Chaste  Release::3.4
VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp
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35 
36 #include "VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp"
37 
40 {
41  if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
42  {
43 #ifdef CHASTE_CVODE
45  mpOdeSolver->Initialise();
46  // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
47  mpOdeSolver->CheckForStoppingEvents();
48  mpOdeSolver->SetMaxSteps(10000);
49 #else
51  mpOdeSolver->Initialise();
52  SetDt(0.00005);
53 #endif //CHASTE_CVODE
54  }
55 }
56 
57 void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem(double wntConcentration, boost::shared_ptr<AbstractCellMutationState> pMutationState)
58 {
59  mpOdeSystem = new VanLeeuwen2009WntSwatCellCycleOdeSystem(1, wntConcentration, pMutationState);
60 }
61 
63 {
64  // Create a new cell-cycle model
66 
67  /*
68  * Set each member variable of the new cell-cycle model that inherits
69  * its value from the parent.
70  *
71  * Note 1: some of the new cell-cycle model's member variables (namely
72  * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mDt, mpOdeSolver)
73  * will already have been correctly initialized in its constructor.
74  *
75  * Note 2: one or more of the new cell-cycle model's member variables
76  * may be set/overwritten as soon as InitialiseDaughterCell() is called on
77  * the new cell-cycle model.
78  */
79  p_model->SetBirthTime(mBirthTime);
80  p_model->SetDimension(mDimension);
84  p_model->SetSDuration(mSDuration);
85  p_model->SetG2Duration(mG2Duration);
86  p_model->SetMDuration(mMDuration);
87  p_model->SetDivideTime(mDivideTime);
90  p_model->SetLastTime(mLastTime);
91 
92  /*
93  * Create the new cell-cycle model's ODE system and use the current values
94  * of the state variables in mpOdeSystem as an initial condition.
95  */
96  assert(mpOdeSystem);
97  double wnt_level = GetWntLevel();
98  p_model->InitialiseOdeSystem(wnt_level, mpCell->GetMutationState());
100 
101  return p_model;
102 }
103 
105 {
106  // No new parameters to output, so just call method on direct parent class
108 }
109 
110 // Declare identifier for the serializer
113 #include "CellCycleModelOdeSolverExportWrapper.hpp"
114 EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(VanLeeuwen2009WntSwatCellCycleModelHypothesisOne)
void SetStateVariables(const std::vector< double > &rStateVariables)
boost::shared_ptr< AbstractCellCycleModelOdeSolver > mpOdeSolver
virtual void SetStemCellG1Duration(double stemCellG1Duration)
void SetMinimumGapDuration(double minimumGapDuration)
void SetMDuration(double mDuration)
void SetG2Duration(double g2Duration)
VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
static boost::shared_ptr< CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER > > Instance()
void SetDimension(unsigned dimension)
void SetFinishedRunningOdes(bool finishedRunningOdes)
virtual void SetTransitCellG1Duration(double transitCellG1Duration)
#define CHASTE_CLASS_EXPORT(T)
void InitialiseOdeSystem(double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)
void SetG2PhaseStartTime(double g2PhaseStartTime)
void SetSDuration(double sDuration)