TissueSimulation< DIM > Class Template Reference

#include <TissueSimulation.hpp>

Inheritance diagram for TissueSimulation< DIM >:

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List of all members.

Public Member Functions

 TissueSimulation (AbstractTissue< DIM > &rTissue, std::vector< AbstractForce< DIM > * > forceCollection, bool deleteTissueAndForceCollection=false, bool initialiseCells=true)
virtual ~TissueSimulation ()
std::vector< double > GetNodeLocation (const unsigned &rNodeIndex)
c_vector< unsigned,
NUM_CELL_MUTATION_STATES > 		GetCellMutationStateCount ()
c_vector< unsigned,
NUM_CELL_TYPES > 		GetCellTypeCount ()
c_vector< unsigned, 5 > GetCellCyclePhaseCount ()
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 SetOutputCellMutationStates (bool outputCellMutationStates)
void SetOutputCellAncestors (bool outputCellAncestors)
void SetOutputCellTypes (bool outputCellTypes)
void SetOutputCellVariables (bool outputCellVariables)
void SetOutputCellCyclePhases (bool outputCellCyclePhases)
void SetUpdateTissueRule (bool updateTissue)
void AddCellKiller (AbstractCellKiller< DIM > *pCellKiller)
void Solve ()
AbstractTissue< DIM > & rGetTissue ()
const AbstractTissue< DIM > & rGetTissue () const
const std::vector
< AbstractForce< DIM > * > 		rGetForceCollection () const

Protected Member Functions

template<class Archive>
void serialize (Archive &archive, const unsigned int version)
virtual void WriteVisualizerSetupFile ()
unsigned DoCellBirth ()
virtual c_vector< double, DIM > CalculateDividingCellCentreLocations (TissueCell *pParentCell)
unsigned DoCellRemoval ()
virtual void UpdateNodePositions (const std::vector< c_vector< double, DIM > > &rNodeForces)
virtual void ApplyTissueBoundaryConditions (const std::vector< c_vector< double, DIM > > &rOldLocations)
virtual void PostSolve ()
virtual void SetupSolve ()
virtual void AfterSolve ()
virtual bool StoppingEventHasOccurred ()

Protected Attributes

double mDt
double mEndTime
AbstractTissue< DIM > & mrTissue
bool mDeleteTissue
bool mAllocatedMemoryForForceCollection
bool mInitialiseCells
bool mNoBirth
bool mUpdateTissue
bool mOutputCellMutationStates
bool mOutputCellAncestors
bool mOutputCellTypes
bool mOutputCellVariables
bool mOutputCellCyclePhases
std::string mOutputDirectory
std::string mSimulationOutputDirectory
out_stream mpSetupFile
CancerParameters * mpParams
RandomNumberGenerator * mpRandomGenerator
unsigned mNumBirths
unsigned mNumDeaths
unsigned mSamplingTimestepMultiple
std::vector
< AbstractCellKiller< DIM > * > 		mCellKillers
std::vector< AbstractForce
< DIM > * > 		mForceCollection

Friends

class TestCryptSimulation2d
class TestTissueSimulation3d
class boost::serialization::access

Detailed Description

template<unsigned DIM>
class TissueSimulation< DIM >

Run a 2D or 3D tissue simulation, currently based on the Meineke Paper (doi:10.1046/j.0960-7722.2001.00216.x)

Cells are represented by their centres in space, they are connected by springs defined by the cells' Delaunay/Voronoi tesselation.

The spring lengths are governed by the equations dr/dt = stem_cycle_time*(mu/eta) sum_j r_hat_i,j*(|r_i,j|-s0) = alpha sum_j r_hat_i,j*(|r_i,j|-s0)

where alpha = stem_cycle_time*(mu/eta) = stem_cycle_time*meineke_lambda. s0 = natural length of the spring.

Length is scaled by natural length. Time is in hours.

meineke_lambda = mu (spring constant) / eta (damping) = 0.01 (from Meineke - note that the value we use for Meineke lambda is completely different because we have nondimensionalised)

The TissueSimulation accepts a tissue (facade class), containing either a mesh or just a vector of nodes, where nodes are associated with TissueCells or are ghost nodes. The TissueSimulation then accesses only the TissueCells via an iterator in the tissue facade class.

If simulating a crypt with a mesh-based tissue, the mesh should be surrounded by at least one layer of ghost nodes. These are nodes which do not correspond to a cell, but are necessary for remeshing (because the remesher tries to create a convex hull of the set of nodes) and visualization purposes. The MeshBasedTissueWithGhostNodes class deals with ghost nodes.

Cells can divide (at a time governed by their cell cycle models).

Cells can die - at a time/position specified by cell killers which can be added to the simulation.

Definition at line 84 of file TissueSimulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
TissueSimulation< DIM >::TissueSimulation ( AbstractTissue< DIM > &  rTissue,
std::vector< AbstractForce< DIM > * >  forceCollection,
bool  deleteTissueAndForceCollection = false,
bool  initialiseCells = true 
) [inline]

Constructor.

Parameters:
rTissue A tissue facade class (contains a mesh and cells)
forceCollection The mechanics to use in the simulation
deleteTissueAndForceCollection Whether to delete the tissue and force collection on destruction to free up memory
initialiseCells Whether to initialise cells (set to false when loading from an archive)

Definition at line 41 of file TissueSimulation.cpp.

References CancerParameters::Instance(), TissueSimulation< DIM >::mAllocatedMemoryForForceCollection, TissueSimulation< DIM >::mDeleteTissue, TissueSimulation< DIM >::mDt, TissueSimulation< DIM >::mEndTime, TissueSimulation< DIM >::mForceCollection, TissueSimulation< DIM >::mInitialiseCells, TissueSimulation< DIM >::mNoBirth, TissueSimulation< DIM >::mNumBirths, TissueSimulation< DIM >::mNumDeaths, TissueSimulation< DIM >::mOutputCellAncestors, TissueSimulation< DIM >::mOutputCellCyclePhases, TissueSimulation< DIM >::mOutputCellMutationStates, TissueSimulation< DIM >::mOutputCellTypes, TissueSimulation< DIM >::mOutputCellVariables, TissueSimulation< DIM >::mOutputDirectory, TissueSimulation< DIM >::mpParams, TissueSimulation< DIM >::mpRandomGenerator, TissueSimulation< DIM >::mrTissue, TissueSimulation< DIM >::mSamplingTimestepMultiple, TissueSimulation< DIM >::mSimulationOutputDirectory, and TissueSimulation< DIM >::mUpdateTissue.

template<unsigned DIM>
TissueSimulation< DIM >::~TissueSimulation (  )  [inline, virtual]

Destructor.

This frees the tissue and cell killers, if they were created by de-serialization.

Definition at line 97 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mAllocatedMemoryForForceCollection, TissueSimulation< DIM >::mCellKillers, TissueSimulation< DIM >::mDeleteTissue, TissueSimulation< DIM >::mForceCollection, and TissueSimulation< DIM >::mrTissue.

Member Function Documentation

template<unsigned DIM>
template<class Archive>
void TissueSimulation< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, protected]

Archive the member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:
archive 
version 

Reimplemented in CryptSimulation2d.

Definition at line 179 of file TissueSimulation.hpp.

template<unsigned DIM>
virtual void TissueSimulation< DIM >::WriteVisualizerSetupFile (  )  [inline, protected, virtual]

Writes out special information about the mesh to the visualizer.

Reimplemented in CryptSimulation2d.

Definition at line 211 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::DoCellBirth (  )  [inline, protected]

During a simulation time step, process any cell divisions that need to occur. If the simulation includes cell birth, causes (almost) all cells that are ready to divide to produce daughter cells.

Returns:
the number of births that occurred.

Definition at line 123 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), TissueSimulation< DIM >::mNoBirth, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::AfterSolve(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
c_vector< double, DIM > TissueSimulation< DIM >::CalculateDividingCellCentreLocations ( TissueCell *  pParentCell  )  [inline, protected, virtual]

Calculates the new locations of a dividing cell's cell centres. Moves the dividing node a bit and returns co-ordinates for the new node. It does this by picking a random direction (0->2PI) and placing the parent and daughter in opposing directions on this axis.

Parameters:
pParentCell pointer to the parent cell
Returns:
daughter_coords The coordinates for the daughter cell.

Reimplemented in CryptSimulation2d.

Definition at line 191 of file TissueSimulation.cpp.

References CancerParameters::GetDivisionSeparation(), CancerParameters::Instance(), and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::DoCellBirth().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::DoCellRemoval (  )  [inline, protected]

During a simulation time step, process any cell sloughing or death

This uses the cell killers to remove cells and associated nodes from the facade class.

Returns:
the number of deaths that occurred.

Definition at line 164 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mCellKillers, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::AfterSolve(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
void TissueSimulation< DIM >::UpdateNodePositions ( const std::vector< c_vector< double, DIM > > &  rNodeForces  )  [inline, protected, virtual]

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

Parameters:
rNodeForces the forces on nodes

Definition at line 240 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::ApplyTissueBoundaryConditions(), TissueSimulation< DIM >::mDt, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::ApplyTissueBoundaryConditions ( const std::vector< c_vector< double, DIM > > &  rOldLocations  )  [inline, protected, virtual]

Apply any tissue boundary conditions. Can be overridden in subclasses.

Parameters:
rOldLocations 

Definition at line 261 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::UpdateNodePositions().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::PostSolve (  )  [inline, protected, virtual]

A method for subclasses to do something at the end of each timestep

Reimplemented in CryptSimulation2d.

Definition at line 268 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::SetupSolve (  )  [inline, protected, virtual]

A method for subclasses to do something at before the start of the time loop

Reimplemented in CryptSimulation2d.

Definition at line 275 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
void TissueSimulation< DIM >::AfterSolve (  )  [inline, protected, virtual]

Implements out cell birth, cell death and a tissue update if necessary for a final time. This method may be overridden in subclasses to do something at the end of each time loop. Note that each subclass should also call the base class method.

Reimplemented in CryptSimulation2d.

Definition at line 628 of file TissueSimulation.cpp.

References GenericEventHandler< 9, CancerEventHandler >::BeginEvent(), TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< DIM >::DoCellRemoval(), GenericEventHandler< 9, CancerEventHandler >::EndEvent(), SimulationTime::Instance(), TissueSimulation< DIM >::mNumBirths, TissueSimulation< DIM >::mNumDeaths, TissueSimulation< DIM >::mrTissue, and TissueSimulation< DIM >::mUpdateTissue.

Referenced by CryptSimulation2d::AfterSolve(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
bool TissueSimulation< DIM >::StoppingEventHasOccurred (  )  [inline, protected, virtual]

A child class can overload this if they want the simulation to stop based on certain conditions before the specified end time (for example, run until a crypt becomes monoclonal).

Definition at line 670 of file TissueSimulation.cpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
std::vector< double > TissueSimulation< DIM >::GetNodeLocation ( const unsigned &  rNodeIndex  )  [inline]

Get a node's location (ONLY FOR TESTING)

Parameters:
rNodeIndex the node index
Returns:
the co-ordinates of this node.

Definition at line 391 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
c_vector< unsigned, NUM_CELL_MUTATION_STATES > TissueSimulation< DIM >::GetCellMutationStateCount (  )  [inline]

Find out how many cells of each mutation state there are

Returns:
The number of cells of each mutation state (evaluated at each visualizer output) [0] = healthy count [1] = labelled cells [2] = APC one hit [3] = APC two hit [4] = beta catenin one hit

Definition at line 677 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellMutationStates, and TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
c_vector< unsigned, NUM_CELL_TYPES > TissueSimulation< DIM >::GetCellTypeCount (  )  [inline]

Find out how many cells of each type there are

Returns:
The number of cells of each type (evaluated at each visualizer output) [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED [3] = APOPTOTIC

Definition at line 688 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellTypes, and TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
c_vector< unsigned, 5 > TissueSimulation< DIM >::GetCellCyclePhaseCount (  )  [inline]

Find out how many cells in each cell cycle phase there are

Returns:
The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 699 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellCyclePhases, and TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
double TissueSimulation< DIM >::GetDt (  )  [inline]

Returns:
the timestep of the simulation

Definition at line 269 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mDt.

template<unsigned DIM>
unsigned TissueSimulation< DIM >::GetNumBirths (  )  [inline]

Returns:
the number of births that have occurred in the entire simulation (since t=0)

Definition at line 276 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNumBirths.

template<unsigned DIM>
unsigned TissueSimulation< DIM >::GetNumDeaths (  )  [inline]

Returns:
the number of deaths that have occurred in the entire simulation (since t=0).

Definition at line 283 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNumDeaths.

template<unsigned DIM>
std::string TissueSimulation< DIM >::GetOutputDirectory ( void   )  [inline]

Get the output directory of the simulation.

Definition at line 306 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputDirectory.

template<unsigned DIM>
void TissueSimulation< DIM >::SetDt ( double  dt  )  [inline]

Set the timestep of the simulation.

Parameters:
dt the timestep to use

Definition at line 261 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mDt.

template<unsigned DIM>
void TissueSimulation< DIM >::SetEndTime ( double  endTime  )  [inline]

Set the end time and resets the timestep to be endtime/100.

Parameters:
endTime the end time to use

Definition at line 290 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mEndTime.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputDirectory ( std::string  outputDirectory  )  [inline]

Set the output directory of the simulation.

Parameters:
outputDirectory the output directory to use

Definition at line 298 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputDirectory, and TissueSimulation< DIM >::mSimulationOutputDirectory.

template<unsigned DIM>
void TissueSimulation< DIM >::SetSamplingTimestepMultiple ( unsigned  samplingTimestepMultiple  )  [inline]

Set the ratio of the number of actual timesteps to the number of timesteps at which results are written to file. Default value is set to 1 by the constructor.

Parameters:
samplingTimestepMultiple the ratio to use

Definition at line 313 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mSamplingTimestepMultiple.

template<unsigned DIM>
void TissueSimulation< DIM >::SetNoBirth ( bool  noBirth  )  [inline]

Set the simulation to run with no birth.

Parameters:
noBirth whether to run with no birth

Definition at line 342 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNoBirth.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputCellMutationStates ( bool  outputCellMutationStates  )  [inline]

Set the simulation to count and store the number of each cell mutation state.

Parameters:
outputCellMutationStates whether to output cell mutation states

Definition at line 349 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellMutationStates.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputCellAncestors ( bool  outputCellAncestors  )  [inline]

Set the simulation to output the cell ancestors if they are set.

Parameters:
outputCellAncestors whether to output cell ancestors

Definition at line 363 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellAncestors.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputCellTypes ( bool  outputCellTypes  )  [inline]

Set the simulation to count and store the number of each cell type.

Parameters:
outputCellTypes whether to output cell types

Definition at line 356 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellTypes.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputCellVariables ( bool  outputCellVariables  )  [inline]

Set the simulation to output the cell-cycle variables.

Parameters:
outputCellVariables whether to output cell-cycle variables

Definition at line 370 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellVariables.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputCellCyclePhases ( bool  outputCellCyclePhases  )  [inline]

Set the simulation to output the cell cycle phases.

The test for this method is in TestCryptSimulation2d::TestStandardResultForArchivingTestsBelow().

Parameters:
outputCellCyclePhases whether to output cell-cycle phases

Definition at line 377 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>
void TissueSimulation< DIM >::SetUpdateTissueRule ( bool  updateTissue  )  [inline]

Set whether to update the topology of the tissue at each time step.

Parameters:
updateTissue whether to update the tissue each time step

Definition at line 335 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mUpdateTissue.

template<unsigned DIM>
void TissueSimulation< DIM >::AddCellKiller ( AbstractCellKiller< DIM > *  pCellKiller  )  [inline]

Add a cell killer to be used in this simulation.

Parameters:
pCellKiller pointer to a cell killer

Definition at line 384 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mCellKillers.

template<unsigned DIM>
void TissueSimulation< DIM >::Solve (  )  [inline]

Main solve method.

This method sets up the simulation time, creates output files, and initialises the tissue. It then iterates through a time loop. At each time step, first any cell death or birth is implemented, then the tissue topology is updated, then the forces are recalculated and the tissue evolved according to whatever force laws are present in the simulation, and finally the results for that time step are output to file. At the end of the time loop, the method closes any output files.

If the tissue has a mesh, then we currently must call the Update() method at each time step. Otherwise, we only need to call Update() after there has been any cell birth or cell death.

Definition at line 403 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::AfterSolve(), GenericEventHandler< 9, CancerEventHandler >::BeginEvent(), TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< DIM >::DoCellRemoval(), GenericEventHandler< 9, CancerEventHandler >::EndEvent(), SimulationTime::GetTime(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::IncrementTimeOneStep(), SimulationTime::Instance(), TissueSimulation< DIM >::mDt, TissueSimulation< DIM >::mEndTime, TissueSimulation< DIM >::mForceCollection, TissueSimulation< DIM >::mNumBirths, TissueSimulation< DIM >::mNumDeaths, TissueSimulation< DIM >::mOutputCellAncestors, TissueSimulation< DIM >::mOutputCellCyclePhases, TissueSimulation< DIM >::mOutputCellMutationStates, TissueSimulation< DIM >::mOutputCellTypes, TissueSimulation< DIM >::mOutputCellVariables, TissueSimulation< DIM >::mOutputDirectory, TissueSimulation< DIM >::mpSetupFile, TissueSimulation< DIM >::mrTissue, TissueSimulation< DIM >::mSamplingTimestepMultiple, TissueSimulation< DIM >::mSimulationOutputDirectory, TissueSimulation< DIM >::mUpdateTissue, OutputFileHandler::OpenOutputFile(), TissueSimulation< DIM >::PostSolve(), SimulationTime::ResetEndTimeAndNumberOfTimeSteps(), SimulationTime::SetEndTimeAndNumberOfTimeSteps(), TissueSimulation< DIM >::SetupSolve(), TissueSimulation< DIM >::StoppingEventHasOccurred(), TissueSimulation< DIM >::UpdateNodePositions(), and TissueSimulation< DIM >::WriteVisualizerSetupFile().

template<unsigned DIM>
AbstractTissue< DIM > & TissueSimulation< DIM >::rGetTissue (  )  [inline]

Returns:
reference to the tissue.

Definition at line 321 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
const AbstractTissue< DIM > & TissueSimulation< DIM >::rGetTissue (  )  const [inline]

Returns:
const reference to the tissue (used in archiving).

Definition at line 328 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
const std::vector< AbstractForce< DIM > * > TissueSimulation< DIM >::rGetForceCollection (  )  const [inline]

Returns:
const reference to mForceCollection (used in archiving).

Definition at line 184 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mForceCollection.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented in CryptSimulation2d.

Definition at line 166 of file TissueSimulation.hpp.

Member Data Documentation

template<unsigned DIM>
double TissueSimulation< DIM >::mDt [protected]

Time step.

Definition at line 94 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetDt(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetDt(), TissueSimulation< DIM >::Solve(), TissueSimulation< DIM >::TissueSimulation(), and TissueSimulation< DIM >::UpdateNodePositions().

template<unsigned DIM>
double TissueSimulation< DIM >::mEndTime [protected]

Time to run the Solve() method up to.

Definition at line 97 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetEndTime(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
AbstractTissue<DIM>& TissueSimulation< DIM >::mrTissue [protected]

Facade encapsulating cells in the tissue being simulated.

Definition at line 100 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AfterSolve(), TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< DIM >::DoCellRemoval(), TissueSimulation< DIM >::GetCellCyclePhaseCount(), TissueSimulation< DIM >::GetCellMutationStateCount(), TissueSimulation< DIM >::GetCellTypeCount(), TissueSimulation< DIM >::GetNodeLocation(), TissueSimulation< DIM >::rGetTissue(), TissueSimulation< DIM >::Solve(), TissueSimulation< DIM >::TissueSimulation(), TissueSimulation< DIM >::UpdateNodePositions(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mDeleteTissue [protected]

Whether to delete the facade in the destructor.

Definition at line 103 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::TissueSimulation(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mAllocatedMemoryForForceCollection [protected]

Whether delete the collection of force laws in the destructor.

Definition at line 106 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::TissueSimulation(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mInitialiseCells [protected]

Whether to initialise the cells.

Definition at line 109 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mNoBirth [protected]

Whether to run the simulation with no birth (defaults to false).

Definition at line 112 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetNoBirth(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mUpdateTissue [protected]

Whether to update the topology of the tissue at each time step (defaults to true).

Definition at line 115 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AfterSolve(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetUpdateTissueRule(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mOutputCellMutationStates [protected]

Whether to count the number of each cell mutation state and output to file

Definition at line 118 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetCellMutationStateCount(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputCellMutationStates(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mOutputCellAncestors [protected]

Whether to output the ancestor of each cell to a visualizer file

Definition at line 121 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputCellAncestors(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mOutputCellTypes [protected]

Whether to count the number of each cell type and output to file

Definition at line 124 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetCellTypeCount(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputCellTypes(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mOutputCellVariables [protected]

Whether to write the cell variables to a file

Definition at line 127 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputCellVariables(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mOutputCellCyclePhases [protected]

Whether to write the cell cycle phases to a file

Definition at line 130 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetCellCyclePhaseCount(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputCellCyclePhases(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
std::string TissueSimulation< DIM >::mOutputDirectory [protected]

Output directory (a subfolder of tmp/[USERNAME]/testoutput)

Definition at line 133 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetOutputDirectory(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputDirectory(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
std::string TissueSimulation< DIM >::mSimulationOutputDirectory [protected]

Simulation Output directory either the same as mOutputDirectory or includes mOutputDirectory/results_from_time_[TIME]

Definition at line 136 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::SetOutputDirectory(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
out_stream TissueSimulation< DIM >::mpSetupFile [protected]

Visualiser setup file

Definition at line 139 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
CancerParameters* TissueSimulation< DIM >::mpParams [protected]

The Meineke and cancer parameters

Definition at line 142 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
RandomNumberGenerator* TissueSimulation< DIM >::mpRandomGenerator [protected]

The singleton RandomNumberGenerator

Definition at line 145 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mNumBirths [protected]

Counts the number of births during the simulation

Definition at line 148 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AfterSolve(), TissueSimulation< DIM >::GetNumBirths(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mNumDeaths [protected]

Counts the number of deaths during the simulation

Definition at line 151 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AfterSolve(), TissueSimulation< DIM >::GetNumDeaths(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mSamplingTimestepMultiple [protected]

The ratio of the number of actual timesteps to the number of timesteps at which results are written to file

Definition at line 157 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetSamplingTimestepMultiple(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
std::vector<AbstractCellKiller<DIM>*> TissueSimulation< DIM >::mCellKillers [protected]

List of cell killers

Definition at line 160 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AddCellKiller(), TissueSimulation< DIM >::DoCellRemoval(), TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
std::vector<AbstractForce<DIM>*> TissueSimulation< DIM >::mForceCollection [protected]

The mechanics used to determine the new location of the cells

Definition at line 163 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::rGetForceCollection(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::Solve(), TissueSimulation< DIM >::TissueSimulation(), and TissueSimulation< DIM >::~TissueSimulation().

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