OnLatticeSimulation.cpp

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*/

#include "OnLatticeSimulation.hpp"
#include "AbstractOnLatticeCellPopulation.hpp"
#include "CellBasedEventHandler.hpp"

template<unsigned DIM>
OnLatticeSimulation<DIM>::OnLatticeSimulation(AbstractCellPopulation<DIM>& rCellPopulation,
                                              bool deleteCellPopulationInDestructor,
                                              bool initialiseCells)
    : AbstractCellBasedSimulation<DIM>(rCellPopulation,
                                       deleteCellPopulationInDestructor,
                                       initialiseCells)
{
    if (!dynamic_cast<AbstractOnLatticeCellPopulation<DIM>*>(&rCellPopulation))
    {
        EXCEPTION("OnLatticeSimulations require a subclass of AbstractOnLatticeCellPopulation.");
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::AddUpdateRule(boost::shared_ptr<AbstractUpdateRule<DIM> > pUpdateRule)
{
    // This static_cast is fine, since otherwise an exception would have been thrown in the constructor
    static_cast<AbstractOnLatticeCellPopulation<DIM>*>(&(this->mrCellPopulation))->AddUpdateRule(pUpdateRule);
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::RemoveAllUpdateRules()
{
    // This static_cast is fine, since otherwise an exception would have been thrown in the constructor
    static_cast<AbstractOnLatticeCellPopulation<DIM>*>(&(this->mrCellPopulation))->RemoveAllUpdateRules();
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::UpdateCellLocationsAndTopology()
{
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::POSITION);
    static_cast<AbstractOnLatticeCellPopulation<DIM>*>(&(this->mrCellPopulation))->UpdateCellLocations(this->mDt);
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::POSITION);
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::UpdateCellPopulation()
{
    bool update_cell_population_this_timestep = (this->mInitialiseCells) || (SimulationTime::Instance()->GetTimeStepsElapsed() != 0);
    if (update_cell_population_this_timestep)
    {
        AbstractCellBasedSimulation<DIM>::UpdateCellPopulation();
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::OutputAdditionalSimulationSetup(out_stream& rParamsFile)
{
    // Loop over the collection of update rules and output info for each
    *rParamsFile << "\n\t<UpdateRules>\n";

    // This static_cast is fine, since otherwise an exception would have been thrown in the constructor
    std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > collection =
            static_cast<AbstractOnLatticeCellPopulation<DIM>*>(&(this->mrCellPopulation))->GetUpdateRuleCollection();

    for (typename std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > >::iterator iter = collection.begin();
         iter != collection.end();
         ++iter)
    {
        (*iter)->OutputUpdateRuleInfo(rParamsFile);
    }

    *rParamsFile << "\t</UpdateRules>\n";
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::OutputSimulationParameters(out_stream& rParamsFile)
{
    // Call method on direct parent class
    AbstractCellBasedSimulation<DIM>::OutputSimulationParameters(rParamsFile);
}

// Explicit instantiation
template class OnLatticeSimulation<1>;
template class OnLatticeSimulation<2>;
template class OnLatticeSimulation<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(OnLatticeSimulation)