VtkMeshWriter.cpp

/*
 
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*/
 
#include <boost/scoped_array.hpp>
#include "VtkMeshWriter.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "MixedDimensionMesh.hpp"
#include "NodesOnlyMesh.hpp"
 
#ifdef CHASTE_VTK
#include "vtkQuadraticTetra.h"
#include "vtkQuadraticTriangle.h"
 
 
// Implementation
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshWriter<ELEMENT_DIM, SPACE_DIM>::VtkMeshWriter(const std::string& rDirectory,
                     const std::string& rBaseName,
                     const bool& rCleanDirectory)
    : AbstractTetrahedralMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, rCleanDirectory),
      mWriteParallelFiles(false),
      mWriteMeshCells(true)
{
    this->mIndexFromZero = true;
 
    // Dubious, since we shouldn't yet know what any details of the mesh are.
    mpVtkUnstructedMesh = vtkUnstructuredGrid::New();
 
    
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::~VtkMeshWriter()
{
    mpVtkUnstructedMesh->Delete(); // Reference counted
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::MakeVtkMesh()
{
    //Construct nodes aka as Points
    vtkPoints* p_pts = vtkPoints::New(VTK_DOUBLE);
    p_pts->GetData()->SetName("Vertex positions");
    for (unsigned item_num=0; item_num<this->GetNumNodes(); item_num++)
    {
        std::vector<double> current_item = this->GetNextNode(); //this->mNodeData[item_num];
        // Add zeroes if the dimension is below 3
        for (unsigned dim=SPACE_DIM; dim<3; dim++)
        {
            current_item.push_back(0.0);//For y and z-coordinates if necessary
        }
        assert(current_item.size() == 3);
        p_pts->InsertPoint(item_num, current_item[0], current_item[1], current_item[2]);
    }
    mpVtkUnstructedMesh->SetPoints(p_pts);
    p_pts->Delete(); //Reference counted
 
    if (mWriteMeshCells == true)
    {
        //Construct elements aka Cells
        for (unsigned item_num=0; item_num<this->GetNumElements(); item_num++)
        {
            std::vector<unsigned> current_element = this->GetNextElement().NodeIndices; // this->mElementData[item_num];
 
            assert((current_element.size() == ELEMENT_DIM + 1) || (current_element.size() == (ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2));
 
            vtkCell* p_cell=nullptr;
            if (ELEMENT_DIM == 3 && current_element.size() == 4)
            {
                p_cell = vtkTetra::New();
            }
            else if (ELEMENT_DIM == 3 && current_element.size() == 10)
            {
                p_cell = vtkQuadraticTetra::New();
            }
            else if (ELEMENT_DIM == 2 && current_element.size() == 3)
            {
                p_cell = vtkTriangle::New();
            }
            else if (ELEMENT_DIM == 2 && current_element.size() == 6)
            {
                p_cell = vtkQuadraticTriangle::New();
            }
            else if (ELEMENT_DIM == 1)
            {
                p_cell = vtkLine::New();
            }
 
            //Set the linear nodes
            vtkIdList* p_cell_id_list = p_cell->GetPointIds();
            for (unsigned j = 0; j < current_element.size(); ++j)
            {
                p_cell_id_list->SetId(j, current_element[j]);
            }
 
            //VTK defines the node ordering in quadratic triangles differently to Chaste, so they must be treated as a special case
            if (SPACE_DIM == 2 && current_element.size() == 6)
            {
                p_cell_id_list->SetId(3, current_element[5]);
                p_cell_id_list->SetId(4, current_element[3]);
                p_cell_id_list->SetId(5, current_element[4]);
            }
 
            mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
            p_cell->Delete(); //Reference counted
        }
    }
 
    if (SPACE_DIM > 1)
    {
        for (unsigned item_num=0; item_num<this->GetNumBoundaryFaces(); item_num++)
        {
            this->GetNextBoundaryElement();
        }
    }
 
    //If necessary, construct cables
    if (this->GetNumCableElements() > 0)
    {
        AugmentCellData();
        //Make a blank cell radius data for the regular elements
        std::vector<double> radii(this->GetNumElements(), 0.0);
        for (unsigned item_num=0; item_num<this->GetNumCableElements(); item_num++)
        {
            ElementData cable_element_data = this->GetNextCableElement();
            std::vector<unsigned> current_element = cable_element_data.NodeIndices;
            radii.push_back(cable_element_data.AttributeValue);
            assert(current_element.size() == 2);
            vtkCell* p_cell=vtkLine::New();
            vtkIdList* p_cell_id_list = p_cell->GetPointIds();
            for (unsigned j = 0; j < 2; ++j)
            {
                p_cell_id_list->SetId(j, current_element[j]);
            }
            mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
            p_cell->Delete(); //Reference counted
        }
        AddCellData("Cable radius", radii);
 
    }
 
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::SetWriteMeshCells(bool writeMeshCells)
{
    mWriteMeshCells = writeMeshCells;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddProvenance(std::string fileName)
{
    std::string comment = "<!-- " + ChasteBuildInfo::GetProvenanceString() + "-->";
 
    out_stream p_vtu_file = this->mpOutputFileHandler->OpenOutputFile(fileName, std::ios::out | std::ios::app);
 
    *p_vtu_file << "\n" << comment << "\n";
    p_vtu_file->close();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::WriteFiles()
{
    // Using separate scope here to make sure file is properly closed before re-opening it to add provenance info.
    {
        MakeVtkMesh();
        assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
        vtkXMLUnstructuredGridWriter* p_writer = vtkXMLUnstructuredGridWriter::New();
#if VTK_MAJOR_VERSION >= 6
        p_writer->SetInputData(mpVtkUnstructedMesh);
#else
        p_writer->SetInput(mpVtkUnstructedMesh);
#endif
        std::string vtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName+".vtu";
        p_writer->SetFileName(vtk_file_name.c_str());
        //p_writer->PrintSelf(std::cout, vtkIndent());
        p_writer->Write();
        p_writer->Delete(); //Reference counted
    }
 
    AddProvenance(this->mBaseName + ".vtu");
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddCellData(std::string dataName, std::vector<double> dataPayload)
{
    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
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AugmentCellData()
{
    unsigned num_cell_arrays = mpVtkUnstructedMesh->GetCellData()->GetNumberOfArrays();
    for (unsigned i = 0; i < num_cell_arrays; i++)
    {
        vtkDataArray* array = mpVtkUnstructedMesh->GetCellData()->GetArray(i);
 
        //Check data was the correct size before the cables were added
        unsigned num_cable_pads = this->GetNumCableElements();
        if (mWriteParallelFiles)
        {
            assert((unsigned)array->GetNumberOfTuples() == this->mpDistributedMesh->GetNumLocalElements());
            num_cable_pads =  this->mpMixedMesh->GetNumLocalCableElements();
        }
        else
        {
            assert((unsigned)array->GetNumberOfTuples() == this->GetNumElements());
        }
 
        //Check that tuples of size 3 will be big enough for padding the rest of the data
        assert(array->GetNumberOfComponents() <= 3);
        double null_data[3] = {0.0, 0.0, 0.0};
 
        //Pad data
        for (unsigned new_index = 0; new_index <  num_cable_pads; new_index++)
        {
            array->InsertNextTuple(null_data);
        }
    }
}
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddCellData(std::string dataName, std::vector<c_vector<double, SPACE_DIM> > dataPayload)
{
    vtkDoubleArray* p_vectors = vtkDoubleArray::New();
    p_vectors->SetName(dataName.c_str());
    p_vectors->SetNumberOfComponents(3);
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        for (unsigned j=0; j<SPACE_DIM; j++)
        {
            p_vectors->InsertNextValue(dataPayload[i][j]);
        }
        //When SPACE_DIM<3, then pad
        for (unsigned j=SPACE_DIM; j<3; j++)
        {
            p_vectors->InsertNextValue(0.0);
        }
    }
 
    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_vectors);
    p_vectors->Delete(); //Reference counted
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddTensorCellData(std::string dataName, std::vector<c_vector<double,SPACE_DIM*(SPACE_DIM+1)/2> > dataPayload)
{
    assert(SPACE_DIM != 1);    // LCOV_EXCL_LINE
 
    vtkDoubleArray* p_vectors = vtkDoubleArray::New();
    p_vectors->SetName(dataName.c_str());
    p_vectors->SetNumberOfComponents(SPACE_DIM*SPACE_DIM);
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        if (SPACE_DIM == 2)
        {
            p_vectors->InsertNextValue(dataPayload[i](0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](1)); //a21
            p_vectors->InsertNextValue(dataPayload[i](2)); //a22
        }
        else if (SPACE_DIM == 3)
        {
            p_vectors->InsertNextValue(dataPayload[i](0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](2)); //a13
            p_vectors->InsertNextValue(dataPayload[i](1)); //a21
            p_vectors->InsertNextValue(dataPayload[i](3)); //a22
            p_vectors->InsertNextValue(dataPayload[i](4)); //a23
            p_vectors->InsertNextValue(dataPayload[i](2)); //a31
            p_vectors->InsertNextValue(dataPayload[i](4)); //a32
            p_vectors->InsertNextValue(dataPayload[i](5)); //a33
        }
    }
 
    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_vectors);
    p_vectors->Delete(); //Reference counted
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddTensorCellData(std::string dataName, std::vector<c_matrix<double,SPACE_DIM,SPACE_DIM> > dataPayload)
{
    assert(SPACE_DIM != 1);    // LCOV_EXCL_LINE
 
    vtkDoubleArray* p_vectors = vtkDoubleArray::New();
    p_vectors->SetName(dataName.c_str());
    p_vectors->SetNumberOfComponents(SPACE_DIM*SPACE_DIM);
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        if (SPACE_DIM == 2)
        {
            p_vectors->InsertNextValue(dataPayload[i](0,0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](0,1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](1,0)); //a21
            p_vectors->InsertNextValue(dataPayload[i](1,1)); //a22
        }
        else if (SPACE_DIM == 3)
        {
            p_vectors->InsertNextValue(dataPayload[i](0,0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](0,1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](0,2)); //a13
            p_vectors->InsertNextValue(dataPayload[i](1,0)); //a21
            p_vectors->InsertNextValue(dataPayload[i](1,1)); //a22
            p_vectors->InsertNextValue(dataPayload[i](1,2)); //a23
            p_vectors->InsertNextValue(dataPayload[i](2,0)); //a31
            p_vectors->InsertNextValue(dataPayload[i](2,1)); //a32
            p_vectors->InsertNextValue(dataPayload[i](2,2)); //a33
        }
    }
 
    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_vectors);
    p_vectors->Delete(); //Reference counted
}
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddPointData(std::string dataName, std::vector<double> dataPayload)
{
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
 
    if (mWriteParallelFiles && this->mpDistributedMesh != nullptr)
    {
        // In parallel, the vector we pass will only contain the values from the privately owned nodes.
        // To get the values from the halo nodes (which will be inserted at the end of the vector we need to
        // communicate with the equivalent vectors on other processes.
 
        // resize the payload data to include halos
        assert( dataPayload.size() == this->mpDistributedMesh->GetNumLocalNodes() );
        dataPayload.resize( this->mpDistributedMesh->GetNumLocalNodes() + this->mpDistributedMesh->GetNumHaloNodes() );
 
 
        // then do the communication
        for ( unsigned rank_offset = 1; rank_offset < PetscTools::GetNumProcs(); rank_offset++ )
        {
            unsigned send_to      = (PetscTools::GetMyRank() + rank_offset) % (PetscTools::GetNumProcs());
            unsigned receive_from = (PetscTools::GetMyRank() + PetscTools::GetNumProcs()- rank_offset ) % (PetscTools::GetNumProcs());
 
            unsigned number_of_nodes_to_send    = mNodesToSendPerProcess[send_to].size();
            unsigned number_of_nodes_to_receive = mNodesToReceivePerProcess[receive_from].size();
 
            boost::scoped_array<double> send_data(new double[number_of_nodes_to_send]);
            boost::scoped_array<double> receive_data(new double[number_of_nodes_to_receive]);
            // Pack
            for (unsigned node = 0; node < number_of_nodes_to_send; node++)
            {
                unsigned global_node_index = mNodesToSendPerProcess[send_to][node];
                unsigned local_node_index = global_node_index
                            - this->mpDistributedMesh->GetDistributedVectorFactory()->GetLow();
                send_data[node] = dataPayload[local_node_index];
            }
            {
                // Send
                int ret;
                MPI_Status status;
                ret = MPI_Sendrecv(send_data.get(), number_of_nodes_to_send,
                                   MPI_DOUBLE,
                                   send_to, 0,
                                   receive_data.get(),  number_of_nodes_to_receive,
                                   MPI_DOUBLE,
                                   receive_from, 0,
                                   PETSC_COMM_WORLD, &status);
                UNUSED_OPT(ret);
                assert ( ret == MPI_SUCCESS );
            }
 
            // Unpack
            for ( unsigned node = 0; node < number_of_nodes_to_receive; node++ )
            {
                unsigned global_node_index = mNodesToReceivePerProcess[receive_from][node];
                unsigned halo_index = mGlobalToNodeIndexMap[global_node_index];
                assert( halo_index >= this->mpDistributedMesh->GetNumLocalNodes() );
                dataPayload[halo_index] = receive_data[node];
            }
 
        }
    }
 
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }
 
    vtkPointData* p_point_data = mpVtkUnstructedMesh->GetPointData();
    p_point_data->AddArray(p_scalars);
    p_scalars->Delete(); //Reference counted
}
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddPointData(std::string dataName, std::vector<c_vector<double, SPACE_DIM> > dataPayload)
{
    vtkDoubleArray* p_vectors = vtkDoubleArray::New();
    p_vectors->SetName(dataName.c_str());
 
    if (mWriteParallelFiles)
    {
        // In parallel, the vector we pass will only contain the values from the privately owned nodes.
        // To get the values from the halo nodes (which will be inserted at the end of the vector we need to
        // communicate with the equivalent vectors on other processes.
 
        // resize the payload data to include halos
        assert( dataPayload.size() == this->mpDistributedMesh->GetNumLocalNodes() );
        dataPayload.resize( this->mpDistributedMesh->GetNumLocalNodes() + this->mpDistributedMesh->GetNumHaloNodes() );
 
        // then do the communication
        for ( unsigned rank_offset = 1; rank_offset < PetscTools::GetNumProcs(); rank_offset++ )
        {
            unsigned send_to      = (PetscTools::GetMyRank() + rank_offset) % (PetscTools::GetNumProcs());
            unsigned receive_from = (PetscTools::GetMyRank() + PetscTools::GetNumProcs()- rank_offset ) % (PetscTools::GetNumProcs());
 
            unsigned number_of_nodes_to_send    = mNodesToSendPerProcess[send_to].size();
            unsigned number_of_nodes_to_receive = mNodesToReceivePerProcess[receive_from].size();
 
            boost::scoped_array<double> send_data(new double[number_of_nodes_to_send * SPACE_DIM]);
            boost::scoped_array<double> receive_data(new double[number_of_nodes_to_receive * SPACE_DIM]);
 
            for (unsigned node = 0; node < number_of_nodes_to_send; node++)
            {
                unsigned global_node_index = mNodesToSendPerProcess[send_to][node];
                unsigned local_node_index = global_node_index
                            - this->mpDistributedMesh->GetDistributedVectorFactory()->GetLow();
                for (unsigned j=0; j<SPACE_DIM; j++)
                {
                    send_data[ node*SPACE_DIM + j ] = dataPayload[local_node_index][j];
                }
            }
 
                int ret;
                MPI_Status status;
                ret = MPI_Sendrecv(send_data.get(), number_of_nodes_to_send * SPACE_DIM,
                                   MPI_DOUBLE,
                                   send_to, 0,
                                   receive_data.get(),  number_of_nodes_to_receive * SPACE_DIM,
                                   MPI_DOUBLE,
                                   receive_from, 0,
                                   PETSC_COMM_WORLD, &status);
                UNUSED_OPT(ret);
                assert ( ret == MPI_SUCCESS );
 
            // Unpack
            for ( unsigned node = 0; node < number_of_nodes_to_receive; node++ )
            {
                unsigned global_node_index = mNodesToReceivePerProcess[receive_from][node];
                unsigned halo_index = mGlobalToNodeIndexMap[global_node_index];
                assert( halo_index >= this->mpDistributedMesh->GetNumLocalNodes() );
                for (unsigned j=0; j<SPACE_DIM; j++)
                {
                    dataPayload[halo_index][j] = receive_data[ node*SPACE_DIM + j ];
                }
            }
        }
    }
 
    p_vectors->SetNumberOfComponents(3);
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        for (unsigned j=0; j<SPACE_DIM; j++)
        {
            p_vectors->InsertNextValue(dataPayload[i][j]);
        }
        //When SPACE_DIM<3, then pad
        for (unsigned j=SPACE_DIM; j<3; j++)
        {
            p_vectors->InsertNextValue(0.0);
        }
    }
 
    vtkPointData* p_point_data = mpVtkUnstructedMesh->GetPointData();
    p_point_data->AddArray(p_vectors);
    p_vectors->Delete(); //Reference counted
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::AddTensorPointData(std::string dataName, std::vector<c_matrix<double,SPACE_DIM,SPACE_DIM> > dataPayload)
{
    assert(SPACE_DIM != 1);    // LCOV_EXCL_LINE
 
    vtkDoubleArray* p_vectors = vtkDoubleArray::New();
    p_vectors->SetName(dataName.c_str());
    p_vectors->SetNumberOfComponents(SPACE_DIM*SPACE_DIM);
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        if (SPACE_DIM == 2)
        {
            p_vectors->InsertNextValue(dataPayload[i](0,0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](0,1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](1,0)); //a21
            p_vectors->InsertNextValue(dataPayload[i](1,1)); //a22
        }
        else if (SPACE_DIM == 3)
        {
            p_vectors->InsertNextValue(dataPayload[i](0,0)); //a11
            p_vectors->InsertNextValue(dataPayload[i](0,1)); //a12
            p_vectors->InsertNextValue(dataPayload[i](0,2)); //a13
            p_vectors->InsertNextValue(dataPayload[i](1,0)); //a21
            p_vectors->InsertNextValue(dataPayload[i](1,1)); //a22
            p_vectors->InsertNextValue(dataPayload[i](1,2)); //a23
            p_vectors->InsertNextValue(dataPayload[i](2,0)); //a31
            p_vectors->InsertNextValue(dataPayload[i](2,1)); //a32
            p_vectors->InsertNextValue(dataPayload[i](2,2)); //a33
        }
    }
 
    vtkPointData* p_point_data = mpVtkUnstructedMesh->GetPointData();
    p_point_data->AddArray(p_vectors);
    p_vectors->Delete(); //Reference counted
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM,SPACE_DIM>::SetParallelFiles( AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh )
{
    //Have we got a distributed mesh?
    this->mpDistributedMesh = dynamic_cast<DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* >(&rMesh);
    mpNodesOnlyMesh = dynamic_cast<NodesOnlyMesh<SPACE_DIM>* >(&rMesh);
 
    if (this->mpDistributedMesh == nullptr && mpNodesOnlyMesh == nullptr)
    {
        EXCEPTION("Cannot write parallel files using a sequential mesh");
    }
 
    if (PetscTools::IsSequential())
    {
        return;     // mWriteParallelFiles is not set sequentially (so we don't set up data exchange machinery)
    }
 
    mWriteParallelFiles = true;
 
    // Populate the global to node index map (as this will be required to add point data)
 
    //Node index that we are writing to VTK (index into mNodes and mHaloNodes as if they were concatenated)
    unsigned index = 0;
 
    // Owned nodes
    for (typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator node_iter = rMesh.GetNodeIteratorBegin();
         node_iter != rMesh.GetNodeIteratorEnd();
         ++node_iter)
    {
        mGlobalToNodeIndexMap[node_iter->GetIndex()] = index;
        index++;
    }
 
    // Halo nodes
    if (this->mpDistributedMesh)
    {
        for (typename DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::HaloNodeIterator halo_iter=this->mpDistributedMesh->GetHaloNodeIteratorBegin();
                halo_iter != this->mpDistributedMesh->GetHaloNodeIteratorEnd();
                ++halo_iter)
        {
            mGlobalToNodeIndexMap[(*halo_iter)->GetIndex()] = index;
            index++;
        }
 
        //Calculate the halo exchange so that node-wise payloads can be communicated
        this->mpDistributedMesh->CalculateNodeExchange( mNodesToSendPerProcess, mNodesToReceivePerProcess );
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMesh(
      AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
      bool keepOriginalElementIndexing)
{
    // Have we got a parallel mesh?
    this->mpDistributedMesh = dynamic_cast<DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* >(&rMesh);
    this->mpMixedMesh = dynamic_cast<MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* >(&rMesh);
 
    if (PetscTools::IsSequential() || !mWriteParallelFiles || (this->mpDistributedMesh == nullptr && mpNodesOnlyMesh == nullptr))
    {
        AbstractTetrahedralMeshWriter<ELEMENT_DIM,SPACE_DIM>::WriteFilesUsingMesh( rMesh,keepOriginalElementIndexing );
    }
    else
    {
        //Make the local mesh into a VtkMesh
        vtkPoints* p_pts = vtkPoints::New(VTK_DOUBLE);
        p_pts->GetData()->SetName("Vertex positions");
 
        // Owned nodes
        for (typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator node_iter = rMesh.GetNodeIteratorBegin();
             node_iter != rMesh.GetNodeIteratorEnd();
             ++node_iter)
        {
            c_vector<double, SPACE_DIM> current_item = node_iter->rGetLocation();
            if (SPACE_DIM == 3)
            {
                p_pts->InsertNextPoint(current_item[0], current_item[1], current_item[2]);
            }
            else if (SPACE_DIM == 2)
            {
                p_pts->InsertNextPoint(current_item[0], current_item[1], 0.0);
            }
            else // (SPACE_DIM == 1)
            {
                p_pts->InsertNextPoint(current_item[0], 0.0, 0.0);
            }
        }
 
        // Halo nodes
        if (this->mpDistributedMesh)
        {
            for (typename DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::HaloNodeIterator halo_iter=this->mpDistributedMesh->GetHaloNodeIteratorBegin();
                    halo_iter != this->mpDistributedMesh->GetHaloNodeIteratorEnd();
                    ++halo_iter)
            {
                c_vector<double, SPACE_DIM> current_item = (*halo_iter)->rGetLocation();
                if (SPACE_DIM == 3)
                {
                    p_pts->InsertNextPoint(current_item[0], current_item[1], current_item[2]);
                }
                else if (SPACE_DIM == 2)
                {
                    p_pts->InsertNextPoint(current_item[0], current_item[1], 0.0);
                }
                else // (SPACE_DIM == 1)
                {
                    p_pts->InsertNextPoint(current_item[0], 0.0, 0.0);
                }
            }
        }
 
        mpVtkUnstructedMesh->SetPoints(p_pts);
        p_pts->Delete(); //Reference counted
 
        for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator elem_iter = rMesh.GetElementIteratorBegin();
             elem_iter != rMesh.GetElementIteratorEnd();
             ++elem_iter)
        {
 
            vtkCell* p_cell=nullptr;
            if (ELEMENT_DIM == 3)
            {
                p_cell = vtkTetra::New();
            }
            else if (ELEMENT_DIM == 2)
            {
                p_cell = vtkTriangle::New();
            }
            else //(ELEMENT_DIM == 1)
            {
                p_cell = vtkLine::New();
            }
            vtkIdList* p_cell_id_list = p_cell->GetPointIds();
            for (unsigned j = 0; j < ELEMENT_DIM+1; ++j)
            {
                unsigned global_node_index = elem_iter->GetNodeGlobalIndex(j);
                p_cell_id_list->SetId(j, mGlobalToNodeIndexMap[global_node_index]);
            }
            mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
            p_cell->Delete(); //Reference counted
        }
        //If necessary, construct cables
        if (this->mpMixedMesh )
        {
            AugmentCellData();
            //Make a blank cell radius data for the regular elements
            std::vector<double> radii(this->mpMixedMesh->GetNumLocalElements(), 0.0);
            for (typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::CableElementIterator elem_iter = this->mpMixedMesh->GetCableElementIteratorBegin();
                 elem_iter != this->mpMixedMesh->GetCableElementIteratorEnd();
                 ++elem_iter)
            {
                radii.push_back((*elem_iter)->GetAttribute());
                vtkCell* p_cell=vtkLine::New();
                vtkIdList* p_cell_id_list = p_cell->GetPointIds();
                for (unsigned j = 0; j < 2; ++j)
                {
                    unsigned global_node_index = (*elem_iter)->GetNodeGlobalIndex(j);
                    p_cell_id_list->SetId(j, mGlobalToNodeIndexMap[global_node_index]);
                }
                mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
                p_cell->Delete(); //Reference counted
            }
            AddCellData("Cable radius", radii);
        }
 
 
        //This block is to guard the mesh writers (vtkXMLPUnstructuredGridWriter) so that they
        //go out of scope, flush buffers and close files
        {
            assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
            vtkXMLPUnstructuredGridWriter* p_writer = vtkXMLPUnstructuredGridWriter::New();
 
            p_writer->SetDataModeToBinary();
 
            p_writer->SetNumberOfPieces(PetscTools::GetNumProcs());
            //p_writer->SetGhostLevel(-1);
            p_writer->SetStartPiece(PetscTools::GetMyRank());
            p_writer->SetEndPiece(PetscTools::GetMyRank());
 
 
#if VTK_MAJOR_VERSION >= 6
            p_writer->SetInputData(mpVtkUnstructedMesh);
#else
            p_writer->SetInput(mpVtkUnstructedMesh);
#endif
            std::string pvtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName+ ".pvtu";
            p_writer->SetFileName(pvtk_file_name.c_str());
            //p_writer->PrintSelf(std::cout, vtkIndent());
            p_writer->Write();
            p_writer->Delete(); //Reference counted
        }
 
        // Add provenance to the individual files
        std::stringstream filepath;
        filepath << this->mBaseName << "_" << PetscTools::GetMyRank() << ".vtu";
        AddProvenance(filepath.str());
        if (PetscTools::AmMaster())
        {
            AddProvenance(this->mBaseName+ ".pvtu");
        }
    }
}
 
// Explicit instantiation
template class VtkMeshWriter<1,1>;
template class VtkMeshWriter<1,2>;
template class VtkMeshWriter<1,3>;
template class VtkMeshWriter<2,2>; // Actually used
template class VtkMeshWriter<2,3>;
template class VtkMeshWriter<3,3>; // Actually used
 
#endif //CHASTE_VTK