Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
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#include <CryptSimulation1d.hpp>
Public Member Functions | |
CryptSimulation1d (AbstractCellPopulation< 1 > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true) | |
virtual | ~CryptSimulation1d () |
void | OutputSimulationParameters (out_stream &rParamsFile) |
Public Member Functions inherited from OffLatticeSimulation< 1 > | |
OffLatticeSimulation (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true) | |
void | AddForce (boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > pForce) |
void | RemoveAllForces () |
void | AddCellPopulationBoundaryCondition (boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, ELEMENT_DIM > > pBoundaryCondition) |
void | RemoveAllCellPopulationBoundaryConditions () |
void | SetNumericalMethod (boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, ELEMENT_DIM > > pNumericalMethod) |
const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, ELEMENT_DIM > > | GetNumericalMethod () const |
void | OutputAdditionalSimulationSetup (out_stream &rParamsFile) |
const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_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 | SetUpdatingTimestepMultiple (unsigned updatingTimestepMultiple) |
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 | AddTopologyUpdateSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > pSimulationModifier) |
std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > > * | GetTopologyUpdateSimulationModifiers () |
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 |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
MeshBasedCellPopulation< 1 > * | mpStaticCastCellPopulation |
Friends | |
class | TestCryptSimulation1d |
class | boost::serialization::access |
A 1D crypt simulation object. The model is a simplified version of a 2D crypt model developed by Meineke et al (doi:10.1046/j.0960-7722.2001.00216.x).
Definition at line 55 of file CryptSimulation1d.hpp.
CryptSimulation1d::CryptSimulation1d | ( | AbstractCellPopulation< 1 > & | rCellPopulation, |
bool | deleteCellPopulationInDestructor = false , |
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bool | initialiseCells = true |
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) |
Constructor.
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 40 of file CryptSimulation1d.cpp.
References OffLatticeSimulation< 1 >::AddCellPopulationBoundaryCondition(), MAKE_PTR, MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mDeleteCellPopulationInDestructor, mpStaticCastCellPopulation, AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::mrCellPopulation, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCentreBasedDivisionRule().
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virtual |
Destructor.
This frees the CryptSimulationBoundaryCondition.
Definition at line 60 of file CryptSimulation1d.cpp.
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virtual |
Outputs simulation parameters to file
As this method is pure virtual, it must be overridden in subclasses.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from OffLatticeSimulation< 1 >.
Definition at line 64 of file CryptSimulation1d.cpp.
References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().
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inlineprivate |
Archive the simulation and member variables.
archive | the archive |
version | the current version of this class |
Definition at line 71 of file CryptSimulation1d.hpp.
References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), and WntConcentration< DIM >::Instance().
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friend |
Needed for serialization.
Definition at line 63 of file CryptSimulation1d.hpp.
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friend |
Definition at line 58 of file CryptSimulation1d.hpp.
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private |
Helper member that is a static cast of the cell population.
Definition at line 80 of file CryptSimulation1d.hpp.
Referenced by CryptSimulation1d().