#include <AbstractCellBasedSimulation.hpp>
Inheritance diagram for AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >: Collaboration diagram for AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >:Public Member Functions | |
| 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) |
| virtual void | OutputSimulationParameters (out_stream &rParamsFile)=0 |
| Public Member Functions inherited from Identifiable | |
| virtual | ~Identifiable () |
| std::string | GetIdentifier () const |
Protected Member Functions | |
| virtual void | WriteVisualizerSetupFile () |
| virtual unsigned | DoCellBirth () |
| unsigned | DoCellRemoval () |
| virtual void | SetupSolve () |
| virtual bool | StoppingEventHasOccurred () |
| virtual void | UpdateCellPopulation () |
| virtual void | UpdateCellLocationsAndTopology ()=0 |
| void | OutputSimulationSetup () |
| virtual void | OutputAdditionalSimulationSetup (out_stream &rParamsFile)=0 |
Protected Attributes | |
| 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 | TestCryptSimulation2d |
| class | TestOffLatticeSimulation3d |
| class | TestOffLatticeSimulation |
| class | boost::serialization::access |
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >
An abstract cell-based simulation class. This class contains common functionality from off lattice and on lattice simulations.
The AbstractCellBasedSimulation 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 CellKillers may be passed to the AbstractCellBasedSimulation object to specify conditions in which Cells may die,
Subclasses use one or more Force laws or update rules (Which are passed to the child class object) to define the mechanical properties of the CellPopulation.
Definition at line 67 of file AbstractCellPopulation.hpp.
Constructor & Destructor Documentation
| AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation | ( | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & | rCellPopulation, |
| bool | deleteCellPopulationInDestructor = false, |
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| bool | initialiseCells = true |
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| ) |
Constructor.
- Parameters
-
rCellPopulation 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 48 of file AbstractCellBasedSimulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDefaultTimeStep(), RandomNumberGenerator::Instance(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mDt, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mInitialiseCells, and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation.
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virtual |
Destructor.
This frees the cell population if it was created by de-serialization.
Definition at line 82 of file AbstractCellBasedSimulation.cpp.
Member Function Documentation
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AddCellKiller | ( | boost::shared_ptr< AbstractCellKiller< SPACE_DIM > > | pCellKiller | ) |
Add a cell killer to be used in this simulation.
- Parameters
-
pCellKiller pointer to a cell killer
Definition at line 266 of file AbstractCellBasedSimulation.cpp.
Referenced by VertexBasedCellPopulation< SPACE_DIM >::SimulationSetupHook().
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AddSimulationModifier | ( | boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > | pSimulationModifier | ) |
Add a SimulationModifier to be used in this simulation.
- Parameters
-
pSimulationModifier pointer to a SimulationModifier
Definition at line 278 of file AbstractCellBasedSimulation.cpp.
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protectedvirtual |
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.
If mOutputDivisionLocations is set to true, then this method also writes the location of each cell division at the present time to mpDivisionLocationFile. This outputs a line of tab-separated values of the form: [time] [div 0 x-pos] [div 0 y-pos] [div 0 z-pos] [div 0 age] [div 1 x-pos] [div 1 y-pos] [div 1 z-pos] [div 1 age] ...
with [y-pos] and [z-pos] included for 2 and 3 dimensional simulations, respectively, and [...age] denoting the age of the dividing cell.
- Returns
- the number of births that occurred.
If required, output this location to file
- Todo:
- (#2578)
For consistency with the rest of the output code, consider removing the AbstractCellBasedSimulation member mOutputDivisionLocations, adding a new member mAgesAndLocationsOfDividingCells to AbstractCellPopulation, adding a new class CellDivisionLocationsWriter to the CellPopulationWriter hierarchy to output the content of mAgesAndLocationsOfDividingCells to file (remembering to clear mAgesAndLocationsOfDividingCells at each timestep), and replacing the following conditional statement with something like
if (mrCellPopulation.HasWriter<CellDivisionLocationsWriter>()) { mCellDivisionLocations.push_back(new_location); }
Definition at line 91 of file AbstractCellBasedSimulation.cpp.
References SimulationTime::GetTime(), and SimulationTime::Instance().
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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 163 of file AbstractCellBasedSimulation.cpp.
| double AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetDt | ( | ) |
- Returns
- the timestep of the simulation
Definition at line 191 of file AbstractCellBasedSimulation.cpp.
| std::vector< double > AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation | ( | const unsigned & | rNodeIndex | ) |
Get a node's location (ONLY FOR TESTING).
- Parameters
-
rNodeIndex the node index
- Returns
- the co-ordinates of this node.
Definition at line 290 of file AbstractCellBasedSimulation.cpp.
| unsigned AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetNumBirths | ( | ) |
- Returns
- the number of births that have occurred in the entire simulation (since t=0)
Definition at line 197 of file AbstractCellBasedSimulation.cpp.
| unsigned AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetNumDeaths | ( | ) |
- Returns
- the number of deaths that have occurred in the entire simulation (since t=0).
Definition at line 203 of file AbstractCellBasedSimulation.cpp.
| bool AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetOutputCellVelocities | ( | ) |
- Returns
- mOutputCellVelocities
Definition at line 619 of file AbstractCellBasedSimulation.cpp.
| std::string AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetOutputDirectory | ( | ) |
- Returns
- the output directory of the simulation.
Definition at line 223 of file AbstractCellBasedSimulation.cpp.
| bool AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetOutputDivisionLocations | ( | ) |
- Returns
- mOutputDivisionLocations
Definition at line 607 of file AbstractCellBasedSimulation.cpp.
| std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > > * AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetSimulationModifiers | ( | ) |
- Returns
- a pointer to the vector of SimulationModifiers used in this simulation.
Definition at line 284 of file AbstractCellBasedSimulation.cpp.
| bool AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::GetUpdateCellPopulationRule | ( | ) |
Return whether to update the topology of the cell population at each time step.
- Returns
- whether to update the cell population each time step
Definition at line 254 of file AbstractCellBasedSimulation.cpp.
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protectedpure virtual |
Helper method to output additional simulations parameters and information defined in subclasses 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
Implemented in OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >, OffLatticeSimulation< 1 >, OffLatticeSimulation< 2 >, and OnLatticeSimulation< DIM >.
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pure 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
Implemented in OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >, OffLatticeSimulation< 1 >, OffLatticeSimulation< 2 >, OnLatticeSimulation< DIM >, CryptSimulation2d, and CryptSimulation1d.
Definition at line 694 of file AbstractCellBasedSimulation.cpp.
Referenced by OnLatticeSimulation< DIM >::OutputSimulationParameters(), and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().
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protected |
Helper method to output all the simulations parameters and information to file.
Definition at line 631 of file AbstractCellBasedSimulation.cpp.
References PetscTools::AmMaster(), ExecutableSupport::GetBuildInfo(), OutputFileHandler::GetOutputDirectoryFullPath(), OutputFileHandler::OpenOutputFile(), ExecutableSupport::SetOutputDirectory(), and ExecutableSupport::WriteMachineInfoFile().
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::RemoveAllCellKillers | ( | ) |
Method to remove all the cell killers.
Definition at line 272 of file AbstractCellBasedSimulation.cpp.
| AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::rGetCellPopulation | ( | ) |
- Returns
- reference to the cell population.
Definition at line 236 of file AbstractCellBasedSimulation.cpp.
| const AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::rGetCellPopulation | ( | ) | const |
- Returns
- const reference to the cell population (used in archiving).
Definition at line 242 of file AbstractCellBasedSimulation.cpp.
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inlineprivate |
Save or restore the simulation.
- Parameters
-
archive the archive version the current version of this class
Definition at line 87 of file AbstractCellBasedSimulation.hpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetDt | ( | double | dt | ) |
Set the timestep of the simulation.
- Parameters
-
dt the timestep to use
Definition at line 184 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetEndTime | ( | double | endTime | ) |
Set the end time and resets the timestep to be endtime/100.
- Parameters
-
endTime the end time to use
Definition at line 209 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetNoBirth | ( | bool | noBirth | ) |
Set the simulation to run with no birth.
- Parameters
-
noBirth whether to run with no birth
Definition at line 260 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetOutputCellVelocities | ( | bool | outputCellVelocities | ) |
Set mOutputCellVelocities.
- Parameters
-
outputCellVelocities the new value of mOutputCellVelocities
Definition at line 625 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetOutputDirectory | ( | std::string | outputDirectory | ) |
Set the output directory of the simulation.
- Parameters
-
outputDirectory the output directory to use
Definition at line 216 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetOutputDivisionLocations | ( | bool | outputDivisionLocations | ) |
Set mOutputDivisionLocations.
- Parameters
-
outputDivisionLocations the new value of mOutputDivisionLocations
Definition at line 613 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetSamplingTimestepMultiple | ( | unsigned | samplingTimestepMultiple | ) |
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 229 of file AbstractCellBasedSimulation.cpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::SetUpdateCellPopulationRule | ( | bool | updateCellPopulation | ) |
Set whether to update the topology of the cell population at each time step.
- Parameters
-
updateCellPopulation whether to update the cell population each time step
Definition at line 248 of file AbstractCellBasedSimulation.cpp.
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inlineprotectedvirtual |
A method for subclasses to do something at before the start of the time loop.
Reimplemented in OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >, OffLatticeSimulation< 1 >, OffLatticeSimulation< 2 >, and CryptSimulation2d.
Definition at line 211 of file AbstractCellBasedSimulation.hpp.
| void AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve | ( | ) |
Main Solve() method, used to evolve the cell population. Note that prior to calling Solve() we must have called SetEndTime(). We may also have optionally called SetDt(); if not, then a default time step is used.
The Solve() method proceeds as follows.
Setting up:
First, we set up SimulationTime, which (i) provides a globally consistent time, accessible to all other classes in the cell_based code and (ii) handles any rounding issues when the time step does not exactly divide the end time.
Next, we create output files. We then call SetupSolve(), which is empty in the parent class but may be overridden, e.g. to open additional output files. We then call SetupSolve() on any member objects inheriting from AbstractCellBasedSimulationModifier. This class hierarchy allows the user to introduce new ways of updating the cell population within the simulation.
Next, we set up each cell by calling ReadyToDivide() on it, which updates the cell's age and cell cycle model. Finally, we call WriteVisualizerSetupFile() and OutputSimulationSetup(), as well as WriteResultsToFiles() on the cell population, to record the initial configration. This completes the set up process.
The main time loop:
At each time step, we begin by calling UpdateCellPopulation(), which implements any cell deaths and cell divisions through DoCellRemoval() and DoCellBirth() respectively. We then update the correspondence between cells and the mesh by calling Update() on the cell population.
If mOutputCellVelocities is set to true and we are at a printing time, then we als write the velocity of each cell at the present time to mpCellVelocitiesFile. This outputs a line of tab-separated values of the form: [time] [cell 0 x-pos] [cell 0 y-pos] [cell 0 z-pos] [cell 0 x-vel] [cell 0 y-vel] [cell 0 z-vel] ...
with [y-pos] and [z-pos] included for 2 and 3 dimensional simulations, respectively, and data for cells being ordered as given by the cell population Iterator.
Next, we call UpdateCellLocationsAndTopology(), which is pure virtual in the parent class so must be overridden. As the cell population has been updated, we then increment SimulationTime by one time step. We then call UpdateAtEndOfTimeStep() on any AbstractCellBasedSimulationModifiers present, e.g. to write additional output. In an analogous manner to the calls to SetupSolve() prior to entering the main time loop.
The last step within the main time loop is to output the present results to file.
Finishing up:
After exiting the main time loop, we call UpdateCellPopulation() in order to carry out a final update of the cell population. We also call UpdateAtEndOfSolve()} on any member objects inheriting from AbstractCellBasedSimulationModifier in an analogous manner to the aforementioned calls to SetupSolve() UpdateAtEndOfTimeStep(). Finally, we close output files. This completes the Solve() method.
Definition at line 301 of file AbstractCellBasedSimulation.cpp.
References PetscTools::AmMaster(), GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), DOUBLE_UNSET, GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), EXCEPTION, SimulationTime::GetTime(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::IncrementTimeOneStep(), SimulationTime::Instance(), SimulationTime::IsEndTimeAndNumberOfTimeStepsSetUp(), SimulationTime::IsFinished(), OutputFileHandler::OpenOutputFile(), SimulationTime::ResetEndTimeAndNumberOfTimeSteps(), and SimulationTime::SetEndTimeAndNumberOfTimeSteps().
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protectedvirtual |
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).
- Returns
- true if stopping event has occurred
Definition at line 566 of file AbstractCellBasedSimulation.cpp.
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protectedpure virtual |
Update the cell locations and topology (connectivity) of the cell population. This method is called within the main time loop of Solve() .
As this method is pure virtual, it must be overridden in subclasses.
In the case of an OffLatticeSimulation, the method computes the force acting on each node (corresponding to a cell in centre-based models and to a vertex in vertex-based models) and integrates equations of motion to find the new position of each node.
In the case of an OnLatticeSimulation, the method performs Monte Carlo updating of the cell population, through a call to UpdateCellLocations() on the cell population object.
Implemented in OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >, OffLatticeSimulation< 1 >, OffLatticeSimulation< 2 >, and OnLatticeSimulation< DIM >.
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protectedvirtual |
Calls the deaths, births and (if mUpdateCellPopulation is true) CellPopulation::Update() methods.
Reimplemented in OnLatticeSimulation< DIM >.
Definition at line 572 of file AbstractCellBasedSimulation.cpp.
References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), and EXCEPTION.
Referenced by OnLatticeSimulation< DIM >::UpdateCellPopulation().
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inlineprotectedvirtual |
Writes out special information about the mesh to the visualizer.
Reimplemented in OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.
Definition at line 177 of file AbstractCellBasedSimulation.hpp.
Friends And Related Function Documentation
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friend |
Needed for serialization.
Definition at line 78 of file AbstractCellBasedSimulation.hpp.
Member Data Documentation
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List of cell killers.
Definition at line 163 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Whether to delete the cell population in the destructor.
Definition at line 121 of file AbstractCellBasedSimulation.hpp.
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protected |
Time step.
Definition at line 112 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation(), and AbstractCellBasedSimulation< DIM >::serialize().
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protected |
Time to run the Solve() method up to.
Definition at line 115 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Whether to initialise the cells.
Definition at line 124 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation().
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Whether to run the simulation with no birth (defaults to false).
Definition at line 127 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Counts the number of births during the simulation.
Definition at line 142 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Counts the number of deaths during the simulation.
Definition at line 145 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Whether to write the cell velocities to a file. Initialised to false in constructor.
Definition at line 157 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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protected |
Output directory (a subfolder of tmp/[USERNAME]/testoutput).
Definition at line 133 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Whether to output the locations of division events (defaults to false).
Definition at line 148 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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Results file for cell velocities.
Definition at line 160 of file AbstractCellBasedSimulation.hpp.
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Output file for location of division events.
Definition at line 151 of file AbstractCellBasedSimulation.hpp.
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Visualizer setup file.
Definition at line 139 of file AbstractCellBasedSimulation.hpp.
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Facade encapsulating cells in the cell population being simulated.
Definition at line 118 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation().
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protected |
The ratio of the number of actual timesteps to the number of timesteps at which results are written to file.
Definition at line 172 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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protected |
List of SimulationModifier rules.
Definition at line 166 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
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protected |
Simulation Output directory either the same as mOutputDirectory or includes mOutputDirectory/results_from_time_[TIME].
Definition at line 136 of file AbstractCellBasedSimulation.hpp.
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Whether to update the topology of the cell population at each time step (defaults to true).
Definition at line 130 of file AbstractCellBasedSimulation.hpp.
Referenced by AbstractCellBasedSimulation< DIM >::serialize().
The documentation for this class was generated from the following files:
- cell_based/src/population/AbstractCellPopulation.hpp
- cell_based/src/simulation/AbstractCellBasedSimulation.hpp
- cell_based/src/simulation/AbstractCellBasedSimulation.cpp
