Cylindrical2dVertexMesh.cpp

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*/
 
#include "Cylindrical2dVertexMesh.hpp"
#include "Cylindrical2dMesh.hpp"
 
Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(double width,
                                                 std::vector<Node<2>*> nodes,
                                                 std::vector<VertexElement<2, 2>*> vertexElements,
                                                 double cellRearrangementThreshold,
                                                 double t2Threshold)
    : MutableVertexMesh<2,2>(nodes, vertexElements, cellRearrangementThreshold, t2Threshold),
      mWidth(width),
      mpMeshForVtk(nullptr)
{
    // Call ReMesh() to remove any deleted nodes and relabel
    ReMesh();
}
 
Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(Cylindrical2dMesh& rMesh, bool isBounded)
    : mWidth(rMesh.GetWidth(0)),
      mpMeshForVtk(nullptr)
{
    mpDelaunayMesh = &rMesh;
 
    // Reset member variables and clear mNodes, mFaces and mElements
    Clear();
 
    if (!isBounded)
    {
        unsigned num_elements = mpDelaunayMesh->GetNumAllNodes();
        unsigned num_nodes = mpDelaunayMesh->GetNumAllElements();
 
        // Allocate memory for mNodes and mElements
        this->mNodes.reserve(num_nodes);
 
        // Create as many elements as there are nodes in the mesh
        mElements.reserve(num_elements);
 
        for (unsigned elem_index=0; elem_index<num_elements; elem_index++)
        {
            VertexElement<2,2>* p_element = new VertexElement<2,2>(elem_index);
            mElements.push_back(p_element);
        }
 
        // Populate mNodes
        GenerateVerticesFromElementCircumcentres(rMesh);
 
        // Loop over all nodes and check the x locations not outside [0,mWidth]
        for (unsigned i=0; i<mNodes.size(); i++)
        {
            CheckNodeLocation(mNodes[i]);
        }
 
        // Loop over elements of the Delaunay mesh (which are nodes/vertices of this mesh)
        for (unsigned i=0; i<num_nodes; i++)
        {
            // Loop over nodes owned by this triangular element in the Delaunay mesh
            // Add this node/vertex to each of the 3 vertex elements
            for (unsigned local_index=0; local_index<3; local_index++)
            {
                unsigned elem_index = mpDelaunayMesh->GetElement(i)->GetNodeGlobalIndex(local_index);
                unsigned num_nodes_in_elem = mElements[elem_index]->GetNumNodes();
                unsigned end_index = num_nodes_in_elem>0 ? num_nodes_in_elem-1 : 0;
 
                mElements[elem_index]->AddNode(this->mNodes[i], end_index);
            }
        }
    }
    else // Is Bounded
    {
        // First create an extended mesh to include points extended from the boundary
        std::vector<Node<2> *> nodes;
        for (typename TetrahedralMesh<2,2>::NodeIterator node_iter = mpDelaunayMesh->GetNodeIteratorBegin();
            node_iter != mpDelaunayMesh->GetNodeIteratorEnd();
            ++node_iter)
        {
            nodes.push_back(new Node<2>(node_iter->GetIndex(), node_iter->rGetLocation(),node_iter->IsBoundaryNode()));
        }
 
        // Add new nodes
        unsigned new_node_index = mpDelaunayMesh->GetNumNodes();
        for (TetrahedralMesh<2,2>::ElementIterator elem_iter = mpDelaunayMesh->GetElementIteratorBegin();
            elem_iter != mpDelaunayMesh->GetElementIteratorEnd();
            ++elem_iter)
        {
            for (unsigned j=0; j<3; j++)
            {
                Node<2>* p_node_a = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex(j));
                Node<2>* p_node_b = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex((j+1)%3));
 
                std::set<unsigned> node_a_element_indices = p_node_a->rGetContainingElementIndices();
                std::set<unsigned> node_b_element_indices = p_node_b->rGetContainingElementIndices();
 
                std::set<unsigned> shared_elements;
                std::set_intersection(node_a_element_indices.begin(),
                                      node_a_element_indices.end(),
                                      node_b_element_indices.begin(),
                                      node_b_element_indices.end(),
                                      std::inserter(shared_elements, shared_elements.begin()));
 
 
                /*
                 * Note using boundary nodes to identify the boundary edges won't work with
                 * triangles which have 3 boundary nodes
                 * if ((p_node_a->IsBoundaryNode() && p_node_b->IsBoundaryNode()))
                 * wont work with triangles which have 3 boundary nodes so we use a more
                 * general method.
                 */
 
                if (shared_elements.size() == 1) // It's a boundary edge
                {
                    c_vector<double,2> edge = mpDelaunayMesh->GetVectorFromAtoB(p_node_a->rGetLocation(), p_node_b->rGetLocation());
                    c_vector<double,2> normal_vector;
 
                    normal_vector[0]= edge[1];
                    normal_vector[1]= -edge[0];
 
                    double dij = norm_2(normal_vector);
                    assert(dij>1e-5); //Sanity check
                    normal_vector /= dij;
 
                    /*
                     * Here we only add one extra node.
                     *
                     *  ____  one extra image node
                     *   /\
                     *  /__\ edge of mesh
                     *
                     * Changing this can cause issues with stitching the left and right back together.
                     */
 
                    double ratio = 0.5;
                    c_vector<double,2> new_node_location = normal_vector + p_node_a->rGetLocation() + ratio * edge;
 
                    // Check if near other nodes
                    bool node_clear = true;
                    double node_clearance = 0.01;
 
                    for (unsigned i=0; i<nodes.size(); i++)
                    {
                        double distance = norm_2(mpDelaunayMesh->GetVectorFromAtoB(nodes[i]->rGetLocation(), new_node_location));
                        if (distance < node_clearance)
                        {
                            node_clear = false;
                            break;
                        }
                    }
 
                    if (node_clear)
                    {
                        nodes.push_back(new Node<2>(new_node_index, new_node_location));
                        new_node_index++;
                    }
                }
            }
        }
 
        // Add new nodes for voids (note these nodes won't be labeled as boundary nodes here)
        for (TetrahedralMesh<2,2>::ElementIterator elem_iter = mpDelaunayMesh->GetElementIteratorBegin();
            elem_iter != mpDelaunayMesh->GetElementIteratorEnd();
            ++elem_iter)
        {
            bool bad_element = false;
            double edge_threshold = 1.5; //TODO think about making this a setable variable!
 
            for (unsigned j=0; j<3; j++)
            {
                Node<2>* p_node_a = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex(j));
                Node<2>* p_node_b = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex((j+1)%3));
                if (norm_2(mpDelaunayMesh->GetVectorFromAtoB(p_node_a->rGetLocation(), p_node_b->rGetLocation()))>edge_threshold)
                {
                    bad_element = true;
                    break;
                }
            }
 
            if (bad_element)
            {
                for (unsigned j=0; j<3; j++)
                {
                    Node<2>* p_node_a = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex(j));
                    Node<2>* p_node_b = mpDelaunayMesh->GetNode(elem_iter->GetNodeGlobalIndex((j+1)%3));
 
                    c_vector<double,2> edge = mpDelaunayMesh->GetVectorFromAtoB(p_node_a->rGetLocation(), p_node_b->rGetLocation());
                    double edge_length = norm_2(edge);
 
                    // The short edges in these elements are the boundaries of the void
                    if (edge_length<edge_threshold)
                    {
                        /*
                         * Here we only add one extra node.
                         *
                         *  ____  one extra image node
                         *   /\
                         *  /__\ edge of mesh
                         *
                         * Changing this can cause issues with stitching the left and right back together.
                         */
 
                        // Short Edge so add new node
                        c_vector<double,2> normal_vector;
 
                        // Outward Normal
                        normal_vector[0]= edge[1];
                        normal_vector[1]= -edge[0];
 
                        double dij = norm_2(normal_vector);
                        assert(dij>1e-5); //Sanity check
                        normal_vector /= dij;
 
                        double bound_offset = 1.0; //TODO Think about makeing this a setable variable!
                        c_vector<double,2> new_node_location = -bound_offset*normal_vector + p_node_a->rGetLocation() + 0.5 * edge;
 
                        nodes.push_back(new Node<2>(new_node_index, new_node_location));
                        new_node_index++;
                    }
                }
            }
        }
 
        // Loop over all nodes and check they're not outside [0,mWidth)
        for (unsigned i=0; i<nodes.size(); i++)
        {
            CheckNodeLocation(nodes[i]);
        }
 
        Cylindrical2dMesh extended_mesh(mpDelaunayMesh->GetWidth(0),nodes);
 
        unsigned num_elements = mpDelaunayMesh->GetNumAllNodes();
        unsigned num_nodes = extended_mesh.GetNumAllElements();
 
        // Allocate memory for mNodes and mElements
        this->mNodes.reserve(num_nodes);
 
        // Create as many elements as there are nodes in the mesh
        mElements.reserve(num_elements);
        for (unsigned elem_index = 0; elem_index < num_elements; elem_index++)
        {
            VertexElement<2, 2>* p_element = new VertexElement<2, 2>(elem_index);
            mElements.push_back(p_element);
        }
 
        // Populate mNodes
        GenerateVerticesFromElementCircumcentres(extended_mesh);
 
        // Loop over all nodes and check the x locations not outside [0,mWidth]
        for (unsigned i=0; i<mNodes.size(); i++)
        {
            CheckNodeLocation(mNodes[i]);
        }
        // Loop over elements of the Delaunay mesh (which are nodes/vertices of this mesh)
        for (unsigned i = 0; i < num_nodes; i++)
        {
            // Loop over nodes owned by this triangular element in the Delaunay mesh
            // Add this node/vertex to each of the 3 vertex elements
            for (unsigned local_index = 0; local_index < 3; local_index++)
            {
                unsigned elem_index = extended_mesh.GetElement(i)->GetNodeGlobalIndex(local_index);
 
                if (elem_index < num_elements)
                {
                    unsigned num_nodes_in_elem = mElements[elem_index]->GetNumNodes();
                    unsigned end_index = num_nodes_in_elem > 0 ? num_nodes_in_elem - 1 : 0;
 
                    mElements[elem_index]->AddNode(this->mNodes[i], end_index);
                }
            }
        }
    }
 
    // Reorder mNodes anticlockwise
    for (unsigned elem_index=0; elem_index<mElements.size(); elem_index++)
    {
        std::vector<std::pair<double, unsigned> > index_angle_list;
        for (unsigned local_index=0; local_index<mElements[elem_index]->GetNumNodes(); local_index++)
        {
            c_vector<double, 2> vectorA = mpDelaunayMesh->GetNode(elem_index)->rGetLocation();
            c_vector<double, 2> vectorB = mElements[elem_index]->GetNodeLocation(local_index);
            c_vector<double, 2> centre_to_vertex = mpDelaunayMesh->GetVectorFromAtoB(vectorA, vectorB);
 
            double angle = atan2(centre_to_vertex(1), centre_to_vertex(0));
            unsigned global_index = mElements[elem_index]->GetNodeGlobalIndex(local_index);
 
            std::pair<double, unsigned> pair(angle, global_index);
            index_angle_list.push_back(pair);
        }
 
        // Sort the list in order of increasing angle
        sort(index_angle_list.begin(), index_angle_list.end());
 
        // Create a new Voronoi element and pass in the appropriate Nodes, ordered anticlockwise
        VertexElement<2,2>* p_new_element = new VertexElement<2,2>(elem_index);
        for (unsigned count = 0; count < index_angle_list.size(); count++)
        {
            unsigned local_index = count>1 ? count-1 : 0;
            p_new_element->AddNode(mNodes[index_angle_list[count].second], local_index);
        }
 
        // Replace the relevant member of mElements with this Voronoi element
        delete mElements[elem_index];
        mElements[elem_index] = p_new_element;
    }
 
    this->mMeshChangesDuringSimulation = false;
}
 
Cylindrical2dVertexMesh::Cylindrical2dVertexMesh()
    : mpMeshForVtk(nullptr)
{
}
 
Cylindrical2dVertexMesh::~Cylindrical2dVertexMesh()
{
    if (mpMeshForVtk != nullptr)
    {
         delete mpMeshForVtk;
    }
}
 
c_vector<double, 2> Cylindrical2dVertexMesh::GetVectorFromAtoB(const c_vector<double, 2>& rLocation1, const c_vector<double, 2>& rLocation2)
{
    assert(mWidth > 0.0);
 
    c_vector<double, 2> vector = rLocation2 - rLocation1;
    vector[0] = fmod(vector[0], mWidth);
 
    // If the points are more than halfway around the cylinder apart, measure the other way
    if (vector[0] > 0.5 * mWidth)
    {
        vector[0] -= mWidth;
    }
    else if (vector[0] < -0.5 * mWidth)
    {
        vector[0] += mWidth;
    }
    return vector;
}
 
void Cylindrical2dVertexMesh::SetNode(unsigned nodeIndex, ChastePoint<2> point)
{
    double x_coord = point.rGetLocation()[0];
 
    // Perform a periodic movement if necessary
    if (x_coord >= mWidth)
    {
        // Move point to the left
        point.SetCoordinate(0, x_coord - mWidth);
    }
    else if (x_coord < 0.0)
    {
        // Move point to the right
        point.SetCoordinate(0, x_coord + mWidth);
    }
 
    // Update the node's location
    MutableVertexMesh<2,2>::SetNode(nodeIndex, point);
}
 
double Cylindrical2dVertexMesh::GetWidth(const unsigned& rDimension) const
{
    double width = 0.0;
    assert(rDimension==0 || rDimension==1);
    if (rDimension==0)
    {
        width = mWidth;
    }
    else
    {
        width = VertexMesh<2,2>::GetWidth(rDimension);
    }
    return width;
}
 
unsigned Cylindrical2dVertexMesh::AddNode(Node<2>* pNewNode)
{
    CheckNodeLocation(pNewNode);
 
    unsigned node_index = MutableVertexMesh<2,2>::AddNode(pNewNode);
 
    return node_index;
}
 
void Cylindrical2dVertexMesh::CheckNodeLocation(Node<2>* pNode)
{
    double x_location = pNode->rGetLocation()[0];
    if (x_location < 0)
    {
        pNode->rGetModifiableLocation()[0] = x_location + mWidth;
    }
    else if (x_location >= mWidth)
    {
        pNode->rGetModifiableLocation()[0] = x_location - mWidth;
    }
}
 
void Cylindrical2dVertexMesh::Scale(const double xScale, const double yScale, const double zScale)
{
    assert(zScale == 1.0);
 
    AbstractMesh<2, 2>::Scale(xScale, yScale);
 
    // Also rescale the width of the mesh (this effectively scales the domain)
    mWidth *= xScale;
}
 
VertexMesh<2, 2>* Cylindrical2dVertexMesh::GetMeshForVtk()
{
    unsigned num_nodes = GetNumNodes();
 
    std::vector<Node<2>*> temp_nodes(3 * num_nodes);
    std::vector<VertexElement<2, 2>*> elements;
 
    // Create three copies of each node
    for (unsigned index=0; index<num_nodes; index++)
    {
        c_vector<double, 2> location;
        location = GetNode(index)->rGetLocation();
 
        // Node copy at original location
        Node<2>* p_node = new Node<2>(index, false, location[0], location[1]);
        temp_nodes[index] = p_node;
 
        // Node copy shifted right
        p_node = new Node<2>(num_nodes + index, false, location[0] + mWidth, location[1]);
        temp_nodes[num_nodes + index] = p_node;
 
        // Node copy shifted left
        p_node = new Node<2>(2 * num_nodes + index, false, location[0] - mWidth, location[1]);
        temp_nodes[2*num_nodes + index] = p_node;
    }
 
    // Iterate over elements
    for (VertexMesh<2,2>::VertexElementIterator elem_iter = GetElementIteratorBegin();
         elem_iter != GetElementIteratorEnd();
         ++elem_iter)
    {
        unsigned elem_index = elem_iter->GetIndex();
        unsigned num_nodes_in_elem = elem_iter->GetNumNodes();
 
        std::vector<Node<2>*> elem_nodes;
 
        // Compute whether the element straddles either periodic boundary
        bool element_straddles_left_right_boundary = false;
 
        const c_vector<double, 2>& r_this_node_location = elem_iter->GetNode(0)->rGetLocation();
        for (unsigned local_index=0; local_index<num_nodes_in_elem; local_index++)
        {
            const c_vector<double, 2>& r_next_node_location = elem_iter->GetNode((local_index+1)%num_nodes_in_elem)->rGetLocation();
            c_vector<double, 2> vector;
            vector = r_next_node_location - r_this_node_location;
 
            if (fabs(vector[0]) > 0.5 * mWidth)
            {
                element_straddles_left_right_boundary = true;
            }
        }
 
        /* If this is a voronoi tesselation make sure the elements contain
         * the original Delaunay node
         */
        bool element_centre_on_right = true;
        if(mpDelaunayMesh)
        {
                unsigned delaunay_index = this->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
                double element_centre_x_location = this->mpDelaunayMesh->GetNode(delaunay_index)->rGetLocation()[0];
                if (element_centre_x_location < 0.5 * mWidth)
                {
                    element_centre_on_right = false;
                }
        }
 
        // Use the above information when duplicating the element in the vtk mesh
        for (unsigned local_index=0; local_index<num_nodes_in_elem; local_index++)
        {
            unsigned this_node_index = elem_iter->GetNodeGlobalIndex(local_index);
 
            // If the element straddles the left/right periodic boundary...
            if (element_straddles_left_right_boundary)
            {
                // ...and this node is located to the left of the centre of the mesh...
                bool node_is_right_of_centre = (elem_iter->GetNode(local_index)->rGetLocation()[0] - 0.5 * mWidth > 0);
                if (!node_is_right_of_centre && element_centre_on_right)
                {
                    // ...then choose the equivalent node to the right
                    this_node_index += num_nodes;
                }
                else if (node_is_right_of_centre && !element_centre_on_right)
                {
                    // ...then choose the equivalent node to the left
                    this_node_index += 2 * num_nodes;
                }
            }
 
            elem_nodes.push_back(temp_nodes[this_node_index]);
        }
 
        VertexElement<2,2>* p_element = new VertexElement<2,2>(elem_index, elem_nodes);
        elements.push_back(p_element);
    }
 
    // Now delete any nodes from the mesh for VTK that are not contained in any elements
    std::vector<Node<2>*> nodes;
    unsigned count = 0;
    for (unsigned index=0; index<temp_nodes.size(); index++)
    {
        unsigned num_elems_containing_this_node = temp_nodes[index]->rGetContainingElementIndices().size();
 
        if (num_elems_containing_this_node == 0)
        {
            // Avoid memory leak
            delete temp_nodes[index];
        }
        else
        {
            temp_nodes[index]->SetIndex(count);
            nodes.push_back(temp_nodes[index]);
            count++;
        }
    }
 
    if (mpMeshForVtk != nullptr)
    {
        delete mpMeshForVtk;
    }
 
    mpMeshForVtk = new VertexMesh<2,2>(nodes, elements);
    return mpMeshForVtk;
}
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Cylindrical2dVertexMesh)