AdaptiveTetrahedralMesh.cpp

/*

Copyright (C) Fujitsu Laboratories of Europe, 2009-2010

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/*

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#ifdef CHASTE_ADAPTIVITY

#include "AdaptiveTetrahedralMesh.hpp"
#include "HeartConfig.hpp"
#include "OutputFileHandler.hpp"

AdaptiveTetrahedralMesh::AdaptiveTetrahedralMesh() :
    mNumNodes(0),
    mNumElements(0),
    mNumLocalNodes(0),
    mAdaptSuccess(false),
    mpDiscreteGeometryConstraints(NULL),
    mpErrorMeasure(NULL),
    mpAdapt(NULL),
    mGoodEdgeRange(0.0),
    mBadEdgeCriterion(0.0),
    mVerbose(false)

{
        mpVtkUnstructuredGrid = vtkUnstructuredGrid::New();
}

AdaptiveTetrahedralMesh::~AdaptiveTetrahedralMesh()
{
    Reset();//Delete multiple-use pointers
    mpVtkUnstructuredGrid->Delete();
}

void AdaptiveTetrahedralMesh::ConstructFromVtuFile(std::string fileName)
{
    vtkXMLUnstructuredGridReader *p_vtk_reader = vtkXMLUnstructuredGridReader::New();
    p_vtk_reader->SetFileName(fileName.c_str());
    p_vtk_reader->Update();

    mpVtkUnstructuredGrid->DeepCopy(p_vtk_reader->GetOutput());
    mpVtkUnstructuredGrid->Update();

    p_vtk_reader->Delete();

    mNumNodes = mpVtkUnstructuredGrid->GetNumberOfPoints();
    mNumElements = mpVtkUnstructuredGrid->GetNumberOfCells();
    mNumLocalNodes = mNumNodes;       // Since each process has a complete copy of the vtkUnstructuredGrid
}

void AdaptiveTetrahedralMesh::ConstructFromMesh(AbstractTetrahedralMesh<3,3>* rMesh)
{
    vtkPoints *p_pts = vtkPoints::New();
    p_pts->SetDataTypeToDouble();
    for (unsigned i=0; i<rMesh->GetNumNodes(); i++)
    {
        p_pts->InsertPoint(i, rMesh->GetNode(i)->rGetLocation().data());
    }

    mpVtkUnstructuredGrid->Allocate(rMesh->GetNumNodes(), rMesh->GetNumNodes());
    mpVtkUnstructuredGrid->SetPoints(p_pts);
    mpVtkUnstructuredGrid->Update();
    p_pts->Delete();    // Reference counted

    for (unsigned i=0; i<rMesh->GetNumElements(); i++)
    {
        vtkTetra *p_tetra = vtkTetra::New();
        for (int j = 0; j < 4; ++j)
        {
            p_tetra->GetPointIds()->SetId(j, rMesh->GetElement(i)->GetNodeGlobalIndex(j));
        }
        mpVtkUnstructuredGrid->InsertNextCell(p_tetra->GetCellType(), p_tetra->GetPointIds());
        mpVtkUnstructuredGrid->Update();
        p_tetra->Delete();    // Reference counted
    }

    mNumNodes = mpVtkUnstructuredGrid->GetNumberOfPoints();
    mNumElements = mpVtkUnstructuredGrid->GetNumberOfCells();
    mNumLocalNodes = mNumNodes;       // Since each process has a complete copy of the vtkUnstructuredGrid
}

void AdaptiveTetrahedralMesh::ConstructFromDistributedMesh(DistributedTetrahedralMesh<3,3>* rMesh)
{
    vtkPoints *p_pts = vtkPoints::New();
    p_pts->SetDataTypeToDouble();

    std::vector<unsigned> global_node_numbers, halo_nodes;
    std::map<unsigned, unsigned> global_to_local_index_map;

//    vtkUnsignedIntArray *p_scalars = vtkUnsignedIntArray::New();
//    p_scalars->SetName("GlobalNodeNumbers");

    unsigned index = 0;
    for (DistributedTetrahedralMesh<3,3>::NodeIterator it=rMesh->GetNodeIteratorBegin();
         it != rMesh->GetNodeIteratorEnd();
         ++it)
    {
        p_pts->InsertPoint(index, it->rGetLocation().data());
        global_node_numbers.push_back(it->GetIndex());
        global_to_local_index_map[it->GetIndex()] = index;
        index++;
    }

    rMesh->GetHaloNodeIndices(halo_nodes);
    for(unsigned i=0; i<halo_nodes.size(); i++)
    {
        global_node_numbers.push_back(halo_nodes[i]);
        p_pts->InsertPoint(index, rMesh->GetNodeOrHaloNode(halo_nodes[i])->rGetLocation().data());
        global_to_local_index_map[halo_nodes[i]] = index;
        index++;
    }

    AddPointData("GlobalNodeNumbers", global_node_numbers);

    mpVtkUnstructuredGrid->Allocate(global_node_numbers.size(), global_node_numbers.size());
    mpVtkUnstructuredGrid->SetPoints(p_pts);
    mpVtkUnstructuredGrid->Update();
    p_pts->Delete();    // Reference counted

    for (DistributedTetrahedralMesh<3,3>::ElementIterator it=rMesh->GetElementIteratorBegin();
         it != rMesh->GetElementIteratorEnd();
         ++it)
    {
        vtkTetra *p_tetra = vtkTetra::New();
        for (int j = 0; j < 4; ++j)
        {
            p_tetra->GetPointIds()->SetId(j, global_to_local_index_map[it->GetNodeGlobalIndex(j)]);
        }
        mpVtkUnstructuredGrid->InsertNextCell(p_tetra->GetCellType(), p_tetra->GetPointIds());
        mpVtkUnstructuredGrid->Update();
        p_tetra->Delete();    // Reference counted
    }

    mNumNodes = rMesh->GetNumNodes();
    mNumElements = rMesh->GetNumElements();
    mNumLocalNodes = mpVtkUnstructuredGrid->GetNumberOfPoints() - halo_nodes.size();
}

void AdaptiveTetrahedralMesh::AddPointData(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]);
    }

    mpVtkUnstructuredGrid->GetPointData()->AddArray(p_scalars);
    mpVtkUnstructuredGrid->Update();
    p_scalars->Delete(); // Reference counted
}

void AdaptiveTetrahedralMesh::AddPointData(std::string dataName, std::vector<unsigned> dataPayload)
{
    vtkUnsignedIntArray *p_scalars = vtkUnsignedIntArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }

    mpVtkUnstructuredGrid->GetPointData()->AddArray(p_scalars);
    mpVtkUnstructuredGrid->Update();
    p_scalars->Delete(); // Reference counted
}

void AdaptiveTetrahedralMesh::RemoveArray(std::string dataName)
{
    mpVtkUnstructuredGrid->GetPointData()->RemoveArray(dataName.c_str());
}

void AdaptiveTetrahedralMesh::WriteMeshToFile(std::string directory, std::string fileName)

{
    std::string vtk_file_name = directory + fileName;

    vtkXMLUnstructuredGridWriter *vtk_writer = vtkXMLUnstructuredGridWriter::New();
    //Uninitialised stuff arises (see #1079), but you can remove
    //valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    vtk_writer->SetCompressor(NULL);
    // **** REMOVE WITH CAUTION *****
    vtk_writer->SetFileName(vtk_file_name.c_str());
    vtk_writer->SetInput(mpVtkUnstructuredGrid);
    vtk_writer->Write();
    vtk_writer->Delete();
}

void AdaptiveTetrahedralMesh::WriteMeshToDistributedFile(std::string directory, std::string fileName)
{
    std::string vtk_file_name = directory + fileName;

    vtkXMLPUnstructuredGridWriter *vtk_writer = vtkXMLPUnstructuredGridWriter::New();
    //Uninitialised stuff arises (see #1079), but you can remove
    //valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    vtk_writer->SetCompressor(NULL);
    // **** REMOVE WITH CAUTION *****
    vtk_writer->SetFileName(vtk_file_name.c_str());
    vtk_writer->SetDataModeToBinary();

    vtk_writer->SetNumberOfPieces(PetscTools::GetNumProcs());
    vtk_writer->SetGhostLevel(1);
    vtk_writer->SetStartPiece(PetscTools::GetMyRank());
    vtk_writer->SetEndPiece(PetscTools::GetMyRank());

    vtk_writer->SetInput(mpVtkUnstructuredGrid);
    vtk_writer->Write();
    vtk_writer->Delete();
}

vtkUnstructuredGrid* AdaptiveTetrahedralMesh::GetVtkUnstructuredGrid()
{
    return mpVtkUnstructuredGrid;
}

void AdaptiveTetrahedralMesh::SetAdaptCriterion(double range, double criterion)
{
    mGoodEdgeRange = range;
    mBadEdgeCriterion = criterion;
}

unsigned AdaptiveTetrahedralMesh::GetNumNodes()
{
    return mNumNodes;
}

unsigned AdaptiveTetrahedralMesh::GetNumLocalNodes()
{
    return mNumLocalNodes;
}

unsigned AdaptiveTetrahedralMesh::GetNumLocalAndHaloNodes()
{
    return mpVtkUnstructuredGrid->GetNumberOfPoints();
}

unsigned AdaptiveTetrahedralMesh::GetNumElements()
{
    return mNumElements;
}

unsigned AdaptiveTetrahedralMesh::GetNumLocalElements()
{
    return mpVtkUnstructuredGrid->GetNumberOfCells();
}

unsigned AdaptiveTetrahedralMesh::GetNumSurfaceElements()
{
    return sids.size();
}

void AdaptiveTetrahedralMesh::CalculateSENListAndSids(double coplanarTolerance)
{
    DiscreteGeometryConstraints constraints;

    if (mVerbose) constraints.verbose_on();
    constraints.set_coplanar_tolerance( coplanarTolerance );
    constraints.set_volume_input(mpVtkUnstructuredGrid);

    constraints.get_coplanar_ids(sids);
    constraints.get_surface(SENList);
    assert(sids.size()*3==SENList.size());
}

void AdaptiveTetrahedralMesh::GetGeometryConstraints()
{
    assert(mpDiscreteGeometryConstraints==NULL);
    mpDiscreteGeometryConstraints = new DiscreteGeometryConstraints;

    if (mVerbose) mpDiscreteGeometryConstraints->verbose_on();
    mpDiscreteGeometryConstraints->set_surface_input(mpVtkUnstructuredGrid, SENList, sids);
    mpDiscreteGeometryConstraints->get_constraints(max_len);
//    mpDiscreteGeometryConstraints->write_vtk(std::string("sids.vtu"));
}

void AdaptiveTetrahedralMesh::CalculateErrorMetric()
{
    double error           = HeartConfig::Instance()->GetTargetErrorForAdaptivity();
    double sigma           = HeartConfig::Instance()->GetSigmaForAdaptivity();
    double max_edge_length = HeartConfig::Instance()->GetMaxEdgeLengthForAdaptivity();
    double min_edge_length = HeartConfig::Instance()->GetMinEdgeLengthForAdaptivity();
    double gradation       = HeartConfig::Instance()->GetGradationForAdaptivity();
    unsigned max_nodes     = HeartConfig::Instance()->GetMaxNodesForAdaptivity();
    assert(mpErrorMeasure == NULL);
    mpErrorMeasure = new ErrorMeasure;

    if (mVerbose) mpErrorMeasure->verbose_on();
    mpErrorMeasure->set_input(mpVtkUnstructuredGrid);
    mpErrorMeasure->add_field("Vm", error, false, sigma);
    mpErrorMeasure->set_max_length(max_edge_length);
    mpErrorMeasure->set_max_length(&(max_len[0]), mpVtkUnstructuredGrid->GetNumberOfPoints());
    mpErrorMeasure->set_min_length(min_edge_length);
    mpErrorMeasure->apply_gradation(gradation);
    mpErrorMeasure->set_max_nodes(max_nodes);

    mpErrorMeasure->diagnostics();
}

double AdaptiveTetrahedralMesh::GetEdgeLengthDistribution(double range)
{
    //This is a temporary adaptivity class
    Adaptivity an_adapter;
    an_adapter.set_from_vtk(mpVtkUnstructuredGrid, true);
     return an_adapter.edgeLengthDistribution(range);
}

void AdaptiveTetrahedralMesh::Adapt()
{
    mpAdapt = new Adaptivity;
    mAdaptSuccess = false;

    if (mVerbose) mpAdapt->verbose_on();
    mpAdapt->set_from_vtk(mpVtkUnstructuredGrid, true);
    mpAdapt->set_adapt_sweeps(HeartConfig::Instance()->GetNumberOfAdaptiveSweeps());
    mpAdapt->set_surface_mesh(SENList);
    mpAdapt->set_surface_ids(sids);

    if ( mpAdapt->edgeLengthDistribution( mGoodEdgeRange ) > mBadEdgeCriterion )
    {
        mpAdapt->adapt();

        mpAdapt->get_surface_ids(sids);
        mpAdapt->get_surface_mesh(SENList);

        vtkUnstructuredGrid *p_new_vtk_unstructured_grid = mpAdapt->get_adapted_vtu();
        mpVtkUnstructuredGrid->DeepCopy( p_new_vtk_unstructured_grid );
        mpVtkUnstructuredGrid->Update();
        p_new_vtk_unstructured_grid->Delete();

        mAdaptSuccess = true;
    }
    else
    {
        //mpAdapt->get_adapted_vtu()->Initialize();
    }

    mpVtkUnstructuredGrid->GetPointData()->RemoveArray("metric");
    mpVtkUnstructuredGrid->Squeeze();

    // Need to free these pointers as fresh instances are required for the next adapt (else odd things happen)
    Reset();

    // Update private member variables - note: these assume that the adapt happens sequentially
    mNumNodes = mpVtkUnstructuredGrid->GetNumberOfPoints();
    mNumElements = mpVtkUnstructuredGrid->GetNumberOfCells();
    mNumLocalNodes = mNumNodes;       // Since each process has a complete copy of the vtkUnstructuredGrid
}

void AdaptiveTetrahedralMesh::AdaptMesh()
{
    GetGeometryConstraints();

    CalculateErrorMetric();

    RemoveArray("mean_desired_lengths");
    RemoveArray("desired_lengths");
//    SetAdaptCriterion( mGoodEdgeRange, mBadEdgeCriterion );
    Adapt();
}

void AdaptiveTetrahedralMesh::Reset()
{
    delete mpDiscreteGeometryConstraints;
    delete mpErrorMeasure;
    delete mpAdapt;
    mpDiscreteGeometryConstraints=NULL;
    mpErrorMeasure=NULL;
    mpAdapt=NULL;
}

bool AdaptiveTetrahedralMesh::GetAdaptSuccess()
{
    return mAdaptSuccess;
}

void AdaptiveTetrahedralMesh::MakeVerbose(bool verbose)
{
    mVerbose = verbose;
}

#endif // CHASTE_ADAPTIVITY