AdaptiveTetrahedralMesh.cpp

/*

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

*/

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/



#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

---