TrapezoidEdgeVertexMeshWriter.cpp

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*/
 
#include "TrapezoidEdgeVertexMeshWriter.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::TrapezoidEdgeVertexMeshWriter(const std::string& rDirectory,
                                                                                     const std::string& rBaseName,
                                                                                     const bool clearOutputDir)
        : AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir)
{
#ifdef CHASTE_VTK
    // Dubious, since we shouldn't yet know what any details of the mesh are.
    mpVtkUnstructedMesh = vtkUnstructuredGrid::New();
#endif // CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::~TrapezoidEdgeVertexMeshWriter()
{
#ifdef CHASTE_VTK
    mpVtkUnstructedMesh->Delete();
#endif // CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteVtkUsingMesh(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                                                              const std::string& stamp)
{
#ifdef CHASTE_VTK
    assert(SPACE_DIM == 2); // LCOV_EXCL_LINE
 
    // Create VTK mesh
    MakeVtkMesh(rMesh);
 
    // Now write VTK mesh to file
    assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
    vtkXMLUnstructuredGridWriter* p_writer = vtkXMLUnstructuredGridWriter::New();
#if VTK_MAJOR_VERSION >= 6
    p_writer->SetInputData(mpVtkUnstructedMesh);
#else
    p_writer->SetInput(mpVtkUnstructedMesh);
#endif
    // Uninitialised stuff arises (see #1079), but you can remove valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    p_writer->SetCompressor(nullptr);
    // **** REMOVE WITH CAUTION *****
 
    std::string vtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName;
    if (!stamp.empty())
    {
        vtk_file_name += "_" + stamp;
    }
    vtk_file_name += ".vtu";
 
    p_writer->SetFileName(vtk_file_name.c_str());
    // p_writer->PrintSelf(std::cout, vtkIndent());
    p_writer->Write();
    p_writer->Delete(); // Reference counted
#endif // CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::MakeVtkMesh(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
{
    // Only 2D version is supported at the moment
    assert(SPACE_DIM == 2); // LCOV_EXCL_LINE
#ifdef CHASTE_VTK
    // Make the Vtk mesh
    vtkPoints* p_pts = vtkPoints::New(VTK_DOUBLE);
    p_pts->GetData()->SetName("Vertex positions");
    /*
     * Populating points. First, outer points of elements
     */
    const unsigned n_vertices = rMesh.GetNumNodes();
    for (unsigned node_num = 0; node_num < rMesh.GetNumNodes(); node_num++)
    {
        c_vector<double, 2> position;
        position = rMesh.GetNode(node_num)->rGetLocation();
        p_pts->InsertPoint(node_num, position[0], position[1], 0.0);
    }
    /*
     * Populating inner points.
     * [_________________][_____][_________]....[_____]
     *      ^^^^^^^^^^^    ^^^^^  ^^^^^^^^        ^^^^
     *  Outer points       Cell_1  Cell_2        Cell_{num_elements}
     *                              Inner Points
     * cell_offset_dist stores the distance from the beginning of p_pts array for each element
     * Note that the number of inner points equals to the number of nodes of each element
     */
    const unsigned num_elements = rMesh.GetNumElements();
    std::vector<unsigned> cell_offset_dist(rMesh.GetNumElements());
    cell_offset_dist[0] = n_vertices;
    for (unsigned i = 1; i < num_elements; ++i)
        cell_offset_dist[i] = cell_offset_dist[i - 1] + rMesh.GetElement(i - 1)->GetNumNodes();
    // Coefficient 0<=alpha<=1 represents how thin the trapezoid is
    const double alpha = 0.8;
    typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator elem_end = rMesh.GetElementIteratorEnd();
    for (auto elem = rMesh.GetElementIteratorBegin(); elem != elem_end; ++elem)
    {
        const unsigned num_elem_nodes = elem->GetNumNodes();
        const c_vector<double, SPACE_DIM> elem_centroid = rMesh.GetCentroidOfElement(elem->GetIndex());
        for (unsigned elem_node_num = 0; elem_node_num < num_elem_nodes; elem_node_num++)
        {
            c_vector<double, SPACE_DIM> node_position(2);
            node_position = elem->GetNode(elem_node_num)->rGetLocation();
            const double new_x = (node_position[0] - elem_centroid[0]) * alpha + elem_centroid[0];
            const double new_y = (node_position[1] - elem_centroid[1]) * alpha + elem_centroid[1];
            p_pts->InsertPoint(cell_offset_dist[elem->GetIndex()] + elem_node_num,
                               new_x, new_y, 0.0);
        }
    }
    mpVtkUnstructedMesh->SetPoints(p_pts);
    p_pts->Delete(); // Reference counted
    unsigned total_num_edges = 0;
    for (auto elem = rMesh.GetElementIteratorBegin(); elem != elem_end; ++elem)
    {
        // First do the trapezoids for each edge
        for (unsigned edge_index = 0; edge_index < elem->GetNumEdges(); ++edge_index)
        {
            vtkCell* p_cell;
            p_cell = vtkQuad::New();
            const unsigned num_trap_nodes = p_cell->GetNumberOfEdges(); // 4 in 2D, 8 in 3D
            assert(num_trap_nodes == 4);
            vtkIdList* p_cell_id_list = p_cell->GetPointIds();
            p_cell_id_list->SetNumberOfIds(num_trap_nodes);
            auto p_edge = elem->GetEdge(edge_index);
            assert(p_edge->GetNumNodes() == 2);
 
            // See the diagram above for storing pattern
            std::array<unsigned, 2> base_ids = { { p_edge->GetNode(0)->GetIndex(), p_edge->GetNode(1)->GetIndex() } };
            std::array<unsigned, 2> top_ids = { { elem->GetNodeLocalIndex(base_ids[0])
                                                      + cell_offset_dist[elem->GetIndex()],
                                                  elem->GetNodeLocalIndex(base_ids[1]) + cell_offset_dist[elem->GetIndex()] } };
 
            // Assuming counter-clockwise ordering
            p_cell_id_list->SetId(0, base_ids[0]);
            p_cell_id_list->SetId(1, base_ids[1]);
            p_cell_id_list->SetId(2, top_ids[1]);
            p_cell_id_list->SetId(3, top_ids[0]);
            mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
            p_cell->Delete(); // Reference counted
            total_num_edges++;
        }
 
        // Now do the internal cell
        vtkCell* p_cell;
        p_cell = vtkPolygon::New();
        const unsigned num_elem_nodes = elem->GetNumNodes();
        vtkIdList* p_cell_id_list = p_cell->GetPointIds();
        p_cell_id_list->SetNumberOfIds(num_elem_nodes);
        for (unsigned j = 0; j < num_elem_nodes; ++j)
        {
            p_cell_id_list->SetId(j, cell_offset_dist[elem->GetIndex()] + j);
        }
 
        mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
 
        p_cell->Delete(); // Reference counted
    }
 
    // For 2D case. For 3D, we should sum the total number of faces + num_elements
    assert(total_num_edges + num_elements == mpVtkUnstructedMesh->GetNumberOfCells());
#endif // CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::AddCellData(std::string dataName, std::vector<double> dataPayload)
{
#ifdef CHASTE_VTK
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i = 0; i < dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }
 
    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_scalars);
    p_scalars->Delete(); // Reference counted
#endif // CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrapezoidEdgeVertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFiles()
{
    /*
     * Blank as we're only using the class for VTK at the moment, i.e. we don't
     * write mesh information for the case when we have trapezoid edge elements,
     * since trapezoids associated with each edge are only there for
     * visualisation purposes and do not represent the actual mesh. The actual
     * mesh can be written by VertexMeshWriter class and reconstructed by
     * VertexMeshReader class. This method needs to be overriden here, as it is
     * declared as a pure virtual function in the parent class.
     */
}
 
// Explicit instantiation
template class TrapezoidEdgeVertexMeshWriter<1, 1>;
template class TrapezoidEdgeVertexMeshWriter<1, 2>;
template class TrapezoidEdgeVertexMeshWriter<1, 3>;
template class TrapezoidEdgeVertexMeshWriter<2, 2>;
template class TrapezoidEdgeVertexMeshWriter<2, 3>;
template class TrapezoidEdgeVertexMeshWriter<3, 3>;