsigned DIM>

ImmersedBoundarySimulationModifier< DIM >::ImmersedBoundarySimulationModifier ( )

Default constructor.

Definition at line 45 of file ImmersedBoundarySimulationModifier.cpp.

◆ ~ImmersedBoundarySimulationModifier()

template<unsigned DIM>

virtual ImmersedBoundarySimulationModifier< DIM >::~ImmersedBoundarySimulationModifier ( )

virtualdefault

Default destructor.

Member Function Documentation

◆ AddImmersedBoundaryForce()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::AddImmersedBoundaryForce ( boost::shared_ptr< AbstractImmersedBoundaryForce< DIM > > pForce )

Add an immersed boundary force to be used in this modifier.

Parameters

pForce pointer to a force law

Definition at line 797 of file ImmersedBoundarySimulationModifier.cpp.

◆ AddImmersedBoundaryForceContributions()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::AddImmersedBoundaryForceContributions ( )

private

Loops over each immersed boundary force and invokes AddImmersedBoundaryForceContribution()

Definition at line 295 of file ImmersedBoundarySimulationModifier.cpp.

◆ AddNormalNoise()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::AddNormalNoise ( ) const

Add the random noise as generated by mpRandomField

Definition at line 804 of file ImmersedBoundarySimulationModifier.cpp.

References SimulationTime::Instance().

◆ CalculateSourceGradients()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::CalculateSourceGradients	(	const multi_array< double, 3 > &	rRhs,
		multi_array< double, 3 > &	rGradients
	)

private

Calculates the vector of central differences of the fluid source grid

Parameters

rRhs	const reference to rhs grids which contain the fluid source strengths
rGradients	reference to grids storing the graidents

Definition at line 755 of file ImmersedBoundarySimulationModifier.cpp.

◆ ClearForcesAndSources()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::ClearForcesAndSources ( )

private

Helper method for UpdateFluidVelocityGrids() Ensures force applied to each node is reset to zero Ensures fluid force grids and source grid are reset

Definition at line 234 of file ImmersedBoundarySimulationModifier.cpp.

◆ Delta1D()

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::Delta1D	(	double	dist,
		double	spacing
	)

private

Helper method for PropagateForcesToFluidGrid() Calculates the discrete delta approximation based on distance and grid spacing

Parameters

dist	absolute 1-D distance between boundary-node and fluid-node
spacing	the grid spacing

Returns: computed Delta1D value

Definition at line 696 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetAdditiveNormalNoise()

template<unsigned DIM>

bool ImmersedBoundarySimulationModifier< DIM >::GetAdditiveNormalNoise ( ) const

Returns: mAdditiveNormalNoise

Definition at line 855 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetNodeNeighbourUpdateFrequency()

template<unsigned DIM>

unsigned ImmersedBoundarySimulationModifier< DIM >::GetNodeNeighbourUpdateFrequency ( )

Returns: the current number of time steps after which node neighbours are re-calculated

Definition at line 791 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetNoiseLengthScale()

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::GetNoiseLengthScale ( ) const

Returns: mNoiseLengthScale

Definition at line 893 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetNoiseSkip()

template<unsigned DIM>

unsigned ImmersedBoundarySimulationModifier< DIM >::GetNoiseSkip ( ) const

Returns: mNoiseSkip

Definition at line 881 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetNoiseStrength()

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::GetNoiseStrength ( ) const

Returns: mNoiseStrength

Definition at line 868 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetReynoldsNumber()

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::GetReynoldsNumber ( )

Returns: mReynoldsNumber

Definition at line 849 of file ImmersedBoundarySimulationModifier.cpp.

◆ GetZeroFieldSums()

template<unsigned int DIM>

bool ImmersedBoundarySimulationModifier< DIM >::GetZeroFieldSums ( ) const

Returns: mZeroFieldSums

Definition at line 906 of file ImmersedBoundarySimulationModifier.cpp.

◆ OutputSimulationModifierParameters()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< 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 97 of file ImmersedBoundarySimulationModifier.cpp.

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

◆ PropagateFluidSourcesToGrid()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::PropagateFluidSourcesToGrid ( )

private

Helper method for UpdateFluidVelocityGrids() Propagates fluid sources to grid

Definition at line 434 of file ImmersedBoundarySimulationModifier.cpp.

References NEVER_REACHED.

◆ PropagateForcesToFluidGrid()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::PropagateForcesToFluidGrid ( )

private

Helper method for UpdateFluidVelocityGrids() Propagates elastic forces to fluid grid

Definition at line 307 of file ImmersedBoundarySimulationModifier.cpp.

References NEVER_REACHED, Node< SPACE_DIM >::rGetAppliedForce(), and Node< SPACE_DIM >::rGetLocation().

◆ RecalculateAverageNodeSpacings()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::RecalculateAverageNodeSpacings ( )

private

Helper method for UpdateFluidVelocityGrids() Recalculate the average node spacings for elements and laminas. This is performed at each timestep so as to cache the values for safe reuse without re-calculation by force classes and other methods.

Definition at line 277 of file ImmersedBoundarySimulationModifier.cpp.

◆ serialize()

template<unsigned DIM>

template<class Archive >

void ImmersedBoundarySimulationModifier< 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 81 of file ImmersedBoundarySimulationModifier.hpp.

◆ SetAdditiveNormalNoise()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetAdditiveNormalNoise ( bool additiveNormalNoise )

Parameters

additiveNormalNoise whether to include additive normal noise

Definition at line 861 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetNodeNeighbourUpdateFrequency()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetNodeNeighbourUpdateFrequency ( unsigned newFrequency )

Parameters

newFrequency the new number of time steps after which node neighbours are re-calculated

Definition at line 783 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetNoiseLengthScale()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetNoiseLengthScale ( double noiseLengthScale )

Parameters

noiseLengthScale the new value of mNoiseLengthScale

Definition at line 899 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetNoiseSkip()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetNoiseSkip ( unsigned noiseSkip )

Parameters

noiseSkip the new value of mNoiseSkip

Definition at line 887 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetNoiseStrength()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetNoiseStrength ( double noiseStrength )

Parameters

noiseStrength the new value of mNoiseStrength

Definition at line 874 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetReynoldsNumber()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetReynoldsNumber ( double reynoldsNumber )

Parameters

reynoldsNumber the new Reynolds number

Definition at line 841 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetupConstantMemberVariables()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetupConstantMemberVariables ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

private

Helper method for SetupSolve() Sets up all variables which need not change throughout the simulation

Parameters

rCellPopulation reference to the cell population

Definition at line 129 of file ImmersedBoundarySimulationModifier.cpp.

References EXCEPTION, SimulationTime::GetTimeStep(), SimulationTime::Instance(), and NEVER_REACHED.

◆ SetupSolve()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< 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 82 of file ImmersedBoundarySimulationModifier.cpp.

◆ SetZeroFieldSums()

template<unsigned int DIM>

void ImmersedBoundarySimulationModifier< DIM >::SetZeroFieldSums ( bool zeroFieldSums )

Parameters

zeroFieldSums the new value of mZeroFieldSums

Definition at line 912 of file ImmersedBoundarySimulationModifier.cpp.

◆ SolveNavierStokesSpectral()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::SolveNavierStokesSpectral ( )

private

Helper method for UpdateFluidVelocityGrids() Updates fluid velocity grids by solving Navier-Stokes

Definition at line 522 of file ImmersedBoundarySimulationModifier.cpp.

References SimulationTime::GetTimeStep(), and SimulationTime::Instance().

◆ UpdateAtEndOfTimeStep()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< 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 68 of file ImmersedBoundarySimulationModifier.cpp.

References SimulationTime::Instance().

◆ UpdateFluidVelocityGrids()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::UpdateFluidVelocityGrids ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

private

Helper method to calculate elastic forces, propagate these to the fluid grid and solve Navier-Stokes to update the fluid velocity grids

Parameters

rCellPopulation reference to the cell population

Definition at line 105 of file ImmersedBoundarySimulationModifier.cpp.

◆ Upwind2d()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::Upwind2d	(	const multi_array< double, 3 > &	rInput,
		multi_array< double, 3 > &	rOutput
	)

private

Calculates upwind difference of fluid velocity grids

Parameters

rInput	const reference to input grids
rOutput	reference to output grids

Definition at line 704 of file ImmersedBoundarySimulationModifier.cpp.

◆ ZeroFieldSums()

template<unsigned DIM>

void ImmersedBoundarySimulationModifier< DIM >::ZeroFieldSums ( multi_array< double, 3 > & rField )

private

Remove any bias in field sums.

Parameters

rField a reference to the field over which the field sums will be zeroed

Definition at line 657 of file ImmersedBoundarySimulationModifier.cpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 72 of file ImmersedBoundarySimulationModifier.hpp.

◆ TestImmersedBoundarySimulationModifier

template<unsigned DIM>

friend class TestImmersedBoundarySimulationModifier

friend

To allow tests to directly access solver methods

Definition at line 69 of file ImmersedBoundarySimulationModifier.hpp.

Member Data Documentation

◆ mAdditiveNormalNoise

template<unsigned DIM>

bool ImmersedBoundarySimulationModifier< DIM >::mAdditiveNormalNoise

private

Whether to apply additive normal noise to the fluid force grids

Definition at line 105 of file ImmersedBoundarySimulationModifier.hpp.

◆ mFftNorm

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::mFftNorm

private

Normalising constant needed for FFT

Definition at line 102 of file ImmersedBoundarySimulationModifier.hpp.

◆ mForceCollection

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractImmersedBoundaryForce<DIM> > > ImmersedBoundarySimulationModifier< DIM >::mForceCollection

private

A list of force laws to determine the force applied to each node

Definition at line 142 of file ImmersedBoundarySimulationModifier.hpp.

◆ mGridSpacingX

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::mGridSpacingX

private

Number of grid points in the x direction

Definition at line 96 of file ImmersedBoundarySimulationModifier.hpp.

◆ mGridSpacingY

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::mGridSpacingY

private

Number of grid points in the y direction

Definition at line 99 of file ImmersedBoundarySimulationModifier.hpp.

◆ mI

template<unsigned DIM>

std::complex<double> ImmersedBoundarySimulationModifier< DIM >::mI

private

Imaginary unit.

Definition at line 139 of file ImmersedBoundarySimulationModifier.hpp.

◆ mNodeNeighbours

template<unsigned DIM>

std::map<unsigned, std::set<unsigned> > ImmersedBoundarySimulationModifier< DIM >::mNodeNeighbours

private

A map between node indices and a set of their possible neighbours, used calculating cell-cell interactions

Definition at line 129 of file ImmersedBoundarySimulationModifier.hpp.

◆ mNodeNeighbourUpdateFrequency

template<unsigned DIM>

unsigned ImmersedBoundarySimulationModifier< DIM >::mNodeNeighbourUpdateFrequency

private

How often we calculate which cells are neighbours

Definition at line 93 of file ImmersedBoundarySimulationModifier.hpp.

◆ mNodePairs

template<unsigned DIM>

std::vector<std::pair<Node<DIM>*, Node<DIM>*> > ImmersedBoundarySimulationModifier< DIM >::mNodePairs

private

A vector of pairs of pointers to nodes, representing all possible node-node interactions

Definition at line 126 of file ImmersedBoundarySimulationModifier.hpp.

◆ mNoiseLengthScale

template<unsigned DIM>

double ImmersedBoundarySimulationModifier< DIM >::mNoiseLengthScale

private

The length scale on which the Gaussian noise is correlated

Definition at line 117 of file ImmersedBoundarySimulationModifier.hpp.

◆ mNoiseSkip

template<unsigned DIM>

unsigned ImmersedBoundarySimulationModifier< DIM >::mNoiseSkip

private

A random field big enough to have a grid point for every fluid mesh point is likely too big to generate. mNoiseSkip is the sampling ratio such that ever mNoiseSkip^DIM sub-region takes the same noise value

Definition at line 114 of file ImmersedBoundarySimulationModifier.hpp.