FineCoarseMeshPair.cpp

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*/

#include "FineCoarseMeshPair.hpp"

template<unsigned DIM>
FineCoarseMeshPair<DIM>::FineCoarseMeshPair(TetrahedralMesh<DIM,DIM>& rFineMesh, TetrahedralMesh<DIM,DIM>& rCoarseMesh)
    : mrFineMesh(rFineMesh),
      mrCoarseMesh(rCoarseMesh)
{
    mpFineMeshBoxCollection = NULL;
    mpCoarseMeshBoxCollection = NULL;
    ResetStatisticsVariables();
}

template<unsigned DIM>
const TetrahedralMesh<DIM,DIM>& FineCoarseMeshPair<DIM>::GetFineMesh() const
{
    return  mrFineMesh;
}

template<unsigned DIM>
const TetrahedralMesh<DIM,DIM>& FineCoarseMeshPair<DIM>::GetCoarseMesh() const
{
    return  mrCoarseMesh;
}

template<unsigned DIM>
FineCoarseMeshPair<DIM>::~FineCoarseMeshPair()
{
    DeleteFineBoxCollection();
    DeleteCoarseBoxCollection();
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::DeleteFineBoxCollection()
{
    if (mpFineMeshBoxCollection != NULL)
    {
        delete mpFineMeshBoxCollection;
        mpFineMeshBoxCollection = NULL;
    }
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::DeleteCoarseBoxCollection()
{
    if (mpCoarseMeshBoxCollection != NULL)
    {
        delete mpCoarseMeshBoxCollection;
        mpCoarseMeshBoxCollection = NULL;
    }
}

//   Setting up boxes methods

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::SetUpBoxesOnFineMesh(double boxWidth)
{
    SetUpBoxes(mrFineMesh, boxWidth, mpFineMeshBoxCollection);
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::SetUpBoxesOnCoarseMesh(double boxWidth)
{
    SetUpBoxes(mrCoarseMesh, boxWidth, mpCoarseMeshBoxCollection);
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::SetUpBoxes(TetrahedralMesh<DIM,DIM>& rMesh,
                                         double boxWidth,
                                         BoxCollection<DIM>*& rpBoxCollection)
{
    if (rpBoxCollection)
    {
        delete rpBoxCollection;
        rpBoxCollection = NULL;
    }

    // Compute min and max values for the fine mesh nodes
    ChasteCuboid<DIM> bounding_box = rMesh.CalculateBoundingBox();

    // Set up the boxes using a domain that is slightly larger than the fine mesh
    c_vector<double,2*DIM> extended_min_and_max;
    for (unsigned i=0; i<DIM; i++)
    {
        double width = bounding_box.GetWidth(i);

        // Subtract from the minima
        extended_min_and_max(2*i) = bounding_box.rGetLowerCorner()[i] - 0.05*width;

        // Add to the maxima
        extended_min_and_max(2*i+1) = bounding_box.rGetUpperCorner()[i] + 0.05*width;
    }

    if (boxWidth < 0)
    {
        /*
         * Use default value = max(max_edge_length, w20),  where w20 is the width
         * corresponding to 20 boxes in the x-direction.
         *
         * BoxCollection creates an extra box so divide by 19 not 20. Add a little
         * bit on to ensure minor numerical fluctuations don't change the answer.
         */
        boxWidth = (extended_min_and_max(1) - extended_min_and_max(0))/19.000000001;

        // Determine the maximum edge length
        double max_edge_length = -1;

        for (typename TetrahedralMesh<DIM,DIM>::EdgeIterator edge_iterator = rMesh.EdgesBegin();
             edge_iterator!=rMesh.EdgesEnd();
             ++edge_iterator)
        {
            c_vector<double, 3> location1 = edge_iterator.GetNodeA()->rGetLocation();
            c_vector<double, 3> location2 = edge_iterator.GetNodeB()->rGetLocation();
            double edge_length = norm_2(location1-location2);

            if (edge_length>max_edge_length)
            {
                max_edge_length = edge_length;
            }
        }

        if (boxWidth < max_edge_length)
        {
            boxWidth = 1.1*max_edge_length;
        }
    }

    rpBoxCollection = new BoxCollection<DIM>(boxWidth, extended_min_and_max);
    rpBoxCollection->SetupAllLocalBoxes();

    // For each element, if ANY of its nodes are physically in a box, put that element in that box
    for (unsigned i=0; i<rMesh.GetNumElements(); i++)
    {
        Element<DIM,DIM>* p_element = rMesh.GetElement(i);

        std::set<unsigned> box_indices_each_node_this_elem;
        for (unsigned j=0; j<DIM+1; j++) // num vertices per element
        {
            Node<DIM>* p_node = p_element->GetNode(j);
            unsigned box_index = rpBoxCollection->CalculateContainingBox(p_node);
            box_indices_each_node_this_elem.insert(box_index);
        }

        for (std::set<unsigned>::iterator iter = box_indices_each_node_this_elem.begin();
            iter != box_indices_each_node_this_elem.end();
            ++iter)
        {
            rpBoxCollection->rGetBox( *iter ).AddElement(p_element);
        }
    }
}

// ComputeFineElementsAndWeightsForCoarseQuadPoints()
// and
// ComputeFineElementsAndWeightsForCoarseNodes()
// and
// common method

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ComputeFineElementsAndWeightsForCoarseQuadPoints(GaussianQuadratureRule<DIM>& rQuadRule,
                                                                               bool safeMode)
{
    if (mpFineMeshBoxCollection == NULL)
    {
        EXCEPTION("Call SetUpBoxesOnFineMesh() before ComputeFineElementsAndWeightsForCoarseQuadPoints()");
    }

    // Get the quad point (physical) positions
    QuadraturePointsGroup<DIM> quad_point_posns(mrCoarseMesh, rQuadRule);

    // Resize the elements and weights vector.
    mFineMeshElementsAndWeights.resize(quad_point_posns.Size());

    #define COVERAGE_IGNORE
    if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
    {
        std::cout << "\nComputing fine elements and weights for coarse quad points\n";
    }
    #undef COVERAGE_IGNORE


    ResetStatisticsVariables();
    for (unsigned i=0; i<quad_point_posns.Size(); i++)
    {
        #define COVERAGE_IGNORE
        if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
        {
            std::cout << "\r " << i << " of " << quad_point_posns.Size() << std::flush;
        }
        #undef COVERAGE_IGNORE

        // Get the box this point is in
        unsigned box_for_this_point = mpFineMeshBoxCollection->CalculateContainingBox( quad_point_posns.Get(i) );

        // A chaste point version of the c-vector is needed for the GetContainingElement call.
        ChastePoint<DIM> point(quad_point_posns.Get(i));

        ComputeFineElementAndWeightForGivenPoint(point, safeMode, box_for_this_point, i);
    }

    if (mStatisticsCounters[1] > 0)
    {
        WARNING(mStatisticsCounters[1] << " of " << quad_point_posns.Size() << " coarse-mesh quadrature points were outside the fine mesh");
    }
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ComputeFineElementsAndWeightsForCoarseNodes(bool safeMode)
{
    if (mpFineMeshBoxCollection==NULL)
    {
        EXCEPTION("Call SetUpBoxesOnFineMesh() before ComputeFineElementsAndWeightsForCoarseNodes()");
    }

    // Resize the elements and weights vector.
    mFineMeshElementsAndWeights.resize(mrCoarseMesh.GetNumNodes());

    #define COVERAGE_IGNORE
    if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
    {
        std::cout << "\nComputing fine elements and weights for coarse nodes\n";
    }
    #undef COVERAGE_IGNORE


    ResetStatisticsVariables();
    for (unsigned i=0; i<mrCoarseMesh.GetNumNodes(); i++)
    {
        #define COVERAGE_IGNORE
        if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
        {
            std::cout << "\r " << i << " of " << mrCoarseMesh.GetNumNodes() << std::flush;
        }
        #undef COVERAGE_IGNORE

        Node<DIM>* p_node = mrCoarseMesh.GetNode(i);

        // Get the box this point is in
        unsigned box_for_this_point = mpFineMeshBoxCollection->CalculateContainingBox( p_node->rGetModifiableLocation() );

        // A chaste point version of the c-vector is needed for the GetContainingElement call
        ChastePoint<DIM> point(p_node->rGetLocation());

        ComputeFineElementAndWeightForGivenPoint(point, safeMode, box_for_this_point, i);
    }
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ComputeFineElementAndWeightForGivenPoint(ChastePoint<DIM>& rPoint,
                                                                       bool safeMode,
                                                                       unsigned boxForThisPoint,
                                                                       unsigned index)
{
    std::set<unsigned> test_element_indices;

    /*
     * The elements to try (initially) are those contained in the box the point is in.
     *
     * Note: it is possible the point to be in an element not 'in' this box, as it is
     * possible for all element nodes to be in different boxes.
     */
    CollectElementsInContainingBox(mpFineMeshBoxCollection, boxForThisPoint, test_element_indices);

    unsigned elem_index;
    c_vector<double,DIM+1> weight;

    try
    {
        //std::cout << "\n" << "# test elements initially " << test_element_indices.size() << "\n";
        // Try these elements only, initially
        elem_index = mrFineMesh.GetContainingElementIndex(rPoint,
                                                          false,
                                                          test_element_indices,
                                                          true /* quit if not in test_elements */);
        weight = mrFineMesh.GetElement(elem_index)->CalculateInterpolationWeights(rPoint);

        mStatisticsCounters[0]++;
    }
    catch(Exception& e)
    {
        // Now try all elements, trying the elements contained in the boxes local to this element first
        std::set<unsigned> test_element_indices;

        CollectElementsInLocalBoxes(mpFineMeshBoxCollection, boxForThisPoint, test_element_indices);

        try
        {
            elem_index = mrFineMesh.GetContainingElementIndex(rPoint, false, test_element_indices, true);
            weight = mrFineMesh.GetElement(elem_index)->CalculateInterpolationWeights(rPoint);
            mStatisticsCounters[0]++;
        }
        catch(Exception& e)
        {
            if (safeMode)
            {
                // Try the remaining elements
                try
                {
                    elem_index = mrFineMesh.GetContainingElementIndex(rPoint, false);
                    weight = mrFineMesh.GetElement(elem_index)->CalculateInterpolationWeights(rPoint);
                    mStatisticsCounters[0]++;

                }
                catch (Exception& e)
                {
                    // The point is not in ANY element, so store the nearest element and corresponding weights
                    elem_index = mrFineMesh.GetNearestElementIndexFromTestElements(rPoint,test_element_indices);
                    weight = mrFineMesh.GetElement(elem_index)->CalculateInterpolationWeights(rPoint);

                    mNotInMesh.push_back(index);
                    mNotInMeshNearestElementWeights.push_back(weight);
                    mStatisticsCounters[1]++;
                }
            }
            else
            {
                assert(test_element_indices.size() > 0); // boxes probably too small if this fails

                /*
                 * Immediately assume it isn't in the rest of the mesh - this should be the
                 * case assuming the box width was chosen suitably. Store the nearest element
                 * and corresponding weights.
                 */
                elem_index = mrFineMesh.GetNearestElementIndexFromTestElements(rPoint,test_element_indices);
                weight = mrFineMesh.GetElement(elem_index)->CalculateInterpolationWeights(rPoint);

                mNotInMesh.push_back(index);
                mNotInMeshNearestElementWeights.push_back(weight);
                mStatisticsCounters[1]++;
            }
        }
    }

    mFineMeshElementsAndWeights[index].ElementNum = elem_index;
    mFineMeshElementsAndWeights[index].Weights = weight;
}

// ComputeCoarseElementsForFineNodes
// and
// ComputeCoarseElementsForFineElementCentroids
// and
// common method

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ComputeCoarseElementsForFineNodes(bool safeMode)
{
    if (mpCoarseMeshBoxCollection==NULL)
    {
        EXCEPTION("Call SetUpBoxesOnCoarseMesh() before ComputeCoarseElementsForFineNodes()");
    }

    #define COVERAGE_IGNORE
    if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
    {
        std::cout << "\nComputing coarse elements for fine nodes\n";
    }
    #undef COVERAGE_IGNORE

    mCoarseElementsForFineNodes.resize(mrFineMesh.GetNumNodes());

    ResetStatisticsVariables();
    for (unsigned i=0; i<mCoarseElementsForFineNodes.size(); i++)
    {
        #define COVERAGE_IGNORE
        if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
        {
            std::cout << "\r " << i << " of " << mCoarseElementsForFineNodes.size() << std::flush;
        }
        #undef COVERAGE_IGNORE

        ChastePoint<DIM> point = mrFineMesh.GetNode(i)->GetPoint();

        // Get the box this point is in
        unsigned box_for_this_point = mpCoarseMeshBoxCollection->CalculateContainingBox(mrFineMesh.GetNode(i)->rGetModifiableLocation());

        mCoarseElementsForFineNodes[i] = ComputeCoarseElementForGivenPoint(point, safeMode, box_for_this_point);
    }
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ComputeCoarseElementsForFineElementCentroids(bool safeMode)
{
    if (mpCoarseMeshBoxCollection==NULL)
    {
        EXCEPTION("Call SetUpBoxesOnCoarseMesh() before ComputeCoarseElementsForFineElementCentroids()");
    }

    #define COVERAGE_IGNORE
    if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
    {
        std::cout << "\nComputing coarse elements for fine element centroids\n";
    }
    #undef COVERAGE_IGNORE

    mCoarseElementsForFineElementCentroids.resize(mrFineMesh.GetNumElements());

    ResetStatisticsVariables();
    for (unsigned i=0; i<mrFineMesh.GetNumElements(); i++)
    {
        #define COVERAGE_IGNORE
        if(CommandLineArguments::Instance()->OptionExists("-mesh_pair_verbose"))
        {
            std::cout << "\r " << i << " of " << mrFineMesh.GetNumElements() << std::flush;
        }
        #undef COVERAGE_IGNORE

        c_vector<double,DIM> point_cvec = mrFineMesh.GetElement(i)->CalculateCentroid();
        ChastePoint<DIM> point(point_cvec);

        // Get the box this point is in
        unsigned box_for_this_point = mpCoarseMeshBoxCollection->CalculateContainingBox( point_cvec );

        mCoarseElementsForFineElementCentroids[i] = ComputeCoarseElementForGivenPoint(point, safeMode, box_for_this_point);
    }
}

template<unsigned DIM>
unsigned FineCoarseMeshPair<DIM>::ComputeCoarseElementForGivenPoint(ChastePoint<DIM>& rPoint,
                                                                    bool safeMode,
                                                                    unsigned boxForThisPoint)
{
    std::set<unsigned> test_element_indices;
    CollectElementsInContainingBox(mpCoarseMeshBoxCollection, boxForThisPoint, test_element_indices);

    unsigned elem_index;

    try
    {
        elem_index = mrCoarseMesh.GetContainingElementIndex(rPoint,
                                                            false,
                                                            test_element_indices,
                                                            true /* quit if not in test_elements */);

        mStatisticsCounters[0]++;
    }
    catch(Exception& e)
    {
        // Now try all elements, trying the elements contained in the boxes local to this element first
        std::set<unsigned> test_element_indices;
        CollectElementsInLocalBoxes(mpCoarseMeshBoxCollection, boxForThisPoint, test_element_indices);

        try
        {
            elem_index = mrCoarseMesh.GetContainingElementIndex(rPoint, false, test_element_indices, true);
            mStatisticsCounters[0]++;
        }
        catch(Exception& e)
        {
            if (safeMode)
            {
                // Try the remaining elements
                try
                {
                    elem_index = mrCoarseMesh.GetContainingElementIndex(rPoint, false);

                    mStatisticsCounters[0]++;
                }
                catch (Exception& e)
                {
                    // The point is not in ANY element, so store the nearest element and corresponding weights
                    elem_index = mrCoarseMesh.GetNearestElementIndexFromTestElements(rPoint,test_element_indices);
                    mStatisticsCounters[1]++;
                }
            }
            else
            {
                assert(test_element_indices.size() > 0); // boxes probably too small if this fails

                /*
                 * Immediately assume it isn't in the rest of the mesh - this should be the
                 * case assuming the box width was chosen suitably. Store the nearest element
                 * and corresponding weights.
                 */
                elem_index = mrCoarseMesh.GetNearestElementIndexFromTestElements(rPoint,test_element_indices);
                mStatisticsCounters[1]++;
            }
        }
    }

    return elem_index;
}

// Helper methods for code

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::CollectElementsInContainingBox(BoxCollection<DIM>*& rpBoxCollection,
                                                             unsigned boxIndex,
                                                             std::set<unsigned>& rElementIndices)
{
    for (typename std::set<Element<DIM,DIM>*>::iterator elem_iter = rpBoxCollection->rGetBox(boxIndex).rGetElementsContained().begin();
         elem_iter != rpBoxCollection->rGetBox(boxIndex).rGetElementsContained().end();
         ++elem_iter)
    {
        rElementIndices.insert((*elem_iter)->GetIndex());
    }
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::CollectElementsInLocalBoxes(BoxCollection<DIM>*& rpBoxCollection,
                                                          unsigned boxIndex,
                                                          std::set<unsigned>& rElementIndices)
{
    std::set<unsigned> local_boxes = rpBoxCollection->GetLocalBoxes(boxIndex);
    for (std::set<unsigned>::iterator local_box_iter = local_boxes.begin();
         local_box_iter != local_boxes.end();
         ++local_box_iter)
    {
        for (typename std::set<Element<DIM,DIM>*>::iterator elem_iter = rpBoxCollection->rGetBox(*local_box_iter).rGetElementsContained().begin();
             elem_iter != rpBoxCollection->rGetBox(*local_box_iter).rGetElementsContained().end();
             ++elem_iter)
        {
            rElementIndices.insert((*elem_iter)->GetIndex());
        }
    }
}

// Statistics related methods

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::ResetStatisticsVariables()
{
    mNotInMesh.clear();
    mNotInMeshNearestElementWeights.clear();
    mStatisticsCounters.resize(2, 0u);
}

template<unsigned DIM>
void FineCoarseMeshPair<DIM>::PrintStatistics()
{
    std::cout << "\nFineCoarseMeshPair statistics for the last-called method:\n";

//    std::cout << "\tNum points for which containing element was found, using box containing that point = " << mStatisticsCounters[0] << "\n";
//    std::cout << "\tNum points for which containing element was in local box = " << mStatisticsCounters[1] << "\n";
//    std::cout << "\tNum points for which containing element was in an element in a non-local box = " << mStatisticsCounters[2] << "\n";
//    std::cout << "\tNum points for which no containing element was found = " << mStatisticsCounters[3] << "\n";

    std::cout << "\tNum points for which containing element was found: " << mStatisticsCounters[0] << "\n";
    std::cout << "\tNum points for which no containing element was found = " << mStatisticsCounters[1] << "\n";

    if (mNotInMesh.size() > 0)
    {
        std::cout << "\tIndices and weights for points (nodes/quad points) for which no containing element was found:\n";
        for (unsigned i=0; i<mNotInMesh.size(); i++)
        {
            std::cout << "\t\t" << mNotInMesh[i] << ", " << mNotInMeshNearestElementWeights[i] << "\n";
        }
    }
}

// Explicit instantiation

template class FineCoarseMeshPair<1>;
template class FineCoarseMeshPair<2>;
template class FineCoarseMeshPair<3>;