#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	SetNumericalMethod (boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > pNumericalMethod)

const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > >	GetNumericalMethod () const

void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

virtual void	OutputSimulationParameters (out_stream &rParamsFile)

const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > &	rGetForceCollection () const

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 ()

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 ()

void	RevertToOldLocations (std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)

void	ApplyBoundaries (std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)

virtual void	SetupSolve ()

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

boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > >	mpNumericalMethod

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

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

Friends
class	boost::serialization::access

class	TestOffLatticeSimulation

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 an off-lattice 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. Alternative cell populations may be defined by the user.

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 71 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 45 of file OffLatticeSimulation.cpp.

References EXCEPTION.

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 69 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mBoundaryConditions.

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 57 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::ApplyBoundaries ( std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions )

protected

Applies any boundary conditions.

Parameters

oldNodeLoctions Mapping between node indices and old node locations

Definition at line 169 of file OffLatticeSimulation.cpp.

References EXCEPTION, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mBoundaryConditions.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellLocationsAndTopology().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::GetNumericalMethod ( ) const

Returns: the current numerical method.

Definition at line 87 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overridden OutputAdditionalSimulationSetup() method.

Output any force, boundary condition or numerical method information.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 226 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mBoundaryConditions, OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overridden OutputSimulationParameters() method.

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 257 of file OffLatticeSimulation.cpp.

References EXPORT_TEMPLATE_CLASS_ALL_DIMS, and 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 75 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mBoundaryConditions.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Remove all the forces.

Definition at line 63 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RevertToOldLocations ( std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions )

protected

Sends nodes back to the positions given in the input map. Used after a failed step when adaptivity is turned on.

Parameters

oldNodeLoctions A map linking nodes to their old positions.

Definition at line 158 of file OffLatticeSimulation.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellLocationsAndTopology().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > & OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::rGetForceCollection ( ) const

Directly access the forces attached to this simulation, to allow their manipulation after archiving.

Returns: mForceCollection the vector of pointers to forces attached to this simulation

Definition at line 93 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection.

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 87 of file OffLatticeSimulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetNumericalMethod ( boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > pNumericalMethod )

Set the numerical method to be used in this simulation (use this to solve the mechanics system).

Parameters

pNumericalMethod pointer to a numerical method object

Definition at line 81 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod.

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 206 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection, OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod, and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation.

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.

Todo:: #2087 Make this a settable member variable

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 99 of file OffLatticeSimulation.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::ApplyBoundaries(), GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), EXCEPTION, StepSizeException::GetSuggestedNewStep(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mDt, OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation, OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RevertToOldLocations(), and StepSizeException::what().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protectedvirtual

Overridden WriteVisualizerSetupFile() method.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 192 of file OffLatticeSimulation.cpp.

References PetscTools::AmMaster(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mForceCollection, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mpVizSetupFile, and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation.

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 76 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 101 of file OffLatticeSimulation.hpp.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationBoundaryCondition(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::ApplyBoundaries(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputAdditionalSimulationSetup(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RemoveAllCellPopulationBoundaryConditions(), and 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 98 of file OffLatticeSimulation.hpp.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::AddForce(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputAdditionalSimulationSetup(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::RemoveAllForces(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::rGetForceCollection(), OffLatticeSimulation< 2 >::serialize(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve(), and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::WriteVisualizerSetupFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNumericalMethod

protected

The numerical method to use in this simulation. Defaults to the explicit forward Euler method.

Definition at line 104 of file OffLatticeSimulation.hpp.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::GetNumericalMethod(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputAdditionalSimulationSetup(), OffLatticeSimulation< 2 >::serialize(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetNumericalMethod(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve(), and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellLocationsAndTopology().

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 >