Cylindrical2dNodesOnlyMesh.cpp

/*

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/

#include <map>
#include "Cylindrical2dNodesOnlyMesh.hpp"

Cylindrical2dNodesOnlyMesh::Cylindrical2dNodesOnlyMesh(double width)
        : NodesOnlyMesh<2>(),
          mWidth(width)
{
    assert(width > 0.0);
}

void Cylindrical2dNodesOnlyMesh::SetUpBoxCollection(double cutOffLength, c_vector<double, 2*2> domainSize, int numLocalRows, bool isPeriodic)
{
    NodesOnlyMesh<2>::SetUpBoxCollection(cutOffLength, domainSize, PETSC_DECIDE, true);    // Only difference is that this "true" makes the boxes periodic.

    this->AddNodesToBoxes();
}

double Cylindrical2dNodesOnlyMesh::GetWidth(const unsigned& rDimension) const
{
    double width = 0.0;
    assert(rDimension==0 || rDimension==1);
    if (rDimension==0)
    {
        width = mWidth;
    }
    else
    {
        width = MutableMesh<2,2>::GetWidth(rDimension);
    }
    return width;
}


void Cylindrical2dNodesOnlyMesh::SetNode(unsigned nodeIndex, ChastePoint<2> point, bool concreteMove)
{
    // concreteMove should always be false for NodesOnlyMesh as no elements to check
    assert(!concreteMove);

    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
    this->GetNode(nodeIndex)->SetPoint(point);
}

unsigned Cylindrical2dNodesOnlyMesh::AddNode(Node<2>* pNewNode)
{
    // Call method on parent class
    unsigned node_index = NodesOnlyMesh<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;

}

c_vector<double, 2> Cylindrical2dNodesOnlyMesh::GetVectorFromAtoB(const c_vector<double, 2>& rLocation1, const c_vector<double, 2>& rLocation2)
{
    c_vector<double, 2> vector = rLocation2 - rLocation1;
    vector[0] = fmod(vector[0], mWidth);

    /*
     * Handle the cylindrical condition here: 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;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Cylindrical2dNodesOnlyMesh)