void CellIdWriter<ELEMENT_DIM, SPACE_DIM>::VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
unsigned cell_id = pCell->GetCellId();
unsigned location_index = pCellPopulation->GetLocationIndexUsingCell(pCell);
*this->mpOutStream << " " << cell_id << " " << location_index;
c_vector<double, SPACE_DIM> coords = pCellPopulation->GetLocationOfCellCentre(pCell);
for (unsigned i=0; i<SPACE_DIM; i++)
{
*this->mpOutStream << " " << coords[i];
}
}
void CellDataItemWriter<ELEMENT_DIM, SPACE_DIM>::VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
// Output the location index corresponding to this cell
unsigned location_index = pCellPopulation->GetLocationIndexUsingCell(pCell);
*this->mpOutStream << location_index << " ";
// Output this cell's ID
unsigned cell_id = pCell->GetCellId();
*this->mpOutStream << cell_id << " ";
// Output the position of this cell's centre
c_vector<double, SPACE_DIM> centre_location = pCellPopulation->GetLocationOfCellCentre(pCell);
for (unsigned i=0; i<SPACE_DIM; i++)
{
*this->mpOutStream << centre_location[i] << " ";
}
// Output this cell's level of mCellDataVariableName
double value = pCell->GetCellData()->GetItem(mCellDataVariableName);
*this->mpOutStream << value << " ";
}
void RandomCellKillerInCuboid<DIM>::CheckAndLabelSingleCellForApoptosis(CellPtr pCell)
{
/*
* We assume a constant time step and that there are an integer number (n = 1/dt)
* of time steps per hour. We also assume that this method is called every time step
* and that the probabilities of dying at different times are independent.
*
* Let q=mProbabilityOfDeathInAnHour and p="probability of death in a given time step".
*
* Probability of not dying in an hour:
* (1-q) = (1-p)^n = (1-p)^(1/dt).
*
* Rearranging for p:
* p = 1 - (1-q)^dt.
*/
double death_prob_this_timestep = 1.0 - pow((1.0 - mProbabilityOfDeathInAnHour), SimulationTime::Instance()->GetTimeStep());
if (!pCell->HasApoptosisBegun() &&
RandomNumberGenerator::Instance()->ranf() < death_prob_this_timestep)
{
OUTPUT<<SimulationTime::Instance()->GetTime()<<" "<<pCell->GetCellId()<<std::endl;
pCell->StartApoptosis();
}
}
double CellIdWriter<ELEMENT_DIM, SPACE_DIM>::GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
double cell_id = pCell->GetCellId();
return cell_id;
}