sampledTriSurfaceMesh.C

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/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
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     \\/     M anipulation  |
-------------------------------------------------------------------------------
    Copyright (C) 2011-2016 OpenFOAM Foundation
    Copyright (C) 2016-2018 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
    This file is part of OpenFOAM.
 
    OpenFOAM is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    OpenFOAM 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 General Public License
    for more details.
 
    You should have received a copy of the GNU General Public License
    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
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#include "sampledTriSurfaceMesh.H"
#include "meshSearch.H"
#include "Tuple2.H"
#include "globalIndex.H"
#include "treeDataCell.H"
#include "treeDataFace.H"
#include "meshTools.H"
 
#include "addToRunTimeSelectionTable.H"
 
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
const Foam::Enum
<
    Foam::sampledTriSurfaceMesh::samplingSource
>
Foam::sampledTriSurfaceMesh::samplingSourceNames_
({
    { samplingSource::cells, "cells" },
    { samplingSource::insideCells, "insideCells" },
    { samplingSource::boundaryFaces, "boundaryFaces" },
});
 
 
namespace Foam
{
    defineTypeNameAndDebug(sampledTriSurfaceMesh, 0);
    addToRunTimeSelectionTable
    (
        sampledSurface,
        sampledTriSurfaceMesh,
        word
    );
 
    //- Private class for finding nearest
    //  Comprising:
    //  - global index
    //  - sqr(distance)
    typedef Tuple2<scalar, label> nearInfo;
 
    class nearestEqOp
    {
    public:
 
        void operator()(nearInfo& x, const nearInfo& y) const
        {
            if (y.first() < x.first())
            {
                x = y;
            }
        }
    };
}
 
 
// * * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * //
 
void Foam::sampledTriSurfaceMesh::setZoneMap
(
    const surfZoneList& zoneLst,
    labelList& zoneIds
)
{
    label sz = 0;
    for (const surfZone& zn : zoneLst)
    {
        sz += zn.size();
    }
 
    zoneIds.setSize(sz);
    forAll(zoneLst, zonei)
    {
        const surfZone& zn = zoneLst[zonei];
 
        // Assign sub-zone Ids
        SubList<label>(zoneIds, zn.size(), zn.start()) = zonei;
    }
}
 
 
// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
const Foam::indexedOctree<Foam::treeDataFace>&
Foam::sampledTriSurfaceMesh::nonCoupledboundaryTree() const
{
    // Variant of meshSearch::boundaryTree() that only does non-coupled
    // boundary faces.
 
    if (!boundaryTreePtr_.valid())
    {
        // all non-coupled boundary faces (not just walls)
        const polyBoundaryMesh& patches = mesh().boundaryMesh();
 
        labelList bndFaces(patches.nFaces());
        label bndI = 0;
        for (const polyPatch& pp : patches)
        {
            if (!pp.coupled())
            {
                forAll(pp, i)
                {
                    bndFaces[bndI++] = pp.start()+i;
                }
            }
        }
        bndFaces.setSize(bndI);
 
 
        treeBoundBox overallBb(mesh().points());
        Random rndGen(123456);
        // Extend slightly and make 3D
        overallBb = overallBb.extend(rndGen, 1e-4);
        overallBb.min() -= point(ROOTVSMALL, ROOTVSMALL, ROOTVSMALL);
        overallBb.max() += point(ROOTVSMALL, ROOTVSMALL, ROOTVSMALL);
 
        boundaryTreePtr_.reset
        (
            new indexedOctree<treeDataFace>
            (
                treeDataFace    // all information needed to search faces
                (
                    false,                      // do not cache bb
                    mesh(),
                    bndFaces                    // boundary faces only
                ),
                overallBb,                      // overall search domain
                8,                              // maxLevel
                10,                             // leafsize
                3.0                             // duplicity
            )
        );
    }
 
    return *boundaryTreePtr_;
}
 
 
bool Foam::sampledTriSurfaceMesh::update(const meshSearch& meshSearcher)
{
    // Find the cells the triangles of the surface are in.
    // Does approximation by looking at the face centres only
    const pointField& fc = surface_.faceCentres();
 
    List<nearInfo> nearest(fc.size());
 
    // Global numbering for cells/faces - only used to uniquely identify local
    // elements
    globalIndex globalCells(onBoundary() ? mesh().nFaces() : mesh().nCells());
 
    for (nearInfo& near : nearest)
    {
        near.first()  = GREAT;
        near.second() = labelMax;
    }
 
    if (sampleSource_ == cells)
    {
        // Search for nearest cell
 
        const indexedOctree<treeDataCell>& cellTree = meshSearcher.cellTree();
 
        forAll(fc, triI)
        {
            pointIndexHit nearInfo = cellTree.findNearest
            (
                fc[triI],
                sqr(GREAT)
            );
            if (nearInfo.hit())
            {
                nearest[triI].first()  = magSqr(nearInfo.hitPoint()-fc[triI]);
                nearest[triI].second() = globalCells.toGlobal(nearInfo.index());
            }
        }
    }
    else if (sampleSource_ == insideCells)
    {
        // Search for cell containing point
 
        const indexedOctree<treeDataCell>& cellTree = meshSearcher.cellTree();
 
        forAll(fc, triI)
        {
            if (cellTree.bb().contains(fc[triI]))
            {
                const label index = cellTree.findInside(fc[triI]);
                if (index != -1)
                {
                    nearest[triI].first()  = 0.0;
                    nearest[triI].second() = globalCells.toGlobal(index);
                }
            }
        }
    }
    else
    {
        // Search for nearest boundaryFace
 
        //const indexedOctree<treeDataFace>& bTree = meshSearcher.boundaryTree()
        //- Search on all non-coupled boundary faces
        const indexedOctree<treeDataFace>& bTree = nonCoupledboundaryTree();
 
        forAll(fc, triI)
        {
            pointIndexHit nearInfo = bTree.findNearest
            (
                fc[triI],
                sqr(GREAT)
            );
            if (nearInfo.hit())
            {
                nearest[triI].first()  = magSqr(nearInfo.hitPoint()-fc[triI]);
                nearest[triI].second() = globalCells.toGlobal
                (
                    bTree.shapes().faceLabels()[nearInfo.index()]
                );
            }
        }
    }
 
 
    // See which processor has the nearest. Mark and subset
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
    Pstream::listCombineGather(nearest, nearestEqOp());
    Pstream::listCombineScatter(nearest);
 
    labelList cellOrFaceLabels(fc.size(), -1);
 
    label nFound = 0;
    forAll(nearest, triI)
    {
        if (nearest[triI].second() == labelMax)
        {
            // Not found on any processor. How to map?
        }
        else if (globalCells.isLocal(nearest[triI].second()))
        {
            cellOrFaceLabels[triI] = globalCells.toLocal
            (
                nearest[triI].second()
            );
            nFound++;
        }
    }
 
 
    if (debug)
    {
        Pout<< "Local out of faces:" << cellOrFaceLabels.size()
            << " keeping:" << nFound << endl;
    }
 
    // Now subset the surface. Do not use triSurface::subsetMesh since requires
    // original surface to be in compact numbering.
 
    const triSurface& s = surface_;
 
    // Compact to original triangle
    labelList faceMap(s.size());
    // Compact to original points
    labelList pointMap(s.points().size());
    // From original point to compact points
    labelList reversePointMap(s.points().size(), -1);
 
    // Handle region-wise sorting (makes things slightly more complicated)
    zoneIds_.setSize(s.size(), -1);
 
    // Better not to use triSurface::sortedZones here,
    // since we'll sort ourselves
 
    // Get zone/region sizes used, store under the original region Id
    Map<label> zoneSizes;
 
    // Recover region names from the input surface
    Map<word> zoneNames;
    {
        const geometricSurfacePatchList& patches = s.patches();
 
        forAll(patches, patchi)
        {
            zoneNames.set
            (
                patchi,
                (
                    patches[patchi].name().empty()
                  ? word::printf("patch%d", patchi)
                  : patches[patchi].name()
                )
            );
 
            zoneSizes.set(patchi, 0);
        }
    }
 
 
    {
        label newPointi = 0;
        label newFacei = 0;
 
        forAll(s, facei)
        {
            if (cellOrFaceLabels[facei] != -1)
            {
                const triSurface::FaceType& f = s[facei];
                const label regionid = f.region();
 
                auto fnd = zoneSizes.find(regionid);
                if (fnd.found())
                {
                    ++(*fnd);
                }
                else
                {
                    // This shouldn't happen
                    zoneSizes.insert(regionid, 1);
                    zoneNames.set(regionid, word::printf("patch%d", regionid));
                }
 
                // Store new faces compact
                faceMap[newFacei] = facei;
                zoneIds_[newFacei] = regionid;
                ++newFacei;
 
                // Renumber face points
                for (const label labi : f)
                {
                    if (reversePointMap[labi] == -1)
                    {
                        pointMap[newPointi] = labi;
                        reversePointMap[labi] = newPointi++;
                    }
                }
            }
        }
 
        // Trim
        faceMap.setSize(newFacei);
        zoneIds_.setSize(newFacei);
        pointMap.setSize(newPointi);
    }
 
 
    // Assign start/size (and name) to the newZones
    // re-use the lookup to map (zoneId => zoneI)
    surfZoneList zoneLst(zoneSizes.size());
    label start = 0;
    label zoneI = 0;
    forAllIters(zoneSizes, iter)
    {
        // No negative regionids, so Map<label> usually sorts properly
        const label regionid = iter.key();
 
        word name;
        auto fnd = zoneNames.cfind(regionid);
        if (fnd.found())
        {
            name = *fnd;
        }
        if (name.empty())
        {
            name = word::printf("patch%d", regionid);
        }
 
        zoneLst[zoneI] = surfZone
        (
            name,
            0,           // initialize with zero size
            start,
            zoneI
        );
 
        // Adjust start for the next zone and save (zoneId => zoneI) mapping
        start += iter();
        iter() = zoneI++;
    }
 
 
    // At this stage:
    // - faceMap to map the (unsorted) compact to original triangle
    // - zoneIds for the next sorting
    // - zoneSizes contains region -> count information
 
    // Rebuild the faceMap for the sorted order
    labelList sortedFaceMap(faceMap.size());
 
    forAll(zoneIds_, facei)
    {
        const label zonei = zoneIds_[facei];
        label sortedFacei = zoneLst[zonei].start() + zoneLst[zonei].size()++;
        sortedFaceMap[sortedFacei] = faceMap[facei];
    }
 
    // zoneIds are now simply flat values
    setZoneMap(zoneLst, zoneIds_);
 
    // Replace the faceMap with the properly sorted face map
    faceMap.transfer(sortedFaceMap);
 
    if (keepIds_)
    {
        originalIds_ = faceMap;
    }
 
    // Subset cellOrFaceLabels (for compact faces)
    cellOrFaceLabels = labelUIndList(cellOrFaceLabels, faceMap)();
 
    // Store any face per point (without using pointFaces())
    labelList pointToFace(pointMap.size());
 
    // Create faces and points for subsetted surface
    faceList& surfFaces = this->storedFaces();
    surfFaces.setSize(faceMap.size());
 
    this->storedZones().transfer(zoneLst);
 
    forAll(faceMap, facei)
    {
        const labelledTri& origF = s[faceMap[facei]];
        face& f = surfFaces[facei];
 
        f = triFace
        (
            reversePointMap[origF[0]],
            reversePointMap[origF[1]],
            reversePointMap[origF[2]]
        );
 
        for (const label labi : f)
        {
            pointToFace[labi] = facei;
        }
    }
 
    this->storedPoints() = pointField(s.points(), pointMap);
 
    if (debug)
    {
        print(Pout);
        Pout<< endl;
    }
 
 
 
    // Collect the samplePoints and sampleElements
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
    if (sampledSurface::interpolate())
    {
        samplePoints_.setSize(pointMap.size());
        sampleElements_.setSize(pointMap.size(), -1);
 
        if (sampleSource_ == cells)
        {
            // samplePoints_   : per surface point a location inside the cell
            // sampleElements_ : per surface point the cell
 
            forAll(points(), pointi)
            {
                const point& pt = points()[pointi];
                label celli = cellOrFaceLabels[pointToFace[pointi]];
                sampleElements_[pointi] = celli;
 
                // Check if point inside cell
                if
                (
                    mesh().pointInCell
                    (
                        pt,
                        sampleElements_[pointi],
                        meshSearcher.decompMode()
                    )
                )
                {
                    samplePoints_[pointi] = pt;
                }
                else
                {
                    // Find nearest point on faces of cell
                    const cell& cFaces = mesh().cells()[celli];
 
                    scalar minDistSqr = VGREAT;
 
                    forAll(cFaces, i)
                    {
                        const face& f = mesh().faces()[cFaces[i]];
                        pointHit info = f.nearestPoint(pt, mesh().points());
                        if (info.distance() < minDistSqr)
                        {
                            minDistSqr = info.distance();
                            samplePoints_[pointi] = info.rawPoint();
                        }
                    }
                }
            }
        }
        else if (sampleSource_ == insideCells)
        {
            // samplePoints_   : per surface point a location inside the cell
            // sampleElements_ : per surface point the cell
 
            forAll(points(), pointi)
            {
                const point& pt = points()[pointi];
                label celli = cellOrFaceLabels[pointToFace[pointi]];
                sampleElements_[pointi] = celli;
                samplePoints_[pointi] = pt;
            }
        }
        else
        {
            // samplePoints_   : per surface point a location on the boundary
            // sampleElements_ : per surface point the boundary face containing
            //                   the location
 
            forAll(points(), pointi)
            {
                const point& pt = points()[pointi];
                label facei = cellOrFaceLabels[pointToFace[pointi]];
                sampleElements_[pointi] = facei;
                samplePoints_[pointi] = mesh().faces()[facei].nearestPoint
                (
                    pt,
                    mesh().points()
                ).rawPoint();
            }
        }
    }
    else
    {
        // if sampleSource_ == cells:
        //      sampleElements_ : per surface triangle the cell
        //      samplePoints_   : n/a
        // if sampleSource_ == insideCells:
        //      sampleElements_ : -1 or per surface triangle the cell
        //      samplePoints_   : n/a
        // else:
        //      sampleElements_ : per surface triangle the boundary face
        //      samplePoints_   : n/a
        sampleElements_.transfer(cellOrFaceLabels);
        samplePoints_.clear();
    }
 
 
    if (debug)
    {
        this->clearOut();
        OFstream str(mesh().time().path()/"surfaceToMesh.obj");
        Info<< "Dumping correspondence from local surface (points or faces)"
            << " to mesh (cells or faces) to " << str.name() << endl;
 
        const vectorField& centres =
        (
            onBoundary()
          ? mesh().faceCentres()
          : mesh().cellCentres()
        );
 
        if (sampledSurface::interpolate())
        {
            label vertI = 0;
            forAll(samplePoints_, pointi)
            {
                meshTools::writeOBJ(str, points()[pointi]);
                vertI++;
 
                meshTools::writeOBJ(str, samplePoints_[pointi]);
                vertI++;
 
                label elemi = sampleElements_[pointi];
                meshTools::writeOBJ(str, centres[elemi]);
                vertI++;
                str << "l " << vertI-2 << ' ' << vertI-1 << ' ' << vertI << nl;
            }
        }
        else
        {
            label vertI = 0;
            forAll(sampleElements_, triI)
            {
                meshTools::writeOBJ(str, faceCentres()[triI]);
                vertI++;
 
                label elemi = sampleElements_[triI];
                meshTools::writeOBJ(str, centres[elemi]);
                vertI++;
                str << "l " << vertI-1 << ' ' << vertI << nl;
            }
        }
    }
 
    needsUpdate_ = false;
    return true;
}
 
 
// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
Foam::sampledTriSurfaceMesh::sampledTriSurfaceMesh
(
    const word& name,
    const polyMesh& mesh,
    const word& surfaceName,
    const samplingSource sampleSource
)
:
    sampledSurface(name, mesh),
    MeshStorage(),
    surface_
    (
        IOobject
        (
            surfaceName,
            mesh.time().constant(), // instance
            "triSurface",           // local
            mesh.time(),            // registry
            IOobject::MUST_READ,
            IOobject::NO_WRITE,
            false
        )
    ),
    sampleSource_(sampleSource),
    needsUpdate_(true),
    keepIds_(false),
    originalIds_(),
    zoneIds_(),
    sampleElements_(),
    samplePoints_()
{}
 
 
Foam::sampledTriSurfaceMesh::sampledTriSurfaceMesh
(
    const word& name,
    const polyMesh& mesh,
    const dictionary& dict
)
:
    sampledSurface(name, mesh, dict),
    MeshStorage(),
    surface_
    (
        IOobject
        (
            dict.get<word>("surface"),
            mesh.time().constant(), // instance
            "triSurface",           // local
            mesh.time(),            // registry
            IOobject::MUST_READ,
            IOobject::NO_WRITE,
            false
        ),
        dict
    ),
    sampleSource_(samplingSourceNames_.get("source", dict)),
    needsUpdate_(true),
    keepIds_(dict.lookupOrDefault("keepIds", false)),
    originalIds_(),
    zoneIds_(),
    sampleElements_(),
    samplePoints_()
{}
 
 
Foam::sampledTriSurfaceMesh::sampledTriSurfaceMesh
(
    const word& name,
    const polyMesh& mesh,
    const triSurface& surface,
    const word& sampleSourceName
)
:
    sampledSurface(name, mesh),
    MeshStorage(),
    surface_
    (
        IOobject
        (
            name,
            mesh.time().constant(), // instance
            "triSurface",           // local
            mesh.time(),            // registry
            IOobject::NO_READ,
            IOobject::NO_WRITE,
            false
        ),
        surface
    ),
    sampleSource_(samplingSourceNames_[sampleSourceName]),
    needsUpdate_(true),
    keepIds_(false),
    originalIds_(),
    zoneIds_(),
    sampleElements_(),
    samplePoints_()
{}
 
 
// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
Foam::sampledTriSurfaceMesh::~sampledTriSurfaceMesh()
{}
 
 
// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
bool Foam::sampledTriSurfaceMesh::needsUpdate() const
{
    return needsUpdate_;
}
 
 
bool Foam::sampledTriSurfaceMesh::expire()
{
    // already marked as expired
    if (needsUpdate_)
    {
        return false;
    }
 
    sampledSurface::clearGeom();
    MeshStorage::clear();
    zoneIds_.clear();
 
    originalIds_.clear();
    boundaryTreePtr_.clear();
    sampleElements_.clear();
    samplePoints_.clear();
 
    needsUpdate_ = true;
    return true;
}
 
 
bool Foam::sampledTriSurfaceMesh::update()
{
    if (!needsUpdate_)
    {
        return false;
    }
 
    // Calculate surface and mesh overlap bounding box
    treeBoundBox bb
    (
        surface_.triSurface::points(),
        surface_.triSurface::meshPoints()
    );
 
    // Check for overlap with (global!) mesh bb
    const bool intersect = bb.intersect(mesh().bounds());
 
    if (!intersect)
    {
        // Surface and mesh do not overlap at all. Guarantee a valid
        // bounding box so we don't get any 'invalid bounding box' errors.
 
        WarningInFunction
            << "Surface " << surface_.searchableSurface::name()
            << " does not overlap bounding box of mesh " << mesh().bounds()
            << endl;
 
        bb = treeBoundBox(mesh().bounds());
        const vector span(bb.span());
 
        bb.min() += (0.5-1e-6)*span;
        bb.max() -= (0.5-1e-6)*span;
    }
    else
    {
        // Extend a bit
        const vector span(bb.span());
        bb.min() -= 0.5*span;
        bb.max() += 0.5*span;
 
        bb.inflate(1e-6);
    }
 
    // Mesh search engine, no triangulation of faces.
    meshSearch meshSearcher(mesh(), bb, polyMesh::FACE_PLANES);
 
    return update(meshSearcher);
}
 
 
bool Foam::sampledTriSurfaceMesh::update(const treeBoundBox& bb)
{
    if (!needsUpdate_)
    {
        return false;
    }
 
    // Mesh search engine on subset, no triangulation of faces.
    meshSearch meshSearcher(mesh(), bb, polyMesh::FACE_PLANES);
 
    return update(meshSearcher);
}
 
 
Foam::tmp<Foam::scalarField> Foam::sampledTriSurfaceMesh::sample
(
    const interpolation<scalar>& sampler
) const
{
    return sampleOnFaces(sampler);
}
 
 
Foam::tmp<Foam::vectorField> Foam::sampledTriSurfaceMesh::sample
(
    const interpolation<vector>& sampler
) const
{
    return sampleOnFaces(sampler);
}
 
 
Foam::tmp<Foam::sphericalTensorField> Foam::sampledTriSurfaceMesh::sample
(
    const interpolation<sphericalTensor>& sampler
) const
{
    return sampleOnFaces(sampler);
}
 
 
Foam::tmp<Foam::symmTensorField> Foam::sampledTriSurfaceMesh::sample
(
    const interpolation<symmTensor>& sampler
) const
{
    return sampleOnFaces(sampler);
}
 
 
Foam::tmp<Foam::tensorField> Foam::sampledTriSurfaceMesh::sample
(
    const interpolation<tensor>& sampler
) const
{
    return sampleOnFaces(sampler);
}
 
 
Foam::tmp<Foam::scalarField> Foam::sampledTriSurfaceMesh::interpolate
(
    const interpolation<scalar>& interpolator
) const
{
    return sampleOnPoints(interpolator);
}
 
 
Foam::tmp<Foam::vectorField> Foam::sampledTriSurfaceMesh::interpolate
(
    const interpolation<vector>& interpolator
) const
{
    return sampleOnPoints(interpolator);
}
 
Foam::tmp<Foam::sphericalTensorField> Foam::sampledTriSurfaceMesh::interpolate
(
    const interpolation<sphericalTensor>& interpolator
) const
{
    return sampleOnPoints(interpolator);
}
 
 
Foam::tmp<Foam::symmTensorField> Foam::sampledTriSurfaceMesh::interpolate
(
    const interpolation<symmTensor>& interpolator
) const
{
    return sampleOnPoints(interpolator);
}
 
 
Foam::tmp<Foam::tensorField> Foam::sampledTriSurfaceMesh::interpolate
(
    const interpolation<tensor>& interpolator
) const
{
    return sampleOnPoints(interpolator);
}
 
 
void Foam::sampledTriSurfaceMesh::print(Ostream& os) const
{
    os  << "sampledTriSurfaceMesh: " << name() << " :"
        << " surface:" << surface_.objectRegistry::name()
        << " faces:"   << faces().size()
        << " points:"  << points().size()
        << " zoneids:" << zoneIds().size();
}
 
 
// ************************************************************************* //