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)
{
    // ReMesh to remove any deleted nodes and relabel
    ReMesh();
}

Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(Cylindrical2dMesh& rMesh)
    : mWidth(rMesh.GetWidth(0))
{
    mpDelaunayMesh = &rMesh;

    // Reset member variables and clear mNodes, mFaces and mElements
    Clear();

    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 generated nodes and check they're not outside [0,mWidth]
    for (unsigned i=0; i<num_nodes; i++)
    {
        double x_location = mNodes[i]->rGetLocation()[0];
        if (x_location < 0 )
        {
            mNodes[i]->rGetModifiableLocation()[0] = x_location + mWidth;
        }
        else if (x_location > mWidth )
        {
            mNodes[i]->rGetModifiableLocation()[0] = x_location - mWidth;
        }
    }

    // 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);
        }
    }

    // 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()
{
}

Cylindrical2dVertexMesh::~Cylindrical2dVertexMesh()
{
}

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)
{
    unsigned node_index = MutableVertexMesh<2,2>::AddNode(pNewNode);

    // If necessary move it to be back on the cylinder
    ChastePoint<2> new_node_point = pNewNode->GetPoint();
    SetNode(node_index, new_node_point);

    return node_index;
}

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;
}

MutableVertexMesh<2, 2>* Cylindrical2dVertexMesh::GetMeshForVtk()
{
    unsigned num_nodes = GetNumNodes();

    std::vector<Node<2>*> temp_nodes(2*num_nodes);
    std::vector<VertexElement<2, 2>*> elements;

    // Create four 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;
    }

    // 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;
            }
        }

        // Use the above information when duplicating the element
        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)
                {
                    // ...then choose the equivalent node to the right
                    this_node_index += 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++;
        }
    }

    MutableVertexMesh<2, 2>* p_mesh = new MutableVertexMesh<2,2>(nodes, elements, mCellRearrangementThreshold, mT2Threshold);
    return p_mesh;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Cylindrical2dVertexMesh)