AbstractUnstructuredGridDiscreteContinuumSolver.cpp

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#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning for now (gcc4.3)
#include <vtkDoubleArray.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkProbeFilter.h>
#include <vtkImageData.h>
#include <vtkSmartPointer.h>
#include "AbstractUnstructuredGridDiscreteContinuumSolver.hpp"

template<unsigned DIM>
AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::AbstractUnstructuredGridDiscreteContinuumSolver()
    :   AbstractDiscreteContinuumSolver<DIM>(),
        mpVtkSolution(),
        mpMesh()
{
    this->mHasUnstructuredGrid = true;
}

template<unsigned DIM>
AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::~AbstractUnstructuredGridDiscreteContinuumSolver()
{

}

template<unsigned DIM>
boost::shared_ptr<DiscreteContinuumMesh<DIM> > AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetMesh()
{
    if(!this->mpMesh)
    {
        EXCEPTION("A mesh has not been set.");
    }
    return this->mpMesh;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration> > AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetConcentrationsAtCentroids()
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    std::vector<c_vector<double, DIM> > centroids = mpMesh->GetElementCentroids();
    std::vector<units::quantity<unit::concentration> > sampled_solution(centroids.size(), 0.0*this->mReferenceConcentration);

    // Sample the field at these locations
    vtkSmartPointer<vtkPolyData> p_polydata = vtkSmartPointer<vtkPolyData>::New();
    vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();
    p_points->SetNumberOfPoints(centroids.size());
    for(unsigned idx=0; idx< centroids.size(); idx++)
    {
        if(DIM==3)
        {
            p_points->SetPoint(idx, centroids[idx][0], centroids[idx][1], centroids[idx][2]);
        }
        else
        {
            p_points->SetPoint(idx, centroids[idx][0], centroids[idx][1], 0.0);
        }
    }
    p_polydata->SetPoints(p_points);

    vtkSmartPointer<vtkProbeFilter> p_probe_filter = vtkSmartPointer<vtkProbeFilter>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_probe_filter->SetInput(p_polydata);
        p_probe_filter->SetSource(this->mpVtkSolution);
    #else
        p_probe_filter->SetInputData(p_polydata);
        p_probe_filter->SetSourceData(this->mpVtkSolution);
    #endif
    p_probe_filter->Update();
    vtkSmartPointer<vtkPointData> p_point_data = p_probe_filter->GetOutput()->GetPointData();

    unsigned num_points = p_point_data->GetArray(this->mLabel.c_str())->GetNumberOfTuples();
    for(unsigned idx=0; idx<num_points; idx++)
    {
        sampled_solution[idx] = p_point_data->GetArray(this->mLabel.c_str())->GetTuple1(idx)*this->mReferenceConcentration;
    }
    return sampled_solution;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration> > AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetConcentrations(const std::vector<DimensionalChastePoint<DIM> >& samplePoints)
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    std::vector<units::quantity<unit::concentration> > sampled_solution(samplePoints.size(), 0.0*this->mReferenceConcentration);

    // Sample the field at these locations
    vtkSmartPointer<vtkPolyData> p_polydata = vtkSmartPointer<vtkPolyData>::New();
    vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();

    p_points->SetNumberOfPoints(samplePoints.size());
    for(unsigned idx=0; idx< samplePoints.size(); idx++)
    {
        c_vector<double, DIM> location = samplePoints[idx].GetLocation(this->mpMesh->GetReferenceLengthScale());
        if(DIM==3)
        {
            p_points->SetPoint(idx, location[0], location[1], location[2]);
        }
        else
        {
            p_points->SetPoint(idx, location[0], location[1], 0.0);
        }
    }
    p_polydata->SetPoints(p_points);

    vtkSmartPointer<vtkProbeFilter> p_probe_filter = vtkSmartPointer<vtkProbeFilter>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_probe_filter->SetInput(p_polydata);
        p_probe_filter->SetSource(this->mpVtkSolution);
    #else
        p_probe_filter->SetInputData(p_polydata);
        p_probe_filter->SetSourceData(this->mpVtkSolution);
    #endif
    p_probe_filter->Update();
    vtkSmartPointer<vtkPointData> p_point_data = p_probe_filter->GetOutput()->GetPointData();

    unsigned num_points = p_point_data->GetArray(this->mLabel.c_str())->GetNumberOfTuples();
    for(unsigned idx=0; idx<num_points; idx++)
    {
        sampled_solution[idx] = p_point_data->GetArray(this->mLabel.c_str())->GetTuple1(idx)*this->mReferenceConcentration;
    }
    return sampled_solution;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration> > AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetConcentrations(boost::shared_ptr<RegularGrid<DIM> > pGrid)
{
    return this->GetConcentrations(pGrid->GetLocations());
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration> > AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetConcentrations(boost::shared_ptr<DiscreteContinuumMesh<DIM> > pMesh)
{
    if(this->mpMesh == pMesh)
    {
        return this->GetConcentrations();
    }
    else
    {
        return this->GetConcentrations(pMesh->GetNodeLocationsAsPoints());
    }
}

template<unsigned DIM>
std::vector<double> AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetSolution(const std::vector<DimensionalChastePoint<DIM> >& rSamplePoints)
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    std::vector<double> sampled_solution(rSamplePoints.size(), 0.0);

    // Sample the field at these locations
    vtkSmartPointer<vtkPolyData> p_polydata = vtkSmartPointer<vtkPolyData>::New();
    vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();
    p_points->SetNumberOfPoints(rSamplePoints.size());
    for(unsigned idx=0; idx< rSamplePoints.size(); idx++)
    {
        c_vector<double, DIM> location = rSamplePoints[idx].GetLocation(this->mpMesh->GetReferenceLengthScale());
        if(DIM==3)
        {
            p_points->SetPoint(idx, location[0], location[1], location[2]);
        }
        else
        {
            p_points->SetPoint(idx, location[0], location[1], 0.0);
        }
    }
    p_polydata->SetPoints(p_points);

    vtkSmartPointer<vtkProbeFilter> p_probe_filter = vtkSmartPointer<vtkProbeFilter>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_probe_filter->SetInput(p_polydata);
        p_probe_filter->SetSource(this->mpVtkSolution);
    #else
        p_probe_filter->SetInputData(p_polydata);
        p_probe_filter->SetSourceData(this->mpVtkSolution);
    #endif
    p_probe_filter->Update();
    vtkSmartPointer<vtkPointData> p_point_data = p_probe_filter->GetOutput()->GetPointData();

    unsigned num_points = p_point_data->GetArray(this->mLabel.c_str())->GetNumberOfTuples();
    for(unsigned idx=0; idx<num_points; idx++)
    {
        sampled_solution[idx] = p_point_data->GetArray(this->mLabel.c_str())->GetTuple1(idx);
    }
    return sampled_solution;
}

template<unsigned DIM>
std::vector<double> AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetSolution(boost::shared_ptr<RegularGrid<DIM> > pGrid)
{
    return this->GetSolution(pGrid->GetLocations());
}

template<unsigned DIM>
std::vector<double> AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetSolution(boost::shared_ptr<DiscreteContinuumMesh<DIM> > pMesh)
{
    if(this->mpMesh == pMesh)
    {
        return this->GetSolution();
    }
    else
    {
        return this->GetSolution(pMesh->GetNodeLocationsAsPoints());
    }
}

template<unsigned DIM>
vtkSmartPointer<vtkUnstructuredGrid> AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::GetVtkSolution()
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }
    return this->mpVtkSolution;
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::SetMesh(boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > pMesh)
{
    this->mpMesh = pMesh;
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::Setup()
{
    if(!this->mpMesh)
    {
        EXCEPTION("Mesh needed before Setup can be called.");
    }

    // Set up the VTK solution
    this->mpVtkSolution = mpMesh->GetAsVtkUnstructuredGrid();

    unsigned num_nodes = this->mpMesh->GetNodeLocationsAsPoints().size();
    this->mSolution = std::vector<double>(0.0, num_nodes);

    if(this->mpNetwork)
    {
        this->mpMesh->SetVesselNetwork(this->mpNetwork)  ;
    }
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::UpdateSolution(const std::vector<double>& data)
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    vtkSmartPointer<vtkDoubleArray> pPointData = vtkSmartPointer<vtkDoubleArray>::New();
    pPointData->SetNumberOfComponents(1);
    pPointData->SetNumberOfTuples(data.size());
    pPointData->SetName(this->GetLabel().c_str());
    for (unsigned i = 0; i < data.size(); i++)
    {
        pPointData->SetValue(i, data[i]);
    }
    this->mpVtkSolution->GetPointData()->AddArray(pPointData);

    // Note, if the data vector being passed in is mPointSolution, then it will be overwritten with zeros.
    this->mSolution = std::vector<double>(data.size(), 0.0);
    for (unsigned i = 0; i < data.size(); i++)
    {
        this->mSolution[i] = data[i];
    }
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::UpdateElementSolution(const std::vector<double>& data)
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    vtkSmartPointer<vtkDoubleArray> pPointData = vtkSmartPointer<vtkDoubleArray>::New();
    pPointData->SetNumberOfComponents(1);
    pPointData->SetNumberOfTuples(data.size());
    pPointData->SetName(this->GetLabel().c_str());
    for (unsigned i = 0; i < data.size(); i++)
    {
        pPointData->SetValue(i, data[i]);
    }
    this->mpVtkSolution->GetCellData()->AddArray(pPointData);
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::UpdateSolution(const std::vector<units::quantity<unit::concentration> >& data)
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    vtkSmartPointer<vtkDoubleArray> pPointData = vtkSmartPointer<vtkDoubleArray>::New();
    pPointData->SetNumberOfComponents(1);
    pPointData->SetNumberOfTuples(data.size());
    pPointData->SetName(this->GetLabel().c_str());
    for (unsigned i = 0; i < data.size(); i++)
    {
        pPointData->SetValue(i, data[i]/this->mReferenceConcentration);
    }
    this->mpVtkSolution->GetPointData()->AddArray(pPointData);

    // Note, if the data vector being passed in is mPointSolution, then it will be overwritten with zeros.
    this->mConcentrations = std::vector<units::quantity<unit::concentration> >(data.size(), 0.0*this->mReferenceConcentration);
    for (unsigned i = 0; i < data.size(); i++)
    {
        this->mConcentrations[i] = data[i];
    }
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::UpdateCellData()
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    if(!this->CellPopulationIsSet())
    {
        EXCEPTION("The DiscreteContinuum solver needs a cell population for this operation.");
    }

    // Update for FEM
//    this->mpRegularGrid->SetCellPopulation(*(this->mpCellPopulation));
//    std::vector<std::vector<CellPtr> > point_cell_map = this->mpRegularGrid->GetPointCellMap();
//    for(unsigned idx=0; idx<point_cell_map.size(); idx++)
//    {
//        for(unsigned jdx=0; jdx<point_cell_map[idx].size(); jdx++)
//        {
//            point_cell_map[idx][jdx]->GetCellData()->SetItem(this->mLabel, this->mSolution[idx]);
//        }
//    }
}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::Update()
{

}

template<unsigned DIM>
void AbstractUnstructuredGridDiscreteContinuumSolver<DIM>::Write()
{
    if(!this->mpVtkSolution)
    {
        this->Setup();
    }

    if(!this->mpOutputFileHandler)
    {
        EXCEPTION("An output file handler has not been set for the DiscreteContinuum solver.");
    }

    if(PetscTools::AmMaster())
    {
        vtkSmartPointer<vtkXMLUnstructuredGridWriter> p_writer1 = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
        if(!this->mFilename.empty())
        {
            p_writer1->SetFileName((this->mpOutputFileHandler->GetOutputDirectoryFullPath() + "/" + this->mFilename+".vtu").c_str());
        }
        else
        {
            p_writer1->SetFileName((this->mpOutputFileHandler->GetOutputDirectoryFullPath() + "/solution.vtu").c_str());
        }
        #if VTK_MAJOR_VERSION <= 5
            p_writer1->SetInput(this->mpVtkSolution);
        #else
            p_writer1->SetInputData(this->mpVtkSolution);
        #endif
        p_writer1->Update();
        p_writer1->Write();
    }
}

// Explicit instantiation
template class AbstractUnstructuredGridDiscreteContinuumSolver<2> ;
template class AbstractUnstructuredGridDiscreteContinuumSolver<3> ;