Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
OnLatticeSimulation< DIM > Class Template Reference

#include <OnLatticeSimulation.hpp>

+ Inheritance diagram for OnLatticeSimulation< DIM >:
+ Collaboration diagram for OnLatticeSimulation< DIM >:

Public Member Functions

 OnLatticeSimulation (AbstractCellPopulation< DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
 
void AddUpdateRule (boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule)
 
void RemoveAllUpdateRules ()
 
void OutputAdditionalSimulationSetup (out_stream &rParamsFile)
 
void OutputSimulationParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractCellBasedSimulation< DIM >
 AbstractCellBasedSimulation (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
 
virtual ~AbstractCellBasedSimulation ()
 
std::vector< doubleGetNodeLocation (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 SetUpdatingTimestepMultiple (unsigned updatingTimestepMultiple)
 
void SetNoBirth (bool noBirth)
 
void SetUpdateCellPopulationRule (bool updateCellPopulation)
 
bool GetUpdateCellPopulationRule ()
 
void AddCellKiller (boost::shared_ptr< AbstractCellKiller< ELEMENT_DIM > > pCellKiller)
 
void RemoveAllCellKillers ()
 
void AddSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > pSimulationModifier)
 
std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > > * GetSimulationModifiers ()
 
void AddTopologyUpdateSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > pSimulationModifier)
 
std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > > * GetTopologyUpdateSimulationModifiers ()
 
void Solve ()
 
AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > & rGetCellPopulation ()
 
const AbstractCellPopulation< ELEMENT_DIM, ELEMENT_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

void UpdateCellPopulation ()
 
void UpdateCellLocationsAndTopology ()
 
- Protected Member Functions inherited from AbstractCellBasedSimulation< DIM >
virtual void WriteVisualizerSetupFile ()
 
virtual unsigned DoCellBirth ()
 
unsigned DoCellRemoval ()
 
virtual void SetupSolve ()
 
virtual bool StoppingEventHasOccurred ()
 
void OutputSimulationSetup ()
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from AbstractCellBasedSimulation< DIM >
double mDt
 
double mEndTime
 
AbstractCellPopulation< ELEMENT_DIM, ELEMENT_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< ELEMENT_DIM > > > mCellKillers
 
std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > > mSimulationModifiers
 
std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, ELEMENT_DIM > > > mTopologyUpdateSimulationModifiers
 
unsigned mSamplingTimestepMultiple
 
unsigned mUpdatingTimestepMultiple
 

Detailed Description

template<unsigned DIM>
class OnLatticeSimulation< DIM >

Run an on-lattice 2D or 3D cell-based simulation.

The OnLatticeSimulation 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 Update rules may be passed to the OnLatticeSimulation object, to define the processes which update cells in the CellPopulation. Similarly, one or more CellKillers may be passed to the OnLatticeSimulation object to specify conditions in which Cells may die.

Definition at line 58 of file OnLatticeSimulation.hpp.

Constructor & Destructor Documentation

◆ OnLatticeSimulation()

template<unsigned DIM>
OnLatticeSimulation< DIM >::OnLatticeSimulation ( AbstractCellPopulation< DIM > &  rCellPopulation,
bool  deleteCellPopulationInDestructor = false,
bool  initialiseCells = true 
)

Constructor.

Parameters
rCellPopulationA cell population object
deleteCellPopulationInDestructorWhether to delete the cell population on destruction to free up memory (defaults to false)
initialiseCellsWhether to initialise cells (defaults to true, set to false when loading from an archive)

Definition at line 41 of file OnLatticeSimulation.cpp.

References EXCEPTION.

Member Function Documentation

◆ AddUpdateRule()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractUpdateRule< DIM > >  pUpdateRule)

Add an update rule to be used in this simulation.

Parameters
pUpdateRuleshared pointer to an update rule law

Definition at line 55 of file OnLatticeSimulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::AddUpdateRule().

◆ OutputAdditionalSimulationSetup()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::OutputAdditionalSimulationSetup ( out_stream &  rParamsFile)
virtual

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

Parameters
rParamsFilethe file stream to which the parameters are output

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 87 of file OnLatticeSimulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::GetUpdateRuleCollection().

◆ OutputSimulationParameters()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::OutputSimulationParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputSimulationParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 107 of file OnLatticeSimulation.cpp.

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

◆ RemoveAllUpdateRules()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::RemoveAllUpdateRules ( )

Remove any update rules that have previously been passed to the cell population.

Definition at line 62 of file OnLatticeSimulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::RemoveAllUpdateRules().

◆ serialize()

template<unsigned DIM>
template<class Archive >
void OnLatticeSimulation< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and any member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 71 of file OnLatticeSimulation.hpp.

◆ UpdateCellLocationsAndTopology()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology ( )
protectedvirtual

◆ UpdateCellPopulation()

template<unsigned DIM>
void OnLatticeSimulation< DIM >::UpdateCellPopulation ( )
protectedvirtual

Overridden UpdateCellPopulation() method.

If using a CaBasedCellPopulation, this method does nothing if at the start of a simulation that has just been loaded, to ensure consistency in random number generation.

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 77 of file OnLatticeSimulation.cpp.

References SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellPopulation().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 63 of file OnLatticeSimulation.hpp.


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