AbstractDiscreteContinuumNonLinearEllipticPde.cpp

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#include <algorithm>
#include "AbstractDiscreteContinuumNonLinearEllipticPde.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::AbstractDiscreteContinuumNonLinearEllipticPde() :
            AbstractNonlinearEllipticPde<SPACE_DIM>(),
            mDiffusionTensor(identity_matrix<double>(SPACE_DIM)),
            mDiffusivity(1.0*unit::metre_squared_per_second),
            mConstantInUTerm(),
            mLinearInUTerm(),
            mDiscreteSources(),
            mpRegularGrid(),
            mpMesh(),
            mUseRegularGrid(true),
            mDiscreteConstantSourceStrengths(),
            mDiscreteLinearSourceStrengths()
{
    mDiffusionTensor *= mDiffusivity.value();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::~AbstractDiscreteContinuumNonLinearEllipticPde()
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::AddDiscreteSource(boost::shared_ptr<DiscreteSource<SPACE_DIM> > pDiscreteSource)
{
    mDiscreteSources.push_back(pDiscreteSource);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::diffusivity> AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::ComputeIsotropicDiffusionTerm()
{
    return mDiffusivity;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::concentration_flow_rate> AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::ComputeConstantInUSourceTerm(unsigned gridIndex)
{
    if(mDiscreteConstantSourceStrengths.size()>0)
    {
        if(gridIndex >= mDiscreteConstantSourceStrengths.size())
        {
            EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
        }
        return mConstantInUTerm + mDiscreteConstantSourceStrengths[gridIndex];
    }
    else
    {
        return mConstantInUTerm;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::rate> AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::ComputeLinearInUCoeffInSourceTerm(unsigned gridIndex)
{
    if(mDiscreteLinearSourceStrengths.size()>0)
    {
        if(gridIndex >= mDiscreteLinearSourceStrengths.size())
        {
            EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
        }
        return mLinearInUTerm + mDiscreteLinearSourceStrengths[gridIndex];
    }
    else
    {
        return mLinearInUTerm;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<DiscreteSource<SPACE_DIM> > > AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::GetDiscreteSources()
{
    return mDiscreteSources;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetContinuumConstantInUTerm(units::quantity<unit::concentration_flow_rate> constantInUTerm)
{
    mConstantInUTerm = constantInUTerm;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetIsotropicDiffusionConstant(units::quantity<unit::diffusivity> diffusivity)
{
    mDiffusivity = diffusivity;
    mDiffusionTensor = identity_matrix<double>(SPACE_DIM)* double(mDiffusivity/unit::metre_squared_per_second);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetContinuumLinearInUTerm(units::quantity<unit::rate> linearInUTerm)
{
    mLinearInUTerm = linearInUTerm;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetRegularGrid(boost::shared_ptr<RegularGrid<SPACE_DIM> > pRegularGrid)
{
    mpRegularGrid = pRegularGrid;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetMesh(boost::shared_ptr<TetrahedralMesh<ELEMENT_DIM, SPACE_DIM> > pMesh)
{
    mpMesh = pMesh;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetUseRegularGrid(bool useRegularGrid)
{
    mUseRegularGrid = useRegularGrid;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumNonLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::UpdateDiscreteSourceStrengths()
{
    if(mUseRegularGrid)
    {
        if(!mpRegularGrid)
        {
            EXCEPTION("A grid has not been set for the determination of source strengths.");
        }
        mDiscreteConstantSourceStrengths = std::vector<units::quantity<unit::concentration_flow_rate> >(mpRegularGrid->GetNumberOfPoints(), 0.0*unit::mole_per_metre_cubed_per_second);
        mDiscreteLinearSourceStrengths = std::vector<units::quantity<unit::rate> >(mpRegularGrid->GetNumberOfPoints(), 0.0*unit::per_second);

        for(unsigned idx=0; idx<mDiscreteSources.size(); idx++)
        {
            mDiscreteSources[idx]->SetRegularGrid(mpRegularGrid);
            std::vector<units::quantity<unit::rate> > result = mDiscreteSources[idx]->GetLinearInURegularGridValues();
            std::transform(mDiscreteLinearSourceStrengths.begin( ), mDiscreteLinearSourceStrengths.end( ),
                           result.begin( ), mDiscreteLinearSourceStrengths.begin( ),std::plus<units::quantity<unit::rate> >( ));

            std::vector<units::quantity<unit::concentration_flow_rate> > result2 = mDiscreteSources[idx]->GetConstantInURegularGridValues();
            std::transform(mDiscreteConstantSourceStrengths.begin( ), mDiscreteConstantSourceStrengths.end( ),
                           result2.begin( ), mDiscreteConstantSourceStrengths.begin( ),std::plus<units::quantity<unit::concentration_flow_rate> >( ));
        }
    }
    else
    {
        if(!mpMesh)
        {
            EXCEPTION("A mesh has not been set for the determination of source strengths.");
        }
    }
}

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