OnLatticeSimulation.cpp

/*

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*/

#include "OnLatticeSimulation.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "CellBasedEventHandler.hpp"
#include "LogFile.hpp"
#include "Version.hpp"
#include "ExecutableSupport.hpp"
#include "CaBasedCellPopulation.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.");
    }

    this->mDt = 0.1; // 6 minutes
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::AddCaUpdateRule(boost::shared_ptr<AbstractCaUpdateRule<DIM> > pUpdateRule)
{
    if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->AddUpdateRule(pUpdateRule);
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::RemoveAllCaUpdateRules()
{
    if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->RemoveAllUpdateRules();
    }
}


template<unsigned DIM>
void OnLatticeSimulation<DIM>::AddCaSwitchingUpdateRule(boost::shared_ptr<AbstractCaSwitchingUpdateRule<DIM> > pUpdateRule)
{
    if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->AddSwitchingUpdateRule(pUpdateRule);
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::RemoveAllCaSwitchingUpdateRules()
{
    if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->RemoveAllSwitchingUpdateRules();
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::AddPottsUpdateRule(boost::shared_ptr<AbstractPottsUpdateRule<DIM> > pUpdateRule)
{
    if (bool(dynamic_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->AddUpdateRule(pUpdateRule);
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::RemoveAllPottsUpdateRules()
{
    if (bool(dynamic_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        static_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->RemoveAllUpdateRules();
    }
}

template<unsigned DIM>
c_vector<double, DIM> OnLatticeSimulation<DIM>::CalculateCellDivisionVector(CellPtr pParentCell)
{
    return zero_vector<double>(DIM);
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::WriteVisualizerSetupFile()
{
    if (bool(dynamic_cast<PottsBasedCellPopulation<DIM>*>(&this->mrCellPopulation)))
    {
       *this->mpVizSetupFile << "PottsSimulation\n";
    }
}

template<unsigned DIM>
void OnLatticeSimulation<DIM>::UpdateCellLocationsAndTopology()
{
    // Update cell locations
    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 = true;
    if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        /*
         * If mInitialiseCells is false, then the simulation has been loaded from an archive.
         * In this case, we should not call UpdateCellPopulation() at the first time step. This is
         * because it will have already been called at the final time step prior to saving;
         * if we were to call it again now, then we would have introduced an extra call to
         * the random number generator compared to if we had not saved and loaded the simulation,
         * thus affecting results. This would be bad - we don't want saving and loading to have
         * any effect on the course of a simulation! See #1445.
         */
        if (!this->mInitialiseCells && (SimulationTime::Instance()->GetTimeStepsElapsed() == 0))
        {
            NEVER_REACHED;
//            update_cell_population_this_timestep = false;
        }
    }

    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";
    if (bool(dynamic_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > > collection =
            static_cast<PottsBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->rGetUpdateRuleCollection();

        for (typename std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > >::iterator iter = collection.begin();
             iter != collection.end();
             ++iter)
        {
            (*iter)->OutputUpdateRuleInfo(rParamsFile);
        }
    }
    else if (bool(dynamic_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))))
    {
        std::vector<boost::shared_ptr<AbstractCaUpdateRule<DIM> > > collection =
            static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->rGetUpdateRuleCollection();

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

        std::vector<boost::shared_ptr<AbstractCaSwitchingUpdateRule<DIM> > > switching_collection =
            static_cast<CaBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->rGetSwitchingUpdateRuleCollection();

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

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

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

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)