Toroidal2dVertexMesh.cpp

/*

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*/

#include "Toroidal2dVertexMesh.hpp"

Toroidal2dVertexMesh::Toroidal2dVertexMesh(double width,
                                           double height,
                                           std::vector<Node<2>*> nodes,
                                           std::vector<VertexElement<2, 2>*> vertexElements,
                                           double cellRearrangementThreshold,
                                           double t2Threshold)
    : MutableVertexMesh<2,2>(nodes, vertexElements, cellRearrangementThreshold, t2Threshold),
      mWidth(width),
      mHeight(height),
      mpMeshForVtk(nullptr)
{
    // Call ReMesh() to remove any deleted nodes and relabel
    ReMesh();
}

Toroidal2dVertexMesh::Toroidal2dVertexMesh()
{
}

Toroidal2dVertexMesh::~Toroidal2dVertexMesh()
{
    if (mpMeshForVtk != NULL)
    {
         delete mpMeshForVtk;
    }
}

c_vector<double, 2> Toroidal2dVertexMesh::GetVectorFromAtoB(const c_vector<double, 2>& rLocation1, const c_vector<double, 2>& rLocation2)
{
    assert(mWidth > 0.0);
    assert(mHeight > 0.0);

    c_vector<double, 2> vector = rLocation2 - rLocation1;
    vector[0] = fmod(vector[0], mWidth);
    vector[1] = fmod(vector[1], mHeight);

    // If the points are more than halfway across the domain, measure the other way
    if (vector[0] > 0.5*mWidth)
    {
        vector[0] -= mWidth;
    }
    else if (vector[0] < -0.5*mWidth)
    {
        vector[0] += mWidth;
    }

    // If the points are more than halfway up the domain, measure the other way
    if (vector[1] > 0.5*mHeight)
    {
        vector[1] -= mHeight;
    }
    else if (vector[1] < -0.5*mHeight)
    {
        vector[1] += mHeight;
    }
    return vector;
}

void Toroidal2dVertexMesh::SetNode(unsigned nodeIndex, ChastePoint<2> point)
{
    double x_coord = point.rGetLocation()[0];
    double y_coord = point.rGetLocation()[1];

    // Perform a periodic movement if necessary
    if (x_coord >= mWidth)
    {
        // Move point left
        point.SetCoordinate(0, x_coord - mWidth);
    }
    else if (x_coord < 0.0)
    {
        // Move point right
        point.SetCoordinate(0, x_coord + mWidth);
    }
    if (y_coord >= mHeight)
    {
        // Move point down
        point.SetCoordinate(1, y_coord - mHeight);
    }
    else if (y_coord < 0.0)
    {
        // Move point up
        point.SetCoordinate(1, y_coord + mHeight);
    }

    // Update the node's location
    MutableVertexMesh<2,2>::SetNode(nodeIndex, point);
}

double Toroidal2dVertexMesh::GetWidth(const unsigned& rDimension) const
{
    assert(rDimension==0 || rDimension==1);

    double width = mWidth;
    if (rDimension == 1)
    {
        width = mHeight;
    }

    return width;
}

void Toroidal2dVertexMesh::SetHeight(double height)
{
    assert(height > 0);
    mHeight = height;
}

void Toroidal2dVertexMesh::SetWidth(double width)
{
    assert(width > 0);
    mWidth = width;
}

unsigned Toroidal2dVertexMesh::AddNode(Node<2>* pNewNode)
{
    unsigned node_index = MutableVertexMesh<2,2>::AddNode(pNewNode);

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

    return node_index;
}

VertexMesh<2, 2>* Toroidal2dVertexMesh::GetMeshForVtk()
{
    unsigned num_nodes = GetNumNodes();

    std::vector<Node<2>*> temp_nodes(4*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;

        // Node copy shifted up
        p_node = new Node<2>(2*num_nodes + index, false, location[0], location[1] + mHeight);
        temp_nodes[2*num_nodes + index] = p_node;

        // Node copy shifted right and up
        p_node = new Node<2>(3*num_nodes + index, false, location[0] + mWidth, location[1] + mHeight);
        temp_nodes[3*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;
        bool element_straddles_top_bottom_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 (fabs(vector[1]) > 0.5*mHeight)
            {
                element_straddles_top_bottom_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;
                }
            }

            // If the element straddles the top/bottom periodic boundary...
            if (element_straddles_top_bottom_boundary)
            {
                // ...and this node is located below the centre of the mesh...
                bool node_is_above_centre = (elem_iter->GetNode(local_index)->rGetLocation()[1] - 0.5*mHeight > 0);
                if (!node_is_above_centre)
                {
                    // ...then choose the equivalent node above
                    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;
}

void Toroidal2dVertexMesh::ConstructFromMeshReader(AbstractMeshReader<2,2>& rMeshReader, double width, double height)
{
    assert(rMeshReader.HasNodePermutation() == false);

    // Store numbers of nodes and elements
    unsigned num_nodes = rMeshReader.GetNumNodes();
    unsigned num_elements = rMeshReader.GetNumElements();

    // Reserve memory for nodes
    this->mNodes.reserve(num_nodes);

    rMeshReader.Reset();

    // Add nodes
    std::vector<double> node_data;
    for (unsigned node_idx = 0 ; node_idx < num_nodes ; node_idx++)
    {
        node_data = rMeshReader.GetNextNode();
        node_data.pop_back();
        this->mNodes.push_back(new Node<2>(node_idx, node_data, false));
    }

    rMeshReader.Reset();

    // Reserve memory for elements
    mElements.reserve(rMeshReader.GetNumElements());

    // Add elements
    for (unsigned elem_idx = 0 ; elem_idx < num_elements ; elem_idx++)
    {
        // Get the data for this element
        ElementData element_data = rMeshReader.GetNextElementData();

        // Get the nodes owned by this element
        std::vector<Node<2>*> nodes;
        unsigned num_nodes_in_element = element_data.NodeIndices.size();
        for (unsigned j=0; j<num_nodes_in_element; j++)
        {
            assert(element_data.NodeIndices[j] < this->mNodes.size());
            nodes.push_back(this->mNodes[element_data.NodeIndices[j]]);
        }

        // Use nodes and index to construct this element
        VertexElement<2,2>* p_element = new VertexElement<2,2>(elem_idx, nodes);
        mElements.push_back(p_element);

        if (rMeshReader.GetNumElementAttributes() > 0)
        {
            assert(rMeshReader.GetNumElementAttributes() == 1);
            unsigned attribute_value = (unsigned) element_data.AttributeValue;
            p_element->SetAttribute(attribute_value);
        }
    }

    /*
     * Set width and height from function arguments, and validate by checking area is correct
     */
    this->mWidth = width;
    this->mHeight = height;

    double total_surface_area = 0.0;
    for (unsigned elem_idx = 0 ; elem_idx < num_elements ; elem_idx++)
    {
        total_surface_area += this->GetVolumeOfElement(elem_idx);
    }

    if (fabs(mWidth * mHeight - total_surface_area) > 1e-6)
    {
        EXCEPTION("Mesh width and height do not match sheet surface area.");
    }

    // Set default parameter values
    this->mCellRearrangementRatio = 1.5;
    this->mCellRearrangementThreshold = 0.01;
    this->mT2Threshold = 0.001;
    this->mMeshChangesDuringSimulation = true;
    this->mpMeshForVtk = nullptr;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Toroidal2dVertexMesh)