DiscreteContinuumBoundaryCondition.cpp

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#include "Facet.hpp"
#include "DiscreteContinuumBoundaryCondition.hpp"
#include "VesselSegment.hpp"
#include "UnitCollection.hpp"
#include "BaseUnits.hpp"
#include "GeometryTools.hpp"

template<unsigned DIM>
DiscreteContinuumBoundaryCondition<DIM>::DiscreteContinuumBoundaryCondition()
    :   mpDomain(),
        mPoints(),
        mType(BoundaryConditionType::OUTER),
        mSource(BoundaryConditionSource::PRESCRIBED),
        mLabel("Default"),
        mValue(),
        mpRegularGrid(),
        mpMesh(),
        mpNetwork(),
        mReferenceConcentration(BaseUnits::Instance()->GetReferenceConcentrationScale())
{

}

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

}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetNetwork(boost::shared_ptr<VesselNetwork <DIM> > pNetwork)
{
    mpNetwork = pNetwork;
}

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

template<unsigned DIM>
units::quantity<unit::concentration> DiscreteContinuumBoundaryCondition<DIM>::GetValue()
{
    return mValue;
}

template<unsigned DIM>
BoundaryConditionType::Value DiscreteContinuumBoundaryCondition<DIM>::GetType()
{
    return mType;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateBoundaryConditionContainer(boost::shared_ptr<BoundaryConditionsContainer<DIM, DIM, 1> > pContainer)
{
    double node_distance_tolerance = 1.e-3;
    bool apply_boundary = true;
    bool use_boundry_nodes = false;
    units::quantity<unit::length> length_scale = mpMesh->GetReferenceLengthScale();

    if(mType == BoundaryConditionType::OUTER)
    {
        pContainer->DefineConstantDirichletOnMeshBoundary(mpMesh.get(), mValue/mReferenceConcentration);
        apply_boundary = false;
    }
    else if(mType == BoundaryConditionType::FACET || mType == BoundaryConditionType::VESSEL_VOLUME)
    {
        use_boundry_nodes = true;
    }

    if(apply_boundary)
    {
        if(!use_boundry_nodes)
        {
            // Collect the node locations

            if(mType == BoundaryConditionType::IN_PART)
            {
                if(!mpDomain)
                {
                    EXCEPTION("A part is required for this type of boundary condition");
                }
                else
                {
                    std::vector<DimensionalChastePoint<DIM> > locations(mpMesh->GetNumNodes());
                    std::vector<unsigned> mesh_nodes(mpMesh->GetNumNodes());

                    typename DiscreteContinuumMesh<DIM, DIM>::NodeIterator iter = mpMesh->GetNodeIteratorBegin();
                    unsigned counter=0;
                    while (iter != mpMesh->GetNodeIteratorEnd())
                     {
                         locations[counter] = DimensionalChastePoint<DIM>((*iter).GetPoint().rGetLocation(), length_scale);
                         mesh_nodes[counter] = (*iter).GetIndex();
                         counter++;
                         ++iter;
                     }
                    std::vector<bool> inside_flags = mpDomain->IsPointInPart(locations);
                    for(unsigned idx=0; idx<inside_flags.size(); idx++)
                    {
                        if(inside_flags[idx])
                        {
                            ConstBoundaryCondition<DIM>* p_fixed_boundary_condition = new ConstBoundaryCondition<DIM>(mValue/mReferenceConcentration);
                            pContainer->AddDirichletBoundaryCondition(mpMesh->GetNode(mesh_nodes[idx]), p_fixed_boundary_condition, 0, false);
                        }
                    }
                }
            }
            else
            {
                typename DiscreteContinuumMesh<DIM, DIM>::NodeIterator iter = mpMesh->GetNodeIteratorBegin();

                 while (iter != mpMesh->GetNodeIteratorEnd())
                 {
                     DimensionalChastePoint<DIM> probe_location((*iter).GetPoint().rGetLocation(), length_scale);
                     std::pair<bool,units::quantity<unit::concentration> > result = GetValue(probe_location, node_distance_tolerance);
                     if(result.first)
                     {
                         ConstBoundaryCondition<DIM>* p_fixed_boundary_condition = new ConstBoundaryCondition<DIM>(result.second/mReferenceConcentration);
                         pContainer->AddDirichletBoundaryCondition(&(*iter), p_fixed_boundary_condition, 0, false);
                     }
                     ++iter;
                 }
            }
        }
        else
        {
            typename DiscreteContinuumMesh<DIM, DIM>::BoundaryNodeIterator iter = mpMesh->GetBoundaryNodeIteratorBegin();

            while (iter < mpMesh->GetBoundaryNodeIteratorEnd())
            {
                DimensionalChastePoint<DIM> probe_location((*iter)->GetPoint().rGetLocation(), length_scale);
                std::pair<bool,units::quantity<unit::concentration> > result = GetValue(probe_location, node_distance_tolerance);
                if(result.first)
                {
                    ConstBoundaryCondition<DIM>* p_fixed_boundary_condition = new ConstBoundaryCondition<DIM>(result.second/mReferenceConcentration);
                    pContainer->AddDirichletBoundaryCondition(*iter, p_fixed_boundary_condition);
                }
                ++iter;
            }
        }
    }
}

template<unsigned DIM>
std::pair<bool, units::quantity<unit::concentration> > DiscreteContinuumBoundaryCondition<DIM>::GetValue(DimensionalChastePoint<DIM> location, double tolerance)
{
    units::quantity<unit::length> length_scale = location.GetReferenceLengthScale();
    std::pair<bool, units::quantity<unit::concentration> > result(false, 0.0*unit::mole_per_metre_cubed);
    if(mType == BoundaryConditionType::POINT)
    {
        if(mPoints.size()==0)
        {
            EXCEPTION("A point is required for this type of boundary condition");
        }
        else
        {
            for(unsigned jdx=0; jdx<mPoints.size(); jdx++)
            {
                if(GetDistance<DIM>(location, mPoints[jdx]) < tolerance*length_scale)
                {
                    return std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                }
            }
        }
    }
    else if(mType == BoundaryConditionType::FACET)
    {
        if(!mpDomain)
        {
            EXCEPTION("A part is required for this type of boundary condition");
        }
        else
        {
            std::vector<boost::shared_ptr<Facet<DIM> > > facets =  mpDomain->GetFacets();
            for(unsigned jdx=0; jdx<facets.size();jdx++)
            {
                if(facets[jdx]->ContainsPoint(location) && (facets[jdx]->GetLabel() == mLabel))
                {
                    return std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                }
            }
        }
    }

    else if(mType == BoundaryConditionType::VESSEL_LINE)
    {
        if(!mpNetwork)
        {
            EXCEPTION("A vessel network is required for this type of boundary condition");
        }
        else
        {
            std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments = this->mpNetwork->GetVesselSegments();
            for (unsigned jdx = 0; jdx <  segments.size(); jdx++)
            {
                if (segments[jdx]->GetDistance(location) <= tolerance*length_scale)
                {
                    if(BoundaryConditionSource::PRESCRIBED)
                    {
                        return std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                    }
                }
            }
        }
    }

    else if(mType == BoundaryConditionType::VESSEL_VOLUME)
    {
        if(!mpNetwork)
        {
            EXCEPTION("A vessel network is required for this type of boundary condition");
        }
        else
        {
            std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments = this->mpNetwork->GetVesselSegments();
            for (unsigned jdx = 0; jdx <  segments.size(); jdx++)
            {
                if (segments[jdx]->GetDistance(location) <= segments[jdx]->GetRadius() + tolerance*length_scale)
                {
                    if(BoundaryConditionSource::PRESCRIBED)
                    {
                        return std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                    }
                }
            }
        }
    }

    else if(mType == BoundaryConditionType::CELL)
    {
        EXCEPTION("Cell based boundary conditions are not yet supported.");
    }
    else if(mType == BoundaryConditionType::IN_PART)
    {
        if(!mpDomain)
        {
            EXCEPTION("A part is required for this type of boundary condition");
        }
        else
        {
            if(mpDomain->IsPointInPart(location))
            {
                if(BoundaryConditionSource::PRESCRIBED)
                {
                    return  std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                }
                else
                {
                    return  std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                }
            }
        }
    }
    return result;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridPointBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    if(mPoints.size()==0)
    {
        EXCEPTION("A point is required for this type of boundary condition");
    }
    else
    {
        std::vector<std::vector<unsigned> > point_point_map = mpRegularGrid->GetPointPointMap(mPoints);
        for(unsigned idx=0; idx<point_point_map.size(); idx++)
        {
            if(point_point_map[idx].size()>0)
            {
                (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
            }
        }
    }
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridFacetBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    if(!mpDomain)
    {
        EXCEPTION("A part is required for this type of boundary condition");
    }
    else
    {
        double y_max = double(mpRegularGrid->GetExtents()[1]-1) * mpRegularGrid->GetSpacing()/mpRegularGrid->GetReferenceLengthScale();
        for(unsigned idx=0; idx<mpRegularGrid->GetNumberOfPoints(); idx++)
        {
            if(mpRegularGrid->GetLocationOf1dIndex(idx).GetLocation(mpRegularGrid->GetReferenceLengthScale())[1] == y_max)
            {
                (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
            }

//            std::vector<boost::shared_ptr<Facet<DIM> > > facets =  mpDomain->GetFacets();
//            for(unsigned jdx=0; jdx<facets.size();jdx++)
//            {
//                if(facets[jdx]->ContainsPoint(mpRegularGrid->GetLocationOf1dIndex(idx)))
//                {
//                    if(BoundaryConditionSource::PRESCRIBED)
//                    {
//                        (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
//                        break;
//                    }
//                    else
//                    {
//                        if(facets[jdx]->GetLabel() == mLabel)
//                        {
//                            (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
//                            break;
//                        }
//                    }
//                }
//            }
        }
    }
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridSegmentBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > point_segment_map = mpRegularGrid->GetPointSegmentMap(true, !(mType == BoundaryConditionType::VESSEL_LINE));
    for(unsigned idx=0; idx<point_segment_map.size(); idx++)
    {
        if(point_segment_map[idx].size()>0)
        {
            if(BoundaryConditionSource::PRESCRIBED)
            {
                (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
            }
        }
    }
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridCellBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    EXCEPTION("Cell based boundary conditions are not yet supported.");
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridPartBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    if(!mpDomain)
    {
        EXCEPTION("A part is required for this type of boundary condition");
    }
    else
    {
        for(unsigned idx=0; idx<mpRegularGrid->GetNumberOfPoints(); idx++)
        {
            if(mpDomain->IsPointInPart(mpRegularGrid->GetLocationOf1dIndex(idx)))
            {
                if(BoundaryConditionSource::PRESCRIBED)
                {
                    (*pBoundaryConditions)[idx] =  std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                    break;
                }
                else
                {
                    (*pBoundaryConditions)[idx] =  std::pair<bool, units::quantity<unit::concentration> >(true, mValue);
                    break;
                }
            }
        }
    }
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::UpdateRegularGridBoundaryConditions(boost::shared_ptr<std::vector<std::pair<bool, units::quantity<unit::concentration> > > >pBoundaryConditions)
{
    if(! mpRegularGrid)
    {
        EXCEPTION("A grid has not been set for the determination of boundary condition values. For FE solvers use GetBoundaryConditionContainer()");
    }

    // Check the boundary condition type
    if(mType == BoundaryConditionType::OUTER)
    {
        for(unsigned idx=0; idx<mpRegularGrid->GetNumberOfPoints(); idx++)
        {
            (*pBoundaryConditions)[idx] = std::pair<bool, units::quantity<unit::concentration> > (mpRegularGrid->IsOnBoundary(idx), mValue);
        }
    }
    else if(mType == BoundaryConditionType::POINT)
    {
        UpdateRegularGridPointBoundaryConditions(pBoundaryConditions);
    }
    else if(mType == BoundaryConditionType::FACET)
    {
        UpdateRegularGridFacetBoundaryConditions(pBoundaryConditions);
    }
    else if(mType == BoundaryConditionType::VESSEL_LINE or mType == BoundaryConditionType::VESSEL_VOLUME)
    {
        UpdateRegularGridSegmentBoundaryConditions(pBoundaryConditions);
    }
    else if(mType == BoundaryConditionType::CELL)
    {
        UpdateRegularGridCellBoundaryConditions(pBoundaryConditions);
    }
    else if(mType == BoundaryConditionType::IN_PART)
    {
        UpdateRegularGridPartBoundaryConditions(pBoundaryConditions);
    }
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetDomain(boost::shared_ptr<Part<DIM> > pDomain)
{
    mpDomain = pDomain;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetPoints(std::vector<DimensionalChastePoint<DIM> > points)
{
    mPoints = points;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetSource(BoundaryConditionSource::Value boundarySource)
{
    mSource = boundarySource;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetType(BoundaryConditionType::Value boundaryType)
{
    mType = boundaryType;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetRegularGrid(boost::shared_ptr<RegularGrid<DIM> > pRegularGrid)
{
    mpRegularGrid = pRegularGrid;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetMesh(boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > pMesh)
{
    mpMesh = pMesh;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetLabelName(const std::string& label)
{
    mLabel = label;
}

template<unsigned DIM>
void DiscreteContinuumBoundaryCondition<DIM>::SetValue(units::quantity<unit::concentration> value)
{
    mValue = value;
}

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