MicrovesselSimulationModifier.cpp

/*

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*/

#include "AbstractCellPopulation.hpp"
#include "boost/lexical_cast.hpp"
#include "MicrovesselSimulationModifier.hpp"
#include "BaseUnits.hpp"

template<unsigned DIM>
MicrovesselSimulationModifier<DIM>::MicrovesselSimulationModifier()
    : AbstractCellBasedSimulationModifier<DIM>(),
      mpSolver(),
      mUpdateLabels(),
      mCellPopulationReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale()),
      mCellPopulationReferenceConcentration(BaseUnits::Instance()->GetReferenceConcentrationScale())
{
}

template<unsigned DIM>
MicrovesselSimulationModifier<DIM>::~MicrovesselSimulationModifier()
{
}

template <unsigned DIM>
boost::shared_ptr<MicrovesselSimulationModifier<DIM> > MicrovesselSimulationModifier<DIM>::Create()
{
    MAKE_PTR(MicrovesselSimulationModifier<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    // Do set-up on the vascular tumour modifier
    if(mpSolver)
    {
        mpSolver->SetupFromModifier(rCellPopulation, mCellPopulationReferenceLength, mCellPopulationReferenceConcentration, outputDirectory);

        // Do the first solver increment
        mpSolver->Increment();
    }
    else
    {
        EXCEPTION("A MicrovesselSolver is required for this modifier.");
    }

    rCellPopulation.Update();

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // Store the cell's volume in CellData
        cell_iter->GetCellData()->SetItem("oxygen", 0.0);
    }

    // Update the cell data
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::SetCellDataUpdateLabels(std::vector<std::string> labels)
{
    mUpdateLabels = labels;
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::SetMicrovesselSolver(boost::shared_ptr<MicrovesselSolver<DIM> > pSolver)
{
    mpSolver = pSolver;
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::SetCellPopulationLengthScale(units::quantity<unit::length> cellLengthScale)
{
    mCellPopulationReferenceLength = cellLengthScale;
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::SetCellPopulationConcentrationScale(units::quantity<unit::concentration> cellConcentrationScale)
{
    mCellPopulationReferenceConcentration = cellConcentrationScale;
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Increment the solver
    mpSolver->Increment();

    // Update the cell data
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Make sure the cell population is updated
    rCellPopulation.Update();

    // Update the cell data
    mpSolver->UpdateCellData(mUpdateLabels);
}

template<unsigned DIM>
void MicrovesselSimulationModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

// Explicit instantiation
template class MicrovesselSimulationModifier<2>;
template class MicrovesselSimulationModifier<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS1(MicrovesselSimulationModifier, 2)
EXPORT_TEMPLATE_CLASS1(MicrovesselSimulationModifier, 3)