AbstractDiscreteContinuumLinearEllipticPde.cpp

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#include <algorithm>
#include "AbstractDiscreteContinuumLinearEllipticPde.hpp"
#include "BaseUnits.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::AbstractDiscreteContinuumLinearEllipticPde() :
            AbstractLinearEllipticPde<ELEMENT_DIM, ELEMENT_DIM>(),
            mDiffusionTensor(identity_matrix<double>(SPACE_DIM)),
            mDiffusivity(1.0 * unit::metre_squared_per_second),
            mConstantInUTerm(0.0 * unit::mole_per_metre_cubed_per_second),
            mDiscreteSources(),
            mpRegularGrid(),
            mpMesh(),
            mUseRegularGrid(true),
            mDiscreteConstantSourceStrengths(),
            mReferenceConcentration(BaseUnits::Instance()->GetReferenceConcentrationScale())
{
    mDiffusionTensor *= mDiffusivity.value();
}

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::ComputeConstantInUSourceTerm(const ChastePoint<SPACE_DIM>& rX,
                                                                                                        Element<ELEMENT_DIM, SPACE_DIM>* pElement)
{
    if(mDiscreteConstantSourceStrengths.size()>0)
    {
        if(pElement->GetIndex() >= mDiscreteConstantSourceStrengths.size())
        {
            EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
        }
        units::quantity<unit::concentration_flow_rate> scaling_factor = mReferenceConcentration/BaseUnits::Instance()->GetReferenceTimeScale();
        return (mConstantInUTerm + mDiscreteConstantSourceStrengths[pElement->GetIndex()]) / scaling_factor;
    }
    else
    {
        units::quantity<unit::concentration_flow_rate> scaling_factor = mReferenceConcentration/BaseUnits::Instance()->GetReferenceTimeScale();
        return mConstantInUTerm/scaling_factor;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::concentration_flow_rate> AbstractDiscreteContinuumLinearEllipticPde<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>
c_matrix<double, SPACE_DIM, SPACE_DIM> AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::ComputeDiffusionTerm(const ChastePoint<SPACE_DIM>&)
{
    return mDiffusionTensor;
}

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

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetIsotropicDiffusionConstant(units::quantity<unit::diffusivity> diffusivity)
{
    mDiffusivity = diffusivity;
    units::quantity<unit::diffusivity> scaling_factor = (BaseUnits::Instance()->GetReferenceLengthScale()*BaseUnits::Instance()->GetReferenceLengthScale())/BaseUnits::Instance()->GetReferenceTimeScale();
    mDiffusionTensor = identity_matrix<double>(SPACE_DIM)*(mDiffusivity/scaling_factor);
}

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

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::SetReferenceConcentration(units::quantity<unit::concentration> referenceConcentration)
{
    mReferenceConcentration = referenceConcentration;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractDiscreteContinuumLinearEllipticPde<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);
        for(unsigned idx=0; idx<mDiscreteSources.size(); idx++)
        {
            mDiscreteSources[idx]->SetRegularGrid(mpRegularGrid);
            std::vector<units::quantity<unit::concentration_flow_rate> > result = mDiscreteSources[idx]->GetConstantInURegularGridValues();
            std::transform(mDiscreteConstantSourceStrengths.begin( ), mDiscreteConstantSourceStrengths.end( ),
                           result.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.");
        }

        mDiscreteConstantSourceStrengths = std::vector<units::quantity<unit::concentration_flow_rate> >(mpMesh->GetNumElements(), 0.0*unit::mole_per_metre_cubed_per_second);
        for(unsigned idx=0; idx<mDiscreteSources.size(); idx++)
        {
            mDiscreteSources[idx]->SetMesh(mpMesh);
            std::vector<units::quantity<unit::concentration_flow_rate> > result = mDiscreteSources[idx]->GetConstantInUMeshValues();
            std::transform(mDiscreteConstantSourceStrengths.begin( ), mDiscreteConstantSourceStrengths.end( ),
                           result.begin( ), mDiscreteConstantSourceStrengths.begin( ),std::plus<units::quantity<unit::concentration_flow_rate> >( ));
        }
    }
}

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