#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 ()
bool	GetOutputNodeVelocities ()
void	SetOutputNodeVelocities (bool outputNodeVelocities)
void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)
virtual void	OutputSimulationParameters (out_stream &rParamsFile)
Protected Member Functions
virtual void	UpdateCellLocationsAndTopology ()
virtual void	UpdateNodePositions (const std::vector< c_vector< double, SPACE_DIM > > &rNodeForces)
virtual void	SetupSolve ()
virtual void	UpdateAtEndOfSolve ()
virtual c_vector< double, SPACE_DIM >	CalculateCellDivisionVector (CellPtr pParentCell)
virtual void	WriteVisualizerSetupFile ()
Protected Attributes
std::vector< boost::shared_ptr < AbstractForce< ELEMENT_DIM, SPACE_DIM > > >	mForceCollection
std::vector< boost::shared_ptr < AbstractCellPopulationBoundaryCondition < ELEMENT_DIM, SPACE_DIM > > >	mBoundaryConditions
bool	mOutputNodeVelocities
out_stream	mpNodeVelocitiesFile
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

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 EXCEPTION, and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mDt.

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 86 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 74 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector ( CellPtr pParentCell ) [protected, virtual]

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 returns the zero vector.

Parameters:

pParentCell the parent cell

Returns:: a vector containing information on cell division.

Todo:: 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.

Todo:: do something for vertex models here

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in CryptSimulation1d, and CryptSimulation2d.

Definition at line 137 of file OffLatticeSimulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::GetOutputNodeVelocities ( )

Returns:: mOutputNodeVelocities

Definition at line 392 of file OffLatticeSimulation.cpp.

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 366 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 CryptSimulation1d, and CryptSimulation2d.

Definition at line 404 of file OffLatticeSimulation.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::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 92 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 80 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
	)		`[inline, private]`

Save or restore the simulation.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in DeltaNotchOffLatticeSimulation< DIM >, VolumeTrackedOffLatticeSimulation< DIM >, CryptSimulation1d, and CryptSimulation2d.

Definition at line 83 of file OffLatticeSimulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetOutputNodeVelocities ( bool outputNodeVelocities )

Set mOutputNodeVelocities.

Parameters:

outputNodeVelocities the new value of mOutputNodeVelocities

Definition at line 398 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve ( ) [protected, virtual]

Overridden SetupSolve() method to setup the node velocities file.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in DeltaNotchOffLatticeSimulation< DIM >, VolumeTrackedOffLatticeSimulation< DIM >, and CryptSimulation2d.

Definition at line 347 of file OffLatticeSimulation.cpp.

References PetscTools::AmMaster(), and OutputFileHandler::OpenOutputFile().

Referenced by DeltaNotchOffLatticeSimulation< DIM >::SetupSolve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateAtEndOfSolve ( ) [protected, virtual]

Overridden UpdateAtEndOfSolve() method to close the node velocities file.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in CryptSimulation2d.

Definition at line 357 of file OffLatticeSimulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellLocationsAndTopology ( ) [protected, virtual]

Overridden UpdateCellLocationsAndTopology() method.

Calculate forces and update node positions.

Todo:: Is it faster to preallocate and have forces as a member variable? see #1890

Implements AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 98 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 ( const std::vector< c_vector< double, SPACE_DIM > > & rNodeForces ) [protected, virtual]

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

Parameters:

rNodeForces the forces on nodes

Definition at line 247 of file OffLatticeSimulation.cpp.

References PetscTools::AmMaster(), PetscTools::BeginRoundRobin(), EXCEPTION, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode(), OutputFileHandler::OpenOutputFile(), and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::WriteVisualizerSetupFile ( ) [protected, virtual]

Overridden WriteVisualizerSetupFile() method.

Todo:: Check whether this comment is still valid

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 211 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.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in DeltaNotchOffLatticeSimulation< DIM >, VolumeTrackedOffLatticeSimulation< DIM >, CryptSimulation1d, and CryptSimulation2d.

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().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mOutputNodeVelocities [protected]

Whether to write the node velocities to a file.

Definition at line 100 of file OffLatticeSimulation.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

out_stream OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::mpNodeVelocitiesFile [protected]

Results file node velocities.

Definition at line 103 of file OffLatticeSimulation.hpp.

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 >