AveragedSourceEllipticPde.hpp

/*

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*/

#ifndef AVERAGEDSOURCEELLIPTICPDE_HPP_
#define AVERAGEDSOURCEELLIPTICPDE_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>

#include "AbstractCellPopulation.hpp"
#include "TetrahedralMesh.hpp"
#include "AbstractLinearEllipticPde.hpp"

template<unsigned DIM>
class AveragedSourceEllipticPde : public AbstractLinearEllipticPde<DIM,DIM>
{
    friend class TestCellBasedEllipticPdes;

private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
       archive & boost::serialization::base_object<AbstractLinearEllipticPde<DIM, DIM> >(*this);
       archive & mSourceCoefficient;
       archive & mDiffusionCoefficient;
       archive & mCellDensityOnCoarseElements;
    }

protected:

    AbstractCellPopulation<DIM>& mrCellPopulation;

    double mSourceCoefficient;

    double mDiffusionCoefficient;

    std::vector<double> mCellDensityOnCoarseElements;

public:

    AveragedSourceEllipticPde(AbstractCellPopulation<DIM>& rCellPopulation,
                              double sourceCoefficient=0.0,
                              double diffusionCoefficient=1.0);

    const AbstractCellPopulation<DIM>& rGetCellPopulation() const;

    double GetCoefficient() const;

    void virtual SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap=nullptr);

    double ComputeConstantInUSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement);

    double ComputeLinearInUCoeffInSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement);

    c_matrix<double,DIM,DIM> ComputeDiffusionTerm(const ChastePoint<DIM>& rX);

    double GetUptakeRateForElement(unsigned elementIndex);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(AveragedSourceEllipticPde)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const AveragedSourceEllipticPde<DIM>* t, const unsigned int file_version)
{
    // Save data required to construct instance
    const AbstractCellPopulation<DIM>* p_cell_population = &(t->rGetCellPopulation());
    ar & p_cell_population;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, AveragedSourceEllipticPde<DIM>* t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    AbstractCellPopulation<DIM>* p_cell_population;
    ar >> p_cell_population;

    // Invoke inplace constructor to initialise instance
    ::new(t)AveragedSourceEllipticPde<DIM>(*p_cell_population);
}
}
} // namespace ...

#endif /*AVERAGEDSOURCEELLIPTICPDE_HPP_*/