CellBasedDiscreteSource.cpp

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#include "CellBasedDiscreteSource.hpp"
#include "AbstractCellPopulation.hpp"
#include "VesselNetwork.hpp"
#include "GeometryTools.hpp"
#include "Element.hpp"

template<unsigned DIM>
CellBasedDiscreteSource<DIM>::CellBasedDiscreteSource()
    :   DiscreteSource<DIM>(),
        mCellConstantInUValue(0.0*unit::mole_per_second),
        mCellLinearInUValue(0.0*unit::per_second)
{

}

template<unsigned DIM>
CellBasedDiscreteSource<DIM>::~CellBasedDiscreteSource()
{

}

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

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > CellBasedDiscreteSource<DIM>::GetConstantInUMeshValues()
{
    if(!this->mpMesh)
    {
        EXCEPTION("A mesh is required for this type of source");
    }

    std::vector<units::quantity<unit::concentration_flow_rate> > values(this->mpMesh->GetNumElements(), 0.0*unit::mole_per_metre_cubed_per_second);
    std::vector<std::vector<CellPtr> > element_cell_map = this->mpMesh->GetElementCellMap();
    for(unsigned idx=0; idx<element_cell_map.size(); idx++)
    {
        Element<DIM, DIM>* p_element = this->mpMesh->GetElement(idx);
        double determinant = 0.0;
        c_matrix<double, DIM, DIM> jacobian;
        p_element->CalculateJacobian(jacobian, determinant);
        units::quantity<unit::volume> element_volume = p_element->GetVolume(determinant) * units::pow<3>(this->mpMesh->GetReferenceLengthScale());
        values[idx] += mCellConstantInUValue * double(element_cell_map[idx].size())/element_volume;
    }
    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > CellBasedDiscreteSource<DIM>::GetLinearInUMeshValues()
{
    if(!this->mpMesh)
    {
        EXCEPTION("A mesh is required for this type of source");
    }
    std::vector<units::quantity<unit::rate> > values(this->mpMesh->GetNumElements(), 0.0*unit::per_second);
    std::vector<std::vector<CellPtr> > element_cell_map = this->mpMesh->GetElementCellMap();

    for(unsigned idx=0; idx<element_cell_map.size(); idx++)
    {
        values[idx] += mCellLinearInUValue * double(element_cell_map[idx].size());
    }
    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > CellBasedDiscreteSource<DIM>::GetConstantInURegularGridValues()
{
    if(!this->mpRegularGrid)
    {
        EXCEPTION("A regular grid is required for this type of source");
    }

    std::vector<units::quantity<unit::concentration_flow_rate> > values(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::mole_per_metre_cubed_per_second);
    units::quantity<unit::length> grid_spacing = this->mpRegularGrid->GetSpacing();
    units::quantity<unit::volume> grid_volume = units::pow<3>(grid_spacing);

    std::vector<std::vector<CellPtr> > point_cell_map = this->mpRegularGrid->GetPointCellMap();
    for(unsigned idx=0; idx<point_cell_map.size(); idx++)
    {
        values[idx] += mCellConstantInUValue * double(point_cell_map[idx].size())/grid_volume;
    }
    return values;

}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > CellBasedDiscreteSource<DIM>::GetLinearInURegularGridValues()
{
    if(!this->mpRegularGrid)
    {
        EXCEPTION("A regular grid is required for this type of source");
    }

    std::vector<units::quantity<unit::rate> > values(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::per_second);
    std::vector<std::vector<CellPtr> > point_cell_map = this->mpRegularGrid->GetPointCellMap();
    for(unsigned idx=0; idx<point_cell_map.size(); idx++)
    {
        values[idx] += mCellLinearInUValue * double(point_cell_map[idx].size());
    }
    return values;
}

template<unsigned DIM>
void CellBasedDiscreteSource<DIM>::SetConstantInUConsumptionRatePerCell(units::quantity<unit::molar_flow_rate> value)
{
    mCellConstantInUValue = -value;
}

template<unsigned DIM>
void CellBasedDiscreteSource<DIM>::SetLinearInUConsumptionRatePerCell(units::quantity<unit::rate> value)
{
    mCellLinearInUValue = -value;
}

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