#include <OffLatticeSimulation.hpp>

Inheritance diagram for OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	OffLatticeSimulation (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

void	AddForce (boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce)

void	RemoveAllForces ()

void	AddCellPopulationBoundaryCondition (boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition)

void	RemoveAllCellPopulationBoundaryConditions ()

void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

virtual void	OutputSimulationParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >
	AbstractCellBasedSimulation (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~AbstractCellBasedSimulation ()

void	SetCellBasedPdeHandler (CellBasedPdeHandler< SPACE_DIM > *pCellBasedPdeHandler)

CellBasedPdeHandler< SPACE_DIM > *	GetCellBasedPdeHandler ()

std::vector< double >	GetNodeLocation (const unsigned &rNodeIndex)

double	GetDt ()

unsigned	GetNumBirths ()

unsigned	GetNumDeaths ()

std::string	GetOutputDirectory ()

void	SetDt (double dt)

void	SetEndTime (double endTime)

void	SetOutputDirectory (std::string outputDirectory)

void	SetSamplingTimestepMultiple (unsigned samplingTimestepMultiple)

void	SetNoBirth (bool noBirth)

void	SetUpdateCellPopulationRule (bool updateCellPopulation)

bool	GetUpdateCellPopulationRule ()

void	AddCellKiller (boost::shared_ptr< AbstractCellKiller< SPACE_DIM > > pCellKiller)

void	RemoveAllCellKillers ()

void	AddSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > pSimulationModifier)

std::vector< boost::shared_ptr < AbstractCellBasedSimulationModifier < ELEMENT_DIM, SPACE_DIM > > > *	GetSimulationModifiers ()

void	Solve ()

AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation ()

const AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation () const

bool	GetOutputDivisionLocations ()

void	SetOutputDivisionLocations (bool outputDivisionLocations)

bool	GetOutputCellVelocities ()

void	SetOutputCellVelocities (bool outputCellVelocities)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
virtual void	UpdateCellLocationsAndTopology ()

virtual void	UpdateNodePositions ()

virtual void	SetupSolve ()

virtual c_vector< double, SPACE_DIM >	CalculateCellDivisionVector (CellPtr pParentCell)

virtual void	WriteVisualizerSetupFile ()

Protected Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >
virtual unsigned	DoCellBirth ()

unsigned	DoCellRemoval ()

virtual bool	StoppingEventHasOccurred ()

virtual void	UpdateCellPopulation ()

void	OutputSimulationSetup ()

Protected Attributes
std::vector< boost::shared_ptr < AbstractForce< ELEMENT_DIM, SPACE_DIM > > >	mForceCollection

std::vector< boost::shared_ptr < AbstractCellPopulationBoundaryCondition < ELEMENT_DIM, SPACE_DIM > > >	mBoundaryConditions

Protected Attributes inherited from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >
double	mDt

double	mEndTime

AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	mrCellPopulation

bool	mDeleteCellPopulationInDestructor

bool	mInitialiseCells

bool	mNoBirth

bool	mUpdateCellPopulation

std::string	mOutputDirectory

std::string	mSimulationOutputDirectory

out_stream	mpVizSetupFile

unsigned	mNumBirths

unsigned	mNumDeaths

bool	mOutputDivisionLocations

out_stream	mpDivisionLocationFile

bool	mOutputCellVelocities

out_stream	mpCellVelocitiesFile

std::vector< boost::shared_ptr < AbstractCellKiller < SPACE_DIM > > >	mCellKillers

std::vector< boost::shared_ptr < AbstractCellBasedSimulationModifier < ELEMENT_DIM, SPACE_DIM > > >	mSimulationModifiers

unsigned	mSamplingTimestepMultiple

CellBasedPdeHandler< SPACE_DIM > *	mpCellBasedPdeHandler

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

Friends
class	boost::serialization::access

class	TestOffLatticeSimulationWithNodeBasedCellPopulation

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >

Run an off-lattice 2D or 3D cell-based simulation using a cell-centre- or vertex-based cell population.

In cell-centre-based cell populations, each cell is represented by a single node (corresponding to its centre), and connectivity is defined either by a Delaunay triangulation or a radius of influence. In vertex- based cell populations, each cell is represented by a polytope (corresponding to its membrane) with a variable number of vertices.

The OffLatticeSimulation is constructed with a CellPopulation, which updates the correspondence between each Cell and its spatial representation and handles cell division (governed by the CellCycleModel associated with each cell). Once constructed, one or more Force laws may be passed to the OffLatticeSimulation object, to define the mechanical properties of the CellPopulation. Similarly, one or more CellKillers may be passed to the OffLatticeSimulation object to specify conditions in which Cells may die, and one or more CellPopulationBoundaryConditions to specify regions in space beyond which Cells may not move.

Definition at line 69 of file OffLatticeSimulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OffLatticeSimulation	(	AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &	rCellPopulation,
		bool	deleteCellPopulationInDestructor = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters

rCellPopulation	Reference to a cell population object
deleteCellPopulationInDestructor	Whether to delete the cell population on destruction to free up memory (defaults to false)
initialiseCells	Whether to initialise cells (defaults to true, set to false when loading from an archive)

Definition at line 50 of file OffLatticeSimulation.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AddCellKiller(), EXCEPTION, MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mDt, and NEVER_REACHED.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationBoundaryCondition ( boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition )

Add a cell population boundary condition to be used in this simulation.

Parameters

pBoundaryCondition pointer to a boundary condition

Definition at line 97 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::AddForce ( boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce )

Add a force to be used in this simulation (use this to set the mechanics system).

Parameters

pForce pointer to a force law

Definition at line 85 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector ( CellPtr pParentCell )

protectedvirtual

Overridden CalculateCellDivisionVector() method for determining how cell division occurs. This method returns a vector which is then passed into the CellPopulation method AddCell(). This method may be overridden by subclasses.

For a centre-based cell population, this method calculates the new locations of the cell centres of a dividing cell, moves the parent cell and returns the location of the daughter cell. The new locations are found by picking a random direction and placing the parent and daughter in opposing directions along this axis.

For a vertex-based cell population, the method calls the AbstractVertexBasedDivisionRule which is a member of the cell population.

Parameters

pParentCell the parent cell

Returns: a vector containing information on cell division.

Todo:: #2400 Could remove this dynamic_cast by moving the code block below into AbstractCentreBasedCellPopulation::AddCell(), allowing it to be overruled by this method when overridden in subclasses. See also comment on #1093.

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in CryptSimulation2d, and CryptSimulation1d.

Definition at line 138 of file OffLatticeSimulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation(), VertexBasedCellPopulation< SPACE_DIM >::GetVertexBasedDivisionRule(), RandomNumberGenerator::Instance(), NEVER_REACHED, and RandomNumberGenerator::ranf().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputAdditionalSimulationSetup ( out_stream & rParamsFile )

virtual

Overridden OutputAdditionalSimulationSetup method to output the force and cell population boundary condition information.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 318 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters ( out_stream & rParamsFile )

virtual

Outputs simulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in CryptSimulation2d, and CryptSimulation1d.

Definition at line 344 of file OffLatticeSimulation.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().

Referenced by CryptSimulation1d::OutputSimulationParameters(), and CryptSimulation2d::OutputSimulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RemoveAllCellPopulationBoundaryConditions ( )

Method to remove all the cell population boundary conditions

Definition at line 103 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RemoveAllForces ( )

Method to remove all the Forces

Definition at line 91 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Save or restore the simulation.

Parameters

archive	the archive
version	the current version of this class

Definition at line 84 of file OffLatticeSimulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve ( )

protectedvirtual

Overridden SetupSolve() method to clear the forces applied to the nodes.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in CryptSimulation2d.

Definition at line 305 of file OffLatticeSimulation.cpp.

Referenced by CryptSimulation2d::SetupSolve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellLocationsAndTopology ( )

protectedvirtual

Overridden UpdateCellLocationsAndTopology() method.

Calculate forces and update node positions.

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 109 of file OffLatticeSimulation.cpp.

References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), and GenericEventHandler< 11, CellBasedEventHandler >::EndEvent().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions ( )

protectedvirtual

Moves each node to a new position for this timestep by calling the CellPopulation::UpdateNodeLocations() method then applying any boundary conditions.

Definition at line 267 of file OffLatticeSimulation.cpp.

References EXCEPTION, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::WriteVisualizerSetupFile ( )

protectedvirtual

Overridden WriteVisualizerSetupFile() method.

Todo:: Check whether this comment is still valid

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 231 of file OffLatticeSimulation.cpp.

References PetscTools::AmMaster().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 74 of file OffLatticeSimulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mBoundaryConditions

protected

List of boundary conditions.

Definition at line 97 of file OffLatticeSimulation.hpp.

Referenced by OffLatticeSimulation< 2 >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection

protected

The mechanics used to determine the new location of the cells, a list of the forces.

Definition at line 94 of file OffLatticeSimulation.hpp.

Referenced by OffLatticeSimulation< 2 >::serialize().

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

cell_based/src/simulation/OffLatticeSimulation.hpp
cell_based/src/simulation/OffLatticeSimulation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >