VoronoiVertexMeshGenerator.cpp

/*

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*/

#include "VoronoiVertexMeshGenerator.hpp"

#if BOOST_VERSION >= 105200

using boost::polygon::voronoi_builder;
using boost::polygon::voronoi_diagram;
typedef boost::polygon::point_data<int> boost_point;

VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator(unsigned numElementsX,
                                                       unsigned numElementsY,
                                                       unsigned numRelaxationSteps,
                                                       double elementTargetArea)
        : mpMesh(NULL),
          mpTorMesh(NULL),
          mNumElementsX(numElementsX),
          mNumElementsY(numElementsY),
          mNumRelaxationSteps(numRelaxationSteps),
          mElementTargetArea(elementTargetArea),
          mTol(1e-7),
          mMaxExpectedNumSidesPerPolygon(17)
{
    this->ValidateInputAndSetMembers();
    this->GenerateVoronoiMesh();
}

VoronoiVertexMeshGenerator::~VoronoiVertexMeshGenerator()
{
    if (mpMesh)
    {
        delete mpMesh;
    }
    if (mpTorMesh)
    {
        delete mpTorMesh;
    }
}

void VoronoiVertexMeshGenerator::GenerateVoronoiMesh()
{
    // Get initial seed locations
    std::vector<c_vector<double, 2> > seed_locations = this->GetInitialPointLocations();
    this->ValidateSeedLocations(seed_locations);

    // We now create the initial Voronoi tessellation. This method updates mpMesh.
    this->CreateVoronoiTessellation(seed_locations);

    for (unsigned relaxation = 0 ; relaxation < mNumRelaxationSteps ; relaxation++)
    {
        seed_locations.clear();
        seed_locations = this->GetElementCentroidsFromMesh();

        this->CreateVoronoiTessellation(seed_locations);
    }

    // We need to modify the node locations to achieve the correct target average element area
    double scale_factor = double(mMaxNumElems) * sqrt(mElementTargetArea);
    for (unsigned node_idx = 0 ; node_idx < mpMesh->GetNumNodes() ; node_idx++)
    {
        c_vector<double, 2>& node_location = mpMesh->GetNode(node_idx)->rGetModifiableLocation();
        node_location *= scale_factor;
    }
}

MutableVertexMesh<2,2>* VoronoiVertexMeshGenerator::GetMesh()
{
    return mpMesh;
}

MutableVertexMesh<2,2>* VoronoiVertexMeshGenerator::GetMeshAfterReMesh()
{
    mpMesh->ReMesh();
    return mpMesh;
}

Toroidal2dVertexMesh* VoronoiVertexMeshGenerator::GetToroidalMesh()
{
    /*
     * METHOD OUTLINE:
     *
     * 1. Copy nodes and elements from mpMesh into a new MutableVertexMesh, so no data is shared between mpMesh and the
     *    nodes and elements we will be working with.  There are no available copy constructors, so this is done from
     *    scratch.
     *
     * 2. Identify which nodes on the boundary are congruent to each other.  This is done by recursively using the
     *    helper function CheckForCongruentNodes().
     *
     * 3. Create mpTorMesh by copying the subset of remaining nodes and all elements in the new MutableVertexMesh.
     *    Some elements have been modified to replace nodes by congruent partner nodes and some nodes have been deleted.
     */

    // The width and height of the mesh for periodicity purposes
    double width  = mNumElementsX * sqrt(mElementTargetArea);
    double height = mNumElementsY * sqrt(mElementTargetArea);

    // We need to construct new nodes and elements so we don't have mpTorMesh sharing data with mpMesh
    std::vector<Node<2>*> new_nodes(mpMesh->GetNumNodes());
    std::vector<VertexElement<2,2>*> new_elems(mpMesh->GetNumElements());

    // Copy nodes
    for (unsigned node_counter = 0 ; node_counter < mpMesh->GetNumNodes() ; node_counter++)
    {
        Node<2>* p_node_to_copy = mpMesh->GetNode(node_counter);

        // Get all the information about the node we are copying
        unsigned            copy_index       = p_node_to_copy->GetIndex();
        c_vector<double, 2> copy_location    = p_node_to_copy->rGetLocation();
        bool                copy_is_boundary = p_node_to_copy->IsBoundaryNode();

        // There should not be any 'gaps' in node numbering, but we will assert just to make sure
        assert(copy_index < mpMesh->GetNumNodes());

        // Create a new node and place it in index order. Every node in a periodic mesh is non-boundary.
        new_nodes[copy_index] = new Node<2>(copy_index, copy_location, copy_is_boundary);
    }

    // Copy elements
    for (unsigned elem_counter = 0; elem_counter < mpMesh->GetNumElements(); elem_counter++)
    {
        VertexElement<2,2>* p_elem_to_copy = mpMesh->GetElement(elem_counter);

        // Get the information relating to the element we are copying
        unsigned copy_index     = p_elem_to_copy->GetIndex();
        unsigned copy_num_nodes = p_elem_to_copy->GetNumNodes();

        // There should not be any 'gaps' in element numbering, but we will assert just to make sure
        assert(copy_index < mpMesh->GetNumElements());

        // The vertex element is created from a vector of nodes
        std::vector<Node<2>*> nodes_this_elem;

        // Loop through the nodes in p_elem_to_copy and add the corresponding nodes that we have already copied
        for (unsigned node_local_idx = 0 ; node_local_idx < copy_num_nodes ; node_local_idx++)
        {
            Node<2>* p_local_node = p_elem_to_copy->GetNode(node_local_idx);
            unsigned local_node_global_idx = p_local_node->GetIndex();
            nodes_this_elem.push_back(new_nodes[local_node_global_idx]);
        }

        // Create a new node and place it in index order
        new_elems[copy_index] = new VertexElement<2,2>(copy_index, nodes_this_elem);
    }

    // We can now create the mesh with new_elements and the subset of new_nodes
    MutableVertexMesh<2,2>* p_temp_mesh = new MutableVertexMesh<2,2>(new_nodes, new_elems);

    /*
     * Recursively associate congruent nodes.
     *
     * For each node currently on the boundary, we loop through all other boundary nodes and check against all eight
     * possible congruent locations.  If any one coincides, we replace the identified node with its congruent partner,
     * delete and remove the identified node from the mesh, and start again from scratch.
     *
     * If a node has no congruent partners, we simply mark it as non-boundary, as it is then a node that needs to appear
     * in the final toroidal mesh.
     *
     * This recursion is guaranteed to terminate as the number of boundary nodes decreases by precisely one each time
     * CheckForCongruentNodes() is called, and CheckForCongruentNodes() returns false if there are no boundary nodes.
     */
    bool re_check = true;

    while (re_check)
    {
        re_check = this->CheckForCongruentNodes(p_temp_mesh, width, height);
    }

    // We now copy the nodes and elements into a new toroidal mesh, and delete p_temp_mesh
    new_nodes.clear();
    new_nodes.resize(p_temp_mesh->GetNumNodes());

    new_elems.clear();
    new_elems.resize(p_temp_mesh->GetNumElements());

    // Copy nodes
    for (unsigned node_counter = 0 ; node_counter < p_temp_mesh->GetNumNodes() ; node_counter++)
    {
        Node<2>* p_node_to_copy = p_temp_mesh->GetNode(node_counter);

        // Get all the information about the node we are copying
        unsigned            copy_index       = p_node_to_copy->GetIndex();
        c_vector<double, 2> copy_location    = p_node_to_copy->rGetLocation();
        bool                copy_is_boundary = p_node_to_copy->IsBoundaryNode();

        // No nodes should be boundary nodes
        assert(!copy_is_boundary);

        // There should not be any 'gaps' in node numbering, but we will assert just to make sure
        assert(copy_index < p_temp_mesh->GetNumNodes());

        // Create a new node and place it in index order. Every node in a periodic mesh is non-boundary.
        new_nodes[copy_index] = new Node<2>(copy_index, copy_location, false);
    }

    // Copy elements
    for (unsigned elem_counter = 0; elem_counter < p_temp_mesh->GetNumElements(); elem_counter++)
    {
        VertexElement<2,2>* p_elem_to_copy = p_temp_mesh->GetElement(elem_counter);

        // Get the information relating to the element we are copying
        unsigned copy_index     = p_elem_to_copy->GetIndex();
        unsigned copy_num_nodes = p_elem_to_copy->GetNumNodes();

        // There should not be any 'gaps' in element numbering, but we will assert just to make sure
        assert(copy_index < p_temp_mesh->GetNumElements());

        // The vertex element is created from a vector of nodes
        std::vector<Node<2>*> nodes_this_elem;

        // Loop through the nodes in p_elem_to_copy and add the corresponding nodes that we have already copied
        for (unsigned node_local_idx = 0 ; node_local_idx < copy_num_nodes ; node_local_idx++)
        {
            Node<2>* p_local_node = p_elem_to_copy->GetNode(node_local_idx);

            unsigned local_node_global_idx = p_local_node->GetIndex();

            nodes_this_elem.push_back(new_nodes[local_node_global_idx]);
        }

        // Create a new node and place it in index order
        new_elems[copy_index] = new VertexElement<2,2>(copy_index, nodes_this_elem);
    }

    delete p_temp_mesh;

    /*
     * We now create the mesh with new_elements and new_nodes.  We immediately call ReMesh() to tidy up any short edges.
     *
     * We then reposition all nodes to be within the box [0, width]x[0, height] to make mesh look nicer when visualised.
     */
    mpTorMesh = new Toroidal2dVertexMesh(width, height, new_nodes, new_elems);
    mpTorMesh->ReMesh();

    c_vector<double, 2> min_x_y;
    min_x_y[0] = DBL_MAX;
    min_x_y[1] = DBL_MAX;

    // First loop is to calculate the correct offset, min_x_y
    for (unsigned node_idx = 0 ; node_idx < mpTorMesh->GetNumNodes() ; node_idx++)
    {
        c_vector<double, 2> this_node_location = mpTorMesh->GetNode(node_idx)->rGetLocation();

        if(this_node_location[0] < min_x_y[0])
        {
            min_x_y[0] = this_node_location[0];
        }
        if(this_node_location[1] < min_x_y[1])
        {
            min_x_y[1] = this_node_location[1];
        }
    }

    // Second loop applies the offset, min_x_y, to each node in the mesh
    for (unsigned node_idx = 0 ; node_idx < mpTorMesh->GetNumNodes() ; node_idx++)
    {
        mpTorMesh->GetNode(node_idx)->rGetModifiableLocation() -= min_x_y;
    }

    // Third loop is to reposition any nodes that are now outside the bounding rectangle
    for (unsigned node_idx = 0 ; node_idx < mpTorMesh->GetNumNodes() ; node_idx++)
    {
        if (mpTorMesh->GetNode(node_idx)->rGetLocation()[0] >= width)
        {
            mpTorMesh->GetNode(node_idx)->rGetModifiableLocation()[0] -= width;
        }
        if (mpTorMesh->GetNode(node_idx)->rGetLocation()[1] >= height)
        {
            mpTorMesh->GetNode(node_idx)->rGetModifiableLocation()[1] -= height;
        }
    }

    return mpTorMesh;
}

bool VoronoiVertexMeshGenerator::CheckForCongruentNodes(MutableVertexMesh<2,2>* pMesh, double width, double height)
{
    // First find all the current boundary nodes in pMesh
    std::vector<Node<2>*> boundary_nodes;
    for (unsigned node_idx = 0 ; node_idx < pMesh->GetNumNodes() ; node_idx++)
    {
        Node<2>* p_node = pMesh->GetNode(node_idx);

        if (p_node->IsBoundaryNode())
        {
            boundary_nodes.push_back(p_node);
        }
    }

    // If there are no boundary nodes, return false (we're done checking congruencies)
    if (boundary_nodes.empty())
    {
        return false;
    }

    // Otherwise, calculate the eight possible congruent locations for the current node
    Node<2>* p_node_a = *(boundary_nodes.begin());
    c_vector<double, 2> node_a_pos = p_node_a->rGetLocation();
    std::vector<c_vector<double,2> > congruent_locations(8, node_a_pos);

    congruent_locations[0][0] += width;

    congruent_locations[1][1] += height;

    congruent_locations[2][0] -= width;

    congruent_locations[3][1] -= height;

    congruent_locations[4][0] += width;
    congruent_locations[4][1] += height;

    congruent_locations[5][0] -= width;
    congruent_locations[5][1] += height;

    congruent_locations[6][0] -= width;
    congruent_locations[6][1] -= height;

    congruent_locations[7][0] += width;
    congruent_locations[7][1] -= height;

    // Loop over all other boundary nodes
    for (unsigned node_b_counter = 0; node_b_counter < boundary_nodes.size(); node_b_counter++)
    {
        // Get the index of the current boundary node, and the corresponding node from the mesh
        unsigned node_b_idx = boundary_nodes[node_b_counter]->GetIndex();
        Node<2>* p_mesh_node_b = pMesh->GetNode(node_b_idx);

        if (p_node_a == p_mesh_node_b)
        {
            continue;
        }

        c_vector<double, 2> node_b_pos = p_mesh_node_b->rGetLocation();

        // Loop over the eight possible congruent locations and check for coincidence of location
        for (unsigned pos = 0 ; pos < congruent_locations.size() ; pos++)
        {
            if (norm_inf(node_b_pos - congruent_locations[pos]) < mTol)
            {
                // Once we find a congruent location, we replace that node in all containing elements
                std::set<unsigned> containing_elems = p_mesh_node_b->rGetContainingElementIndices();

                assert(containing_elems.size() > 0);

                for (std::set<unsigned>::iterator it = containing_elems.begin() ; it != containing_elems.end() ; ++it)
                {
                    VertexElement<2,2>* p_this_elem = pMesh->GetElement(*it);
                    unsigned local_idx = p_this_elem->GetNodeLocalIndex(p_mesh_node_b->GetIndex());

                    assert(local_idx < UINT_MAX);

                    p_this_elem->AddNode(p_node_a, local_idx);
                    p_this_elem->DeleteNode(local_idx);
                }

                // Delete the node_b and remove it from the mesh, and return true to start checking again from scratch
                pMesh->DeleteNodePriorToReMesh(p_mesh_node_b->GetIndex());
                pMesh->RemoveDeletedNodes();
                return true;
            }
        }
    }

    /*
     * If we have checked p_node_a against all node_b candidates and have not found a congruent location, p_node_a can
     * be re-tagged as a non-boundary node, and so will not get checked again next time this function is called.
     */
    p_node_a->SetAsBoundaryNode(false);

    return true;
}

std::vector<c_vector<double, 2> > VoronoiVertexMeshGenerator::GetInitialPointLocations()
{
    // Create a vector which contains mTotalNumElements spaces
    std::vector<c_vector<double, 2> > seed_points(mTotalNumElements);

    RandomNumberGenerator* p_rand_gen = RandomNumberGenerator::Instance();

    // Create the correct number of suitably scaled random numbers
    for (unsigned point_idx = 0 ; point_idx < mTotalNumElements ; point_idx++)
    {
        seed_points[point_idx][0] = p_rand_gen->ranf() * mMultiplierInX;
        seed_points[point_idx][1] = p_rand_gen->ranf() * mMultiplierInY;
    }

    return seed_points;
}

std::vector<c_vector<double, 2> > VoronoiVertexMeshGenerator::GetElementCentroidsFromMesh()
{
    assert(mpMesh->GetNumElements() == mNumElementsX * mNumElementsY);

    std::vector<c_vector<double, 2> > element_centroids;

    // Loop over all elements in the mesh
    for (unsigned elem_idx = 0; elem_idx < mpMesh->GetNumElements(); elem_idx++)
    {
        // Get the current centroid of the element
        c_vector<double, 2> this_centroid = mpMesh->GetCentroidOfElement(elem_idx);

        // Account for possible wrap-around in the x-direction
        if (this_centroid[0] < 0.0)
        {
            this_centroid[0] += mMultiplierInX;
        }
        else if (this_centroid[0] > mMultiplierInX)
        {
            this_centroid[0] -= mMultiplierInX;
        }

        // Account for possible wrap-around in the y-direction
        if (this_centroid[1] < 0.0)
        {
            this_centroid[1] += mMultiplierInY;
        }
        else if (this_centroid[1] > mMultiplierInY)
        {
            this_centroid[1] -= mMultiplierInY;
        }

        element_centroids.push_back(this_centroid);
    }

    return element_centroids;
}

void VoronoiVertexMeshGenerator::CreateVoronoiTessellation(std::vector<c_vector<double, 2> >& rSeedLocations)
{
    // Clear the mesh nodes and elements, as they will be replaced in this method
    std::vector<Node<2>*> nodes;
    std::vector<VertexElement<2, 2>* > elements;

    // Datatype is boost::polygon::point_data<int>
    std::vector<boost_point> points;

    // Take the locations and map them to integers in a subset of [0, INT_MAX/2] x [0, INT_MAX/2]
    for (unsigned point_idx = 0 ; point_idx < rSeedLocations.size() ; point_idx++)
    {
        // Calculate the correct integer gridpoints
        int point_x = int( floor( (rSeedLocations[point_idx][0] * mSamplingMultiplier) + 0.5) );
        int point_y = int( floor( (rSeedLocations[point_idx][1] * mSamplingMultiplier) + 0.5) );

        points.push_back( boost_point(point_x, point_y) );
    }

    // Define offset vectors for the 3 by 3 tessellation
    std::vector<boost_point> offsets;
    offsets.push_back( boost_point(-mMaxIntX,  mMaxIntY) );
    offsets.push_back( boost_point(        0,  mMaxIntY) );
    offsets.push_back( boost_point( mMaxIntX,  mMaxIntY) );
    offsets.push_back( boost_point( mMaxIntX,         0) );
    offsets.push_back( boost_point( mMaxIntX, -mMaxIntY) );
    offsets.push_back( boost_point(        0, -mMaxIntY) );
    offsets.push_back( boost_point(-mMaxIntX, -mMaxIntY) );
    offsets.push_back( boost_point(-mMaxIntX,         0) );

    // Add all the points in the tessellation to the vector of boost points so in total there are 9 copies of each
    // seed location, suitably tiled.
    for (unsigned rep = 0; rep < offsets.size(); rep++)
    {
        boost_point offset = offsets[rep];
        for (unsigned point_idx = 0; point_idx < rSeedLocations.size(); point_idx++)
        {
            boost_point new_point = boost_point(points[point_idx].x() + offset.x(), points[point_idx].y() + offset.y());
            points.push_back(new_point);
        }
    }

    // Construct the Voronoi tessellation of these 9 x mTotalNumElements points
    voronoi_diagram<double> vd;
    construct_voronoi(points.begin(), points.end(), &vd);

    // Loop over the cells in the voronoi diagram to find nodes for our mesh
    for (voronoi_diagram<double>::const_cell_iterator it = vd.cells().begin();
         it != vd.cells().end();
         ++it)
    {
        // Get a reference to the current cell
        const voronoi_diagram<double>::cell_type& cell = *it;

        // The cells we care about are exactly those whose source_index is less than the size of the locations vector
        // (i.e. those cells in the central portion of the 3x3 tessellation of source points)
        if (cell.source_index() < rSeedLocations.size())
        {
            // We create a vector of nodes, which will be used to create a MutableElement
            std::vector<Node<2>*> nodes_this_elem;

            // Loop over the edges of the current cell
            const voronoi_diagram<double>::edge_type *edge = cell.incident_edge();

            do
            {
                if (edge->is_primary())
                {
                    // Calculate the location corresponding to the location of vertex0 of the current edge
                    double x_location = (edge->vertex0()->x()) / mSamplingMultiplier;
                    double y_location = (edge->vertex0()->y()) / mSamplingMultiplier;

                    // Create a node at this location.  Default to non-boundary node; this will be updated later
                    Node<2>* p_this_node = new Node<2>(nodes.size(), false, x_location, y_location);

                    unsigned existing_node_idx = UINT_MAX;

                    for (unsigned node_idx = 0; node_idx < nodes.size(); node_idx++)
                    {
                        // Grab the existing node location
                        c_vector<double, 2> existing_node_location = nodes[node_idx]->rGetLocation();

                        // Equality here is determined entirely on coincidence of position
                        if ( fabs(existing_node_location[0] - p_this_node->rGetLocation()[0]) < DBL_EPSILON )
                        {
                            if ( fabs(existing_node_location[1] - p_this_node->rGetLocation()[1]) < DBL_EPSILON )
                            {
                                // If the nodes match, return the existing node index
                                existing_node_idx = node_idx;
                            }
                        }
                    }

                    if (existing_node_idx < UINT_MAX)
                    {
                        // The node was already in nodes vector, and its index is the variable 'existing_node'
                        nodes_this_elem.push_back(nodes[existing_node_idx]);
                        delete p_this_node;
                    }
                    else
                    {
                        // The node does not yet exist - we add it to the nodes vector
                        nodes.push_back(p_this_node);
                        nodes_this_elem.push_back(p_this_node);
                    }

                    // Move to the next edge
                    edge = edge->next();
                }

            } while (edge != cell.incident_edge());

            // Add a new VertexElement to the mElements vector
            elements.push_back(new VertexElement<2,2>(elements.size(), nodes_this_elem));
        }
    }

    // Loop over the cells in the voronoi diagram to identify boundary nodes
    for (voronoi_diagram<double>::const_cell_iterator it = vd.cells().begin();
         it != vd.cells().end();
         ++it)
    {
        // Get a reference to the current cell
        const voronoi_diagram<double>::cell_type& cell = *it;

        // The cells we care about are exactly those whose source_index is greater than the size of the locations vector
        // (i.e. those cells in the outside eight portions of the 3x3 tessellation of source points)
        if (cell.source_index() >= rSeedLocations.size())
        {
            // Loop over the edges of the current cell
            const voronoi_diagram<double>::edge_type *edge = cell.incident_edge();

            do
            {
                /*
                 * Break out of the do-while if there is an infinite edge; we needn't care about cells at the very edge.
                 */
                if (edge->is_infinite())
                {
                    break;
                }

                if (edge->is_primary())
                {
                    c_vector<double, 2> vertex_location;

                    // Get the location of vertex0 of the current edge
                    vertex_location[0] = (edge->vertex0()->x()) / mSamplingMultiplier;
                    vertex_location[1] = (edge->vertex0()->y()) / mSamplingMultiplier;

                    /*
                     * Check whether this location coincides with one of our nodes; if it does, it must be a boundary
                     * node
                     */
                    for (unsigned node_idx = 0 ; node_idx < nodes.size() ; node_idx++)
                    {
                        // Grab the existing node location
                        c_vector<double, 2> existing_node_location = nodes[node_idx]->rGetLocation();

                        // Equality here is determined entirely on coincidence of position
                        if ( fabs(existing_node_location[0] - vertex_location[0]) < DBL_EPSILON )
                        {
                            if ( fabs(existing_node_location[1] - vertex_location[1]) < DBL_EPSILON )
                            {
                                // If the locations match, tag the node as being on the boundary
                                nodes[node_idx]->SetAsBoundaryNode(true);
                            }
                        }
                    }
                    // Move to the next edge
                    edge = edge->next();
                }

            } while (edge != cell.incident_edge());
        }
    }

    // Create a new mesh with the current vector of nodes and elements
    if (mpMesh)
    {
        delete mpMesh;
    }
    mpMesh = new MutableVertexMesh<2,2>(nodes, elements);
}

void VoronoiVertexMeshGenerator::ValidateInputAndSetMembers()
{
    // Validate inputs
    if ( (mNumElementsX < 2) || (mNumElementsY < 2) )
    {
        EXCEPTION("Need at least 2 by 2 cells");
    }

    if ( mElementTargetArea <= 0.0 )
    {
        EXCEPTION("Specified target area must be strictly positive");
    }

    // The total number of elements requested
    mTotalNumElements = mNumElementsX * mNumElementsY;

    // Max of the numbers of elements across and up
    mMaxNumElems = std::max(mNumElementsX, mNumElementsY);

    // The multipliers necessary in x and y to ensure all seed points are in [0,1]x[0,1]
    mMultiplierInX = double(mNumElementsX) / double(mMaxNumElems);
    mMultiplierInY = double(mNumElementsY) / double(mMaxNumElems);

    // Floating point representation of INT_MAX/2
    mSamplingMultiplier = 0.5 * double(INT_MAX);

    // The max integer that a seed point could be mapped to when discretising
    mMaxIntX = int( floor( (mMultiplierInX * mSamplingMultiplier) + 0.5 ) );
    mMaxIntY = int( floor( (mMultiplierInY * mSamplingMultiplier) + 0.5 ) );
}

void VoronoiVertexMeshGenerator::ValidateSeedLocations(std::vector<c_vector<double, 2> >& rSeedLocations)
{
    unsigned num_seeds = rSeedLocations.size();

    /*
     * Seeds at least 1.0 / mSamplingMultiplier apart from each other
     * are acceptable; the 1.5 term below could just as well be any
     * number that is strictly greater than 1.0.
     */
    double safe_distance = 1.5 / mSamplingMultiplier;

    // If we find a seed that needs to move position, we will move it and start checking again from the beginning
    bool recheck = true;

    while (recheck)
    {
        // If no seeds needs moving (as is overwhelmingly likely), we do not need to check again
        recheck = false;

        // We check each seed against every other, without double counting
        for (unsigned seed_idx_one = 0; seed_idx_one < num_seeds; seed_idx_one++)
        {
            for (unsigned seed_idx_two = seed_idx_one + 1; seed_idx_two < num_seeds; seed_idx_two++)
            {
                // We get the distance between the two seeds currently being considered
                c_vector<double, 2> one_to_two = rSeedLocations[seed_idx_two] - rSeedLocations[seed_idx_one];
                double distance = norm_2(one_to_two);

                if (distance < safe_distance)
                {
                    // We will now need to re-check
                    recheck = true;

                    /*
                     * If the distance is non-zero, we will move the second seed away along the line joining the two
                     * seeds until it's at the safe distance. If the distance is somehow zero, we will just move the
                     * x-location of the second seed by the safe distance.
                     *
                     * In all cases, we also need to ensure the new location is within the boundary box.
                     */
                    if (distance > DBL_EPSILON)
                    {
                        double multiplier = safe_distance / distance;
                        rSeedLocations[seed_idx_two] += (one_to_two * multiplier);

                        rSeedLocations[seed_idx_two][0] = fmod(rSeedLocations[seed_idx_two][0] + mMultiplierInX, mMultiplierInX);
                        rSeedLocations[seed_idx_two][1] = fmod(rSeedLocations[seed_idx_two][1] + mMultiplierInX, mMultiplierInX);
                    }
                    else
                    {
                        rSeedLocations[seed_idx_two][0] += safe_distance;
                        rSeedLocations[seed_idx_two][0] = fmod(rSeedLocations[seed_idx_two][0], mMultiplierInX);
                    }
                }
            }

            // We will re-check now rather than finishing the outer loop first
            if (recheck)
            {
                break;
            }
        }
    }
}

std::vector<double> VoronoiVertexMeshGenerator::GetPolygonDistribution()
{
    assert(mpMesh != NULL);

    // Number of elements in the mesh
    unsigned num_elems = mpMesh->GetNumElements();

    // Store the number of each class of polygons
    std::vector<unsigned> num_polygons(mMaxExpectedNumSidesPerPolygon - 2, 0);

    // Container to return the polygon distribution
    std::vector<double> polygon_dist;

    // Loop over elements in the mesh to get the number of each class of polygon
    for (unsigned elem_idx = 0; elem_idx < num_elems; elem_idx++)
    {
        unsigned num_nodes_this_elem = mpMesh->GetElement(elem_idx)->GetNumNodes();

        // All polygons are assumed to have 3, 4, 5, ..., mMaxExpectedNumSidesPerPolygon sides
        assert(num_nodes_this_elem > 2);
        assert(num_nodes_this_elem <= mMaxExpectedNumSidesPerPolygon);

        // Increment correct place in counter - triangles in place 0, squares in 1, etc
        num_polygons[num_nodes_this_elem - 3]++;
    }

    // Loop over the vector of polygon numbers and calculate the distribution vector to return
    unsigned elems_accounted_for = 0;
    for (unsigned polygon = 0 ; polygon < num_polygons.size() ; polygon++)
    {
        elems_accounted_for += num_polygons[polygon];

        polygon_dist.push_back(static_cast<double>(num_polygons[polygon]) / static_cast<double>(num_elems));

        // Only fill the vector of polygon distributions to the point where there are none of higher class in the mesh
        if (elems_accounted_for == num_elems)
        {
            break;
        }
    }

    return polygon_dist;
}

double VoronoiVertexMeshGenerator::GetAreaCoefficientOfVariation()
{
    assert(mpMesh != NULL);

    // Number of elements in the mesh, and check there are at least two
    unsigned num_elems = mpMesh->GetNumElements();
    assert(num_elems > 1);

    double var = 0.0;

    // Loop over elements in the mesh to get the contributions to the variance
    for (unsigned elem_idx = 0 ; elem_idx < num_elems ; elem_idx++)
    {
        double deviation = mpMesh->GetVolumeOfElement(elem_idx) - mElementTargetArea;
        var += deviation * deviation;
    }

    var /= static_cast<double>(num_elems - 1);

    return sqrt(var) / mElementTargetArea;
}

void VoronoiVertexMeshGenerator::RefreshSeedsAndRegenerateMesh()
{
    this->GenerateVoronoiMesh();
}

void VoronoiVertexMeshGenerator::SetMaxExpectedNumSidesPerPolygon(unsigned maxExpectedNumSidesPerPolygon)
{
    mMaxExpectedNumSidesPerPolygon = maxExpectedNumSidesPerPolygon;
}

unsigned VoronoiVertexMeshGenerator::GetMaxExpectedNumSidesPerPolygon()
{
    return mMaxExpectedNumSidesPerPolygon;
}

#endif // BOOST_VERSION >= 105200
#if BOOST_VERSION < 105200

VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator()
{
    EXCEPTION("This is a dummy class. Build with Boost version 1.52 or above for functionality.");
}

#endif // BOOST_VERSION < 105200