Cylindrical2dVertexMesh.cpp

/*

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*/

#include "Cylindrical2dVertexMesh.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()
{
}

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] > mWidth/2.0)
    {
        vector[0] -= mWidth;
    }
    else if (vector[0] < -mWidth/2.0)
    {
        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;
}

double Cylindrical2dVertexMesh::GetVolumeOfElement(unsigned index)
{
    VertexElement<2, 2>* p_element = GetElement(index);

    c_vector<double, 2> first_node = p_element->GetNodeLocation(0);
    c_vector<double, 2> current_node;
    c_vector<double, 2> anticlockwise_node;
    c_vector<double, 2> transformed_current_node;
    c_vector<double, 2> transformed_anticlockwise_node;

    unsigned num_nodes_in_element = p_element->GetNumNodes();

    double element_area = 0;

    for (unsigned local_index=0; local_index<num_nodes_in_element; local_index++)
    {
        // Find locations of current node and anticlockwise node
        current_node = p_element->GetNodeLocation(local_index);
        anticlockwise_node = p_element->GetNodeLocation((local_index+1)%num_nodes_in_element);

        /*
         * In order to calculate the area we map the origin to (x[0],y[0])
         * then use GetVectorFromAtoB() to get node cooordiantes
         */

        transformed_current_node = GetVectorFromAtoB(first_node, current_node);
        transformed_anticlockwise_node = GetVectorFromAtoB(first_node, anticlockwise_node);

        element_area += 0.5*(transformed_current_node[0]*transformed_anticlockwise_node[1]
                           - transformed_anticlockwise_node[0]*transformed_current_node[1]);
    }

    return element_area;
}

c_vector<double, 2> Cylindrical2dVertexMesh::GetCentroidOfElement(unsigned index)
{
    VertexElement<2, 2>* p_element = GetElement(index);

    c_vector<double, 2> centroid;
    c_vector<double, 2> transformed_centroid = zero_vector<double>(2);
    c_vector<double, 2> first_node = p_element->GetNodeLocation(0);
    c_vector<double, 2> current_node_location;
    c_vector<double, 2> next_node_location;
    c_vector<double, 2> transformed_current_node;
    c_vector<double, 2> transformed_anticlockwise_node;

    double temp_centroid_x = 0;
    double temp_centroid_y = 0;

    unsigned num_nodes_in_element = p_element->GetNumNodes();

    for (unsigned local_index=0; local_index<num_nodes_in_element; local_index++)
    {
        // Find locations of current node and anticlockwise node
        current_node_location = p_element->GetNodeLocation(local_index);
        next_node_location = p_element->GetNodeLocation((local_index+1)%num_nodes_in_element);

        /*
         * In order to calculate the centroid we map the origin to (x[0],y[0])
         * then use  GetVectorFromAtoB() to get node cooordiantes
         */

        transformed_current_node = GetVectorFromAtoB(first_node, current_node_location);
        transformed_anticlockwise_node = GetVectorFromAtoB(first_node, next_node_location);

        temp_centroid_x += (transformed_current_node[0]+transformed_anticlockwise_node[0])*(transformed_current_node[0]*transformed_anticlockwise_node[1]-transformed_current_node[1]*transformed_anticlockwise_node[0]);
        temp_centroid_y += (transformed_current_node[1]+transformed_anticlockwise_node[1])*(transformed_current_node[0]*transformed_anticlockwise_node[1]-transformed_current_node[1]*transformed_anticlockwise_node[0]);
    }

    double vertex_area = GetVolumeOfElement(index);
    double centroid_coefficient = 1.0/(6.0*vertex_area);

    transformed_centroid(0) = centroid_coefficient*temp_centroid_x;
    transformed_centroid(1) = centroid_coefficient*temp_centroid_y;

    centroid = transformed_centroid + first_node;

    return centroid;
}

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