DiscreteContinuumMeshGenerator.cpp

/*

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#include <boost/lexical_cast.hpp>
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning
#include <vtkIdList.h>
#include <vtkCellArray.h>
#include <vtkLine.h>
#include <vtkPoints.h>
#include "Exception.hpp"
#include "Warnings.hpp"
#include "Facet.hpp"
#include "Polygon.hpp"
#include "Element.hpp"
#include "UblasVectorInclude.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "VtkMeshWriter.hpp"
#include "DiscreteContinuumMesh.hpp"
#include "DiscreteContinuumMeshGenerator.hpp"
#include "BaseUnits.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::DiscreteContinuumMeshGenerator() :
    mMaxElementArea(0.0 * unit::metres * unit::metres* unit::metres),
    mpMesh(),
    mpDomain(),
    mpVtkDomain(),
    mStlFilePath(),
    mHoles(),
    mRegions(),
    mAttributes(),
    mReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale())
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM> > DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::Create()
{
    MAKE_PTR(DiscreteContinuumMeshGenerator<ELEMENT_DIM>, pSelf);
    return pSelf;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::~DiscreteContinuumMeshGenerator()
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM> > DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::GetMesh()
{
    if(!mpMesh)
    {
        EXCEPTION("No mesh has been generated.");
    }
    return mpMesh;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetDomain(boost::shared_ptr<Part<SPACE_DIM> > pDomain)
{
    mpDomain = pDomain;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetDomain(vtkSmartPointer<vtkPolyData> pDomain)
{
    mpVtkDomain = pDomain;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetDomain(const std::string& rPathToStl)
{
    mStlFilePath = rPathToStl;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetMaxElementArea(units::quantity<unit::volume> maxElementArea)
{
    mMaxElementArea = maxElementArea;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetHoles(std::vector<DimensionalChastePoint<SPACE_DIM> > holes)
{
    mHoles = holes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::SetRegionMarkers(std::vector<DimensionalChastePoint<SPACE_DIM> > regionMarkers)
{
    mRegions = regionMarkers;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::Update()
{
    // Create a mesh
    mpMesh = boost::shared_ptr<DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM> >(new DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>());

    // For 2D parts use triangle
    if (ELEMENT_DIM == 2)
    {
        if (SPACE_DIM == 2)
        {
            Mesh2d();
        }
        else
        {
            if(mpDomain)
            {
                std::vector<units::quantity<unit::length> > bounding_box = mpDomain->GetBoundingBox();
                if (units::abs(bounding_box[4]) < 1.e-12*unit::metres && units::abs(bounding_box[5]) < 1.e-12*unit::metres)
                {
                   Mesh2d();
                }
                else
                {
                    EXCEPTION("2D meshing is only supported for parts with z=0.");
                }
            }
            else if(mpVtkDomain)
            {
                Mesh2d();
            }
            else
            {
                EXCEPTION("2d meshing is not supported for STL files.");
            }
        }
    }
    // For 3d use tetgen
    else
    {
        if(mpDomain)
        {
            std::vector<units::quantity<unit::length> > bounding_box = mpDomain->GetBoundingBox();
            if (units::abs(bounding_box[4]) < 1.e-12*unit::metres && units::abs(bounding_box[5]) < 1.e-12*unit::metres)
            {
                EXCEPTION("The part is two-dimensional, use the 2D meshing functionality.");
            }
            else
            {
                Mesh3d();
            }
        }
        else if(mpVtkDomain)
        {
            Mesh3d();
        }
        else
        {
            MeshStl3d();
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::Mesh2d()
{
    struct triangulateio mesher_input, mesher_output;
    this->InitialiseTriangulateIo(mesher_input);
    this->InitialiseTriangulateIo(mesher_output);

    // Cases: have just domain, have just vtk domain, have vtk domain and domain
    if(mpDomain and !mpVtkDomain)
    {
        std::vector<DimensionalChastePoint<SPACE_DIM> > vertex_locations = mpDomain->GetVertexLocations();
        unsigned num_vertices = vertex_locations.size();
        mesher_input.pointlist = (double *) malloc(num_vertices * 2 * sizeof(double));
        mesher_input.numberofpoints = int(num_vertices);
        for (unsigned idx = 0; idx < num_vertices; idx++)
        {
            c_vector<double, SPACE_DIM> vertex_location = vertex_locations[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.pointlist[2 * idx + jdx] = vertex_location[jdx];
            }
        }

        std::vector<std::pair<unsigned, unsigned> > segments = mpDomain->GetSegmentIndices();
        unsigned num_segments = segments.size();
        mesher_input.segmentlist = (int *) malloc(num_segments * 2 * sizeof(int));
        mesher_input.numberofsegments = int(num_segments);
        for (unsigned idx = 0; idx < num_segments; idx++)
        {
            mesher_input.segmentlist[2 * idx] = int(segments[idx].first);
            mesher_input.segmentlist[2 * idx + 1] = int(segments[idx].second);
        }
    }
    else if(!mpDomain and mpVtkDomain)
    {
        unsigned num_points = mpVtkDomain->GetNumberOfPoints();
        mesher_input.pointlist = (double *) malloc(num_points * 2 * sizeof(double));
        mesher_input.numberofpoints = int(num_points);
        for (unsigned idx = 0; idx < num_points; idx++)
        {
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.pointlist[2 * idx + jdx] = mpVtkDomain->GetPoints()->GetPoint(idx)[jdx];
            }
        }

        unsigned num_segments = mpVtkDomain->GetNumberOfLines();
        mpVtkDomain->GetLines()->InitTraversal();
        mesher_input.segmentlist = (int *) malloc(num_segments * 2 * sizeof(int));
        mesher_input.numberofsegments = int(num_segments);
        vtkSmartPointer<vtkIdList> p_id_list = vtkSmartPointer<vtkIdList>::New();
        for (unsigned idx = 0; idx < num_segments; idx++)
        {
            mpVtkDomain->GetLines()->GetNextCell(p_id_list);
            mesher_input.segmentlist[2 * idx] = int(p_id_list->GetId(0));
            mesher_input.segmentlist[2 * idx + 1] = int(p_id_list->GetId(1));
        }
    }
    else if(mpDomain and mpVtkDomain)
    {
        unsigned num_points = mpVtkDomain->GetNumberOfPoints();
        std::vector<DimensionalChastePoint<SPACE_DIM> > vertex_locations = mpDomain->GetVertexLocations();
        unsigned num_vertices = vertex_locations.size();

        mesher_input.pointlist = (double *) malloc((num_points+num_vertices) * 2 * sizeof(double));
        mesher_input.numberofpoints = int(num_points+num_vertices);
        for (unsigned idx = 0; idx < num_points; idx++)
        {
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.pointlist[2 * idx + jdx] = mpVtkDomain->GetPoints()->GetPoint(idx)[jdx];
            }
        }
        for (unsigned idx = 0; idx < num_vertices; idx++)
        {
            c_vector<double, SPACE_DIM> vertex_location = vertex_locations[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.pointlist[2 * idx + jdx + 2*num_points] = vertex_location[jdx];
            }
        }

        unsigned num_segments = mpVtkDomain->GetNumberOfLines();
        std::vector<std::pair<unsigned, unsigned> > segments = mpDomain->GetSegmentIndices();
        unsigned num_part_segments = segments.size();
        mpVtkDomain->GetLines()->InitTraversal();

        mesher_input.segmentlist = (int *) malloc((num_segments+num_part_segments) * 2 * sizeof(int));
        mesher_input.numberofsegments = int(num_segments+num_part_segments);
        vtkSmartPointer<vtkIdList> p_id_list = vtkSmartPointer<vtkIdList>::New();
        for (unsigned idx = 0; idx < num_segments; idx++)
        {
            mpVtkDomain->GetLines()->GetNextCell(p_id_list);
            mesher_input.segmentlist[2 * idx] = int(p_id_list->GetId(0));
            mesher_input.segmentlist[2 * idx + 1] = int(p_id_list->GetId(1));
        }
        for (unsigned idx = 0; idx < num_part_segments; idx++)
        {
            mesher_input.segmentlist[2 * idx + 2 * num_segments] = int(segments[idx].first + num_points);
            mesher_input.segmentlist[2 * idx + 1 + 2*num_segments] = int(segments[idx].second + num_points);
        }

    }
    else
    {
        EXCEPTION("Either a part, vtk surface or both are required for 2d meshing");
    }

    if (mHoles.size() > 0)
    {
        mesher_input.holelist = (double *) malloc(mHoles.size() * 2 * sizeof(double));
        mesher_input.numberofholes = int(mHoles.size());
        for (unsigned idx = 0; idx < mHoles.size(); idx++)
        {
            c_vector<double, SPACE_DIM> hole_location = mHoles[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.holelist[2 * idx + jdx] = hole_location[jdx];
            }
        }
    }

    if (mRegions.size() > 0)
    {
        mesher_input.regionlist = (double *) malloc(mRegions.size() * 4 * sizeof(double));
        mesher_input.numberofregions = int(mRegions.size());
        for (unsigned idx = 0; idx < mRegions.size(); idx++)
        {
            c_vector<double, SPACE_DIM> region_location = mRegions[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 2; jdx++)
            {
                mesher_input.regionlist[4 * idx + jdx] = region_location[jdx];
            }
            mesher_input.regionlist[4 * idx + 2] = 1.0;
            mesher_input.regionlist[4 * idx + 3] = mMaxElementArea/units::pow<3>(mReferenceLength);
        }
    }

    std::string mesher_command = "pqQze";
    if (mMaxElementArea > 0.0*unit::metres*unit::metres*unit::metres)
    {
        double mesh_size = mMaxElementArea/units::pow<3>(mReferenceLength);
        mesher_command += "a" + boost::lexical_cast<std::string>(mesh_size);
    }
    if(mRegions.size()>0)
    {
        if(mRegions.size()>0)
        {
            mesher_command += "A";
        }
    }

    triangulate((char*) mesher_command.c_str(), &mesher_input, &mesher_output, NULL);

    mpMesh->ImportFromMesher(mesher_output, mesher_output.numberoftriangles, mesher_output.trianglelist,
                           mesher_output.numberofedges, mesher_output.edgelist, mesher_output.edgemarkerlist);

    mAttributes.clear();
    if(mRegions.size()>0)
    {
        unsigned num_elements = mesher_output.numberoftriangles;
        for(unsigned idx=0; idx< num_elements; idx++)
        {
            mAttributes.push_back(double(mesher_output.triangleattributelist[idx]));
        }
        mpMesh->SetAttributes(mAttributes);
    }

    //Tidy up triangle
    this->FreeTriangulateIo(mesher_input);
    this->FreeTriangulateIo(mesher_output);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::Mesh3d()
{
    std::vector<DimensionalChastePoint<SPACE_DIM> > vertex_locations = mpDomain->GetVertexLocations();
    std::vector<DimensionalChastePoint<SPACE_DIM> > hole_locations = mpDomain->GetHoleMarkers();
    unsigned num_vertices = vertex_locations.size();
    unsigned num_holes = hole_locations.size();
    std::vector<boost::shared_ptr<Facet<SPACE_DIM> > > facets = mpDomain->GetFacets();
    unsigned num_facets = facets.size();

    class tetgen::tetgenio mesher_input, mesher_output;

    tetgen::tetgenio::facet *f;
    tetgen::tetgenio::polygon *p;
    mesher_input.pointlist = new double[(num_vertices) * 3];
    mesher_input.numberofpoints = num_vertices;

    for (unsigned idx = 0; idx < num_vertices; idx++)
    {
        c_vector<double, SPACE_DIM> vertex_location = vertex_locations[idx].GetLocation(mReferenceLength);
        for (unsigned jdx = 0; jdx < 3; jdx++)
        {
            mesher_input.pointlist[3 * idx + jdx] = vertex_location[jdx];
        }
    }

    // Add the holes
    mesher_input.holelist = new double[(num_holes) * 3];
    mesher_input.numberofholes = num_holes;
    for (unsigned idx = 0; idx < num_holes; idx++)
    {
        c_vector<double, SPACE_DIM> hole_location = hole_locations[idx].GetLocation(mReferenceLength);
        for (unsigned jdx = 0; jdx < 3; jdx++)
        {
            mesher_input.holelist[3 * idx + jdx] = hole_location[jdx];
        }
    }

    mesher_input.numberoffacets = num_facets;
    mesher_input.facetlist = new tetgen::tetgenio::facet[num_facets];
    mesher_input.facetmarkerlist = new int[num_facets];
    for (unsigned idx = 0; idx < num_facets; idx++)
    {
        mesher_input.facetmarkerlist[idx] = 0;
        f = &mesher_input.facetlist[idx];
        std::vector<boost::shared_ptr<Polygon<SPACE_DIM> > > polygons = facets[idx]->GetPolygons();
        f->numberofpolygons = polygons.size();
        f->polygonlist = new tetgen::tetgenio::polygon[f->numberofpolygons];
        f->numberofholes = 0;
        f->holelist = NULL;
        for (unsigned jdx = 0; jdx < polygons.size(); jdx++)
        {
            p = &f->polygonlist[jdx];
            p->numberofvertices = polygons[jdx]->GetVertices().size();
            p->vertexlist = new int[p->numberofvertices];
            for (unsigned kdx = 0; kdx < polygons[jdx]->GetVertices().size(); kdx++)
            {
                p->vertexlist[kdx] = int(polygons[jdx]->GetVertices()[kdx]->GetIndex());
            }
        }
    }

    if(mHoles.size() > 0)
    {
        unsigned num_holes = mHoles.size();
        mesher_input.holelist = new double[(num_holes) * 3];
        mesher_input.numberofholes = num_holes;
        for (unsigned idx = 0; idx < num_holes; idx++)
        {
            c_vector<double, SPACE_DIM> hole_location = mHoles[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 3; jdx++)
            {
                mesher_input.holelist[3 * idx + jdx] = hole_location[jdx];
            }
        }
    }

    std::string mesher_command = "pqQz";
    if (mMaxElementArea > 0.0*unit::metres*unit::metres*unit::metres)
    {
        double mesh_size = mMaxElementArea/units::pow<3>(mReferenceLength);
        mesher_command += "a" + boost::lexical_cast<std::string>(mesh_size);
    }

    // Library call
    tetgen::tetrahedralize((char*) mesher_command.c_str(), &mesher_input, &mesher_output);
    mpMesh->ImportDiscreteContinuumMeshFromTetgen(mesher_output, mesher_output.numberoftetrahedra, mesher_output.tetrahedronlist,
                           mesher_output.numberoftrifaces, mesher_output.trifacelist, NULL);

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::MeshStl3d()
{
    class tetgen::tetgenio mesher_input, mesher_output;
    char * writable = new char[mStlFilePath.size() + 1];
    std::copy(mStlFilePath.begin(), mStlFilePath.end(), writable);
    writable[mStlFilePath.size()] = '\0';
    mesher_input.load_stl(writable);

    if(mHoles.size() > 0)
    {
        unsigned num_holes = mHoles.size();
        mesher_input.holelist = new double[(num_holes) * 3];
        mesher_input.numberofholes = num_holes;
        for (unsigned idx = 0; idx < num_holes; idx++)
        {
            c_vector<double, SPACE_DIM> hole_location = mHoles[idx].GetLocation(mReferenceLength);
            for (unsigned jdx = 0; jdx < 3; jdx++)
            {
                mesher_input.holelist[3 * idx + jdx] = hole_location[jdx];
            }
        }
    }

    std::string mesher_command = "pqQz";
    if (mMaxElementArea >  0.0*unit::metres*unit::metres*unit::metres)
    {
        double mesh_size = mMaxElementArea/units::pow<3>(mReferenceLength);
        mesher_command += "a" + boost::lexical_cast<std::string>(mesh_size);
    }

    // Library call
    tetgen::tetrahedralize((char*) mesher_command.c_str(), &mesher_input, &mesher_output);

    mpMesh->ImportDiscreteContinuumMeshFromTetgen(mesher_output, mesher_output.numberoftetrahedra, mesher_output.tetrahedronlist,
                           mesher_output.numberoftrifaces, mesher_output.trifacelist, NULL);

    delete[] writable;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::InitialiseTriangulateIo(triangulateio& mesherIo)
{
    mesherIo.numberofpoints = 0;
    mesherIo.pointlist = NULL;
    mesherIo.numberofpointattributes = 0;
    mesherIo.pointattributelist = (double *) NULL;
    mesherIo.pointmarkerlist = (int *) NULL;
    mesherIo.segmentlist = NULL;
    mesherIo.segmentmarkerlist = (int *) NULL;
    mesherIo.numberofsegments = 0;
    mesherIo.numberofholes = 0;
    mesherIo.numberofregions = 0;
    mesherIo.trianglelist = (int *) NULL;
    mesherIo.triangleattributelist = (double *) NULL;
    mesherIo.numberoftriangleattributes = 0;
    mesherIo.edgelist = (int *) NULL;
    mesherIo.edgemarkerlist = (int *) NULL;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>::FreeTriangulateIo(triangulateio& mesherIo)
{
    if (mesherIo.numberofpoints != 0)
    {
        mesherIo.numberofpoints = 0;
        free(mesherIo.pointlist);
    }

    if (mesherIo.numberofsegments != 0)
    {
        mesherIo.numberofsegments = 0;
        free(mesherIo.segmentlist);
    }

    // These (and the above) should actually be safe since we explicity set to NULL above
    free(mesherIo.pointattributelist);
    free(mesherIo.pointmarkerlist);
    free(mesherIo.segmentmarkerlist);
    free(mesherIo.trianglelist);
    free(mesherIo.triangleattributelist);
    free(mesherIo.edgelist);
    free(mesherIo.edgemarkerlist);
}

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