primitiveMeshCheck.C

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | www.openfoam.com
     \\/     M anipulation  |
-------------------------------------------------------------------------------
    Copyright (C) 2011-2016 OpenFOAM Foundation
    Copyright (C) 2019-2020 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/>.

\*---------------------------------------------------------------------------*/

#include "primitiveMesh.H"
#include "pyramidPointFaceRef.H"
#include "ListOps.H"
#include "unitConversion.H"
#include "SortableList.H"
#include "edgeHashes.H"
#include "primitiveMeshTools.H"

// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //

Foam::scalar Foam::primitiveMesh::closedThreshold_  = 1.0e-6;
Foam::scalar Foam::primitiveMesh::aspectThreshold_  = 1000;
Foam::scalar Foam::primitiveMesh::nonOrthThreshold_ = 70;    // deg
Foam::scalar Foam::primitiveMesh::skewThreshold_    = 4;
Foam::scalar Foam::primitiveMesh::planarCosAngle_   = 1.0e-6;


// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //

bool Foam::primitiveMesh::checkClosedBoundary
(
    const vectorField& areas,
    const bool report,
    const bitSet& internalOrCoupledFaces
) const
{
    DebugInFunction << "Checking if boundary is closed" << endl;

    // Loop through all boundary faces and sum up the face area vectors.
    // For a closed boundary, this should be zero in all vector components

    Vector<solveScalar> sumClosed(Zero);
    solveScalar sumMagClosedBoundary = 0;

    for (label facei = nInternalFaces(); facei < areas.size(); facei++)
    {
        if (!internalOrCoupledFaces.size() || !internalOrCoupledFaces[facei])
        {
            sumClosed += Vector<solveScalar>(areas[facei]);
            sumMagClosedBoundary += mag(areas[facei]);
        }
    }

    reduce(sumClosed, sumOp<Vector<solveScalar>>());
    reduce(sumMagClosedBoundary, sumOp<solveScalar>());

    Vector<solveScalar> openness = sumClosed/(sumMagClosedBoundary + VSMALL);

    if (cmptMax(cmptMag(openness)) > closedThreshold_)
    {
        if (debug || report)
        {
            Info<< " ***Boundary openness " << openness
                << " possible hole in boundary description."
                << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Boundary openness " << openness << " OK."
            << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkClosedCells
(
    const vectorField& faceAreas,
    const scalarField& cellVolumes,
    const bool report,
    labelHashSet* setPtr,
    labelHashSet* aspectSetPtr,
    const Vector<label>& meshD
) const
{
    DebugInFunction << "Checking if cells are closed" << endl;

    // Check that all cells labels are valid
    const cellList& c = cells();

    label nErrorClosed = 0;

    forAll(c, cI)
    {
        const cell& curCell = c[cI];

        if (min(curCell) < 0 || max(curCell) > nFaces())
        {
            if (setPtr)
            {
                setPtr->insert(cI);
            }

            nErrorClosed++;
        }
    }

    if (nErrorClosed > 0)
    {
        if (debug || report)
        {
            Info<< " ***Cells with invalid face labels found, number of cells "
                << nErrorClosed << endl;
        }

        return true;
    }


    scalarField openness;
    scalarField aspectRatio;
    primitiveMeshTools::cellClosedness
    (
        *this,
        meshD,
        faceAreas,
        cellVolumes,
        openness,
        aspectRatio
    );

    label nOpen = 0;
    scalar maxOpennessCell = max(openness);
    label nAspect = 0;
    scalar maxAspectRatio = max(aspectRatio);

    // Check the sums
    forAll(openness, celli)
    {
        if (openness[celli] > closedThreshold_)
        {
            if (setPtr)
            {
                setPtr->insert(celli);
            }

            nOpen++;
        }

        if (aspectRatio[celli] > aspectThreshold_)
        {
            if (aspectSetPtr)
            {
                aspectSetPtr->insert(celli);
            }

            nAspect++;
        }
    }

    reduce(nOpen, sumOp<label>());
    reduce(maxOpennessCell, maxOp<scalar>());

    reduce(nAspect, sumOp<label>());
    reduce(maxAspectRatio, maxOp<scalar>());


    if (nOpen > 0)
    {
        if (debug || report)
        {
            Info<< " ***Open cells found, max cell openness: "
                << maxOpennessCell << ", number of open cells " << nOpen
                << endl;
        }

        return true;
    }

    if (nAspect > 0)
    {
        if (debug || report)
        {
            Info<< " ***High aspect ratio cells found, Max aspect ratio: "
                << maxAspectRatio
                << ", number of cells " << nAspect
                << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Max cell openness = " << maxOpennessCell << " OK." << nl
            << "    Max aspect ratio = " << maxAspectRatio << " OK."
            << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFaceAreas
(
    const vectorField& faceAreas,
    const bool report,
    const bool detailedReport,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face area magnitudes" << endl;

    const scalarField magFaceAreas(mag(faceAreas));

    scalar minArea = GREAT;
    scalar maxArea = -GREAT;

    forAll(magFaceAreas, facei)
    {
        if (magFaceAreas[facei] < VSMALL)
        {
            if (setPtr)
            {
                setPtr->insert(facei);
            }
            if (detailedReport)
            {
                if (isInternalFace(facei))
                {
                    Pout<< "Zero or negative face area detected for "
                        << "internal face "<< facei << " between cells "
                        << faceOwner()[facei] << " and "
                        << faceNeighbour()[facei]
                        << ".  Face area magnitude = " << magFaceAreas[facei]
                        << endl;
                }
                else
                {
                    Pout<< "Zero or negative face area detected for "
                        << "boundary face " << facei << " next to cell "
                        << faceOwner()[facei] << ".  Face area magnitude = "
                        << magFaceAreas[facei] << endl;
                }
            }
        }

        minArea = min(minArea, magFaceAreas[facei]);
        maxArea = max(maxArea, magFaceAreas[facei]);
    }

    reduce(minArea, minOp<scalar>());
    reduce(maxArea, maxOp<scalar>());

    if (minArea < VSMALL)
    {
        if (debug || report)
        {
            Info<< " ***Zero or negative face area detected.  "
                "Minimum area: " << minArea << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Minimum face area = " << minArea
            << ". Maximum face area = " << maxArea
            << ".  Face area magnitudes OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkCellVolumes
(
    const scalarField& vols,
    const bool report,
    const bool detailedReport,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking cell volumes" << endl;

    scalar minVolume = GREAT;
    scalar maxVolume = -GREAT;

    label nNegVolCells = 0;

    forAll(vols, celli)
    {
        if (vols[celli] < VSMALL)
        {
            if (setPtr)
            {
                setPtr->insert(celli);
            }
            if (detailedReport)
            {
                Pout<< "Zero or negative cell volume detected for cell "
                    << celli << ".  Volume = " << vols[celli] << endl;
            }

            nNegVolCells++;
        }

        minVolume = min(minVolume, vols[celli]);
        maxVolume = max(maxVolume, vols[celli]);
    }

    reduce(minVolume, minOp<scalar>());
    reduce(maxVolume, maxOp<scalar>());
    reduce(nNegVolCells, sumOp<label>());

    if (minVolume < VSMALL)
    {
        if (debug || report)
        {
            Info<< " ***Zero or negative cell volume detected.  "
                << "Minimum negative volume: " << minVolume
                << ", Number of negative volume cells: " << nNegVolCells
                << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Min volume = " << minVolume
            << ". Max volume = " << maxVolume
            << ".  Total volume = " << gSum(vols)
            << ".  Cell volumes OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFaceOrthogonality
(
    const vectorField& fAreas,
    const vectorField& cellCtrs,
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking mesh non-orthogonality" << endl;

    tmp<scalarField> tortho = primitiveMeshTools::faceOrthogonality
    (
        *this,
        fAreas,
        cellCtrs
    );
    const scalarField& ortho = tortho();

    // Severe nonorthogonality threshold
    const scalar severeNonorthogonalityThreshold =
        ::cos(degToRad(nonOrthThreshold_));

    scalar minDDotS = min(ortho);

    scalar sumDDotS = sum(ortho);

    label severeNonOrth = 0;

    label errorNonOrth = 0;


    forAll(ortho, facei)
    {
        if (ortho[facei] < severeNonorthogonalityThreshold)
        {
            if (ortho[facei] > SMALL)
            {
                if (setPtr)
                {
                    setPtr->insert(facei);
                }

                severeNonOrth++;
            }
            else
            {
                if (setPtr)
                {
                    setPtr->insert(facei);
                }

                errorNonOrth++;
            }
        }
    }

    reduce(minDDotS, minOp<scalar>());
    reduce(sumDDotS, sumOp<scalar>());
    reduce(severeNonOrth, sumOp<label>());
    reduce(errorNonOrth, sumOp<label>());

    if (debug || report)
    {
        label neiSize = ortho.size();
        reduce(neiSize, sumOp<label>());

        if (neiSize > 0)
        {
            if (debug || report)
            {
                Info<< "    Mesh non-orthogonality Max: "
                    << radToDeg(::acos(minDDotS))
                    << " average: " << radToDeg(::acos(sumDDotS/neiSize))
                    << endl;
            }
        }

        if (severeNonOrth > 0)
        {
            Info<< "   *Number of severely non-orthogonal faces: "
                << severeNonOrth << "." << endl;
        }
    }

    if (errorNonOrth > 0)
    {
        if (debug || report)
        {
            Info<< " ***Number of non-orthogonality errors: "
                << errorNonOrth << "." << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Non-orthogonality check OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFacePyramids
(
    const pointField& points,
    const vectorField& ctrs,
    const bool report,
    const bool detailedReport,
    const scalar minPyrVol,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face orientation" << endl;

    const labelList& own = faceOwner();
    const labelList& nei = faceNeighbour();
    const faceList& f = faces();


    scalarField ownPyrVol;
    scalarField neiPyrVol;
    primitiveMeshTools::facePyramidVolume
    (
        *this,
        points,
        ctrs,
        ownPyrVol,
        neiPyrVol
    );


    label nErrorPyrs = 0;

    forAll(ownPyrVol, facei)
    {
        if (ownPyrVol[facei] < minPyrVol)
        {
            if (setPtr)
            {
                setPtr->insert(facei);
            }
            if (detailedReport)
            {
                Pout<< "Negative pyramid volume: " << ownPyrVol[facei]
                    << " for face " << facei << " " << f[facei]
                    << "  and owner cell: " << own[facei] << endl
                    << "Owner cell vertex labels: "
                    << cells()[own[facei]].labels(faces())
                    << endl;
            }

            nErrorPyrs++;
        }

        if (isInternalFace(facei))
        {
            if (neiPyrVol[facei] < minPyrVol)
            {
                if (setPtr)
                {
                    setPtr->insert(facei);
                }
                if (detailedReport)
                {
                    Pout<< "Negative pyramid volume: " << neiPyrVol[facei]
                        << " for face " << facei << " " << f[facei]
                        << "  and neighbour cell: " << nei[facei] << nl
                        << "Neighbour cell vertex labels: "
                        << cells()[nei[facei]].labels(faces())
                        << endl;
                }
                nErrorPyrs++;
            }
        }
    }

    reduce(nErrorPyrs, sumOp<label>());

    if (nErrorPyrs > 0)
    {
        if (debug || report)
        {
            Info<< " ***Error in face pyramids: "
                << nErrorPyrs << " faces are incorrectly oriented."
                << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Face pyramids OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFaceSkewness
(
    const pointField& points,
    const vectorField& fCtrs,
    const vectorField& fAreas,
    const vectorField& cellCtrs,
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face skewness" << endl;

    // Warn if the skew correction vector is more than skewWarning times
    // larger than the face area vector

    tmp<scalarField> tskewness = primitiveMeshTools::faceSkewness
    (
        *this,
        points,
        fCtrs,
        fAreas,
        cellCtrs
    );
    const scalarField& skewness = tskewness();

    scalar maxSkew = max(skewness);
    label nWarnSkew = 0;

    forAll(skewness, facei)
    {
        // Check if the skewness vector is greater than the PN vector.
        // This does not cause trouble but is a good indication of a poor mesh.
        if (skewness[facei] > skewThreshold_)
        {
            if (setPtr)
            {
                setPtr->insert(facei);
            }

            nWarnSkew++;
        }
    }

    reduce(maxSkew, maxOp<scalar>());
    reduce(nWarnSkew, sumOp<label>());

    if (nWarnSkew > 0)
    {
        if (debug || report)
        {
            Info<< " ***Max skewness = " << maxSkew
                << ", " << nWarnSkew << " highly skew faces detected"
                   " which may impair the quality of the results"
                << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Max skewness = " << maxSkew << " OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFaceAngles
(
    const pointField& points,
    const vectorField& faceAreas,
    const bool report,
    const scalar maxDeg,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face angles" << endl;

    if (maxDeg < -SMALL || maxDeg > 180+SMALL)
    {
        FatalErrorInFunction
            << "maxDeg should be [0..180] but is now " << maxDeg
            << exit(FatalError);
    }

    const scalar maxSin = Foam::sin(degToRad(maxDeg));


    tmp<scalarField> tfaceAngles = primitiveMeshTools::faceConcavity
    (
        maxSin,
        *this,
        points,
        faceAreas
    );
    const scalarField& faceAngles = tfaceAngles();

    scalar maxEdgeSin = max(faceAngles);

    label nConcave = 0;

    forAll(faceAngles, facei)
    {
        if (faceAngles[facei] > SMALL)
        {
            nConcave++;

            if (setPtr)
            {
                setPtr->insert(facei);
            }
        }
    }

    reduce(nConcave, sumOp<label>());
    reduce(maxEdgeSin, maxOp<scalar>());

    if (nConcave > 0)
    {
        scalar maxConcaveDegr =
            radToDeg(Foam::asin(Foam::min(1.0, maxEdgeSin)));

        if (debug || report)
        {
            Info<< "   *There are " << nConcave
                << " faces with concave angles between consecutive"
                << " edges. Max concave angle = " << maxConcaveDegr
                << " degrees." << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    All angles in faces OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkFaceFlatness
(
    const pointField& points,
    const vectorField& faceCentres,
    const vectorField& faceAreas,
    const bool report,
    const scalar warnFlatness,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face flatness" << endl;

    if (warnFlatness < 0 || warnFlatness > 1)
    {
        FatalErrorInFunction
            << "warnFlatness should be [0..1] but is " << warnFlatness
            << exit(FatalError);
    }

    const faceList& fcs = faces();

    tmp<scalarField> tfaceFlatness = primitiveMeshTools::faceFlatness
    (
        *this,
        points,
        faceCentres,
        faceAreas
    );
    const scalarField& faceFlatness = tfaceFlatness();

    scalarField magAreas(mag(faceAreas));

    scalar minFlatness = GREAT;
    scalar sumFlatness = 0;
    label nSummed = 0;
    label nWarped = 0;

    forAll(faceFlatness, facei)
    {
        if (fcs[facei].size() > 3 && magAreas[facei] > VSMALL)
        {
            sumFlatness += faceFlatness[facei];
            nSummed++;

            minFlatness = min(minFlatness, faceFlatness[facei]);

            if (faceFlatness[facei] < warnFlatness)
            {
                nWarped++;

                if (setPtr)
                {
                    setPtr->insert(facei);
                }
            }
        }
    }


    reduce(nWarped, sumOp<label>());
    reduce(minFlatness, minOp<scalar>());

    reduce(nSummed, sumOp<label>());
    reduce(sumFlatness, sumOp<scalar>());

    if (debug || report)
    {
        if (nSummed > 0)
        {
            Info<< "    Face flatness (1 = flat, 0 = butterfly) : min = "
                << minFlatness << "  average = " << sumFlatness / nSummed
                << endl;
        }
    }


    if (nWarped > 0)
    {
        if (debug || report)
        {
            Info<< "   *There are " << nWarped
                << " faces with ratio between projected and actual area < "
                << warnFlatness << endl;

            Info<< "    Minimum ratio (minimum flatness, maximum warpage) = "
                << minFlatness << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    All face flatness OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkConcaveCells
(
    const vectorField& fAreas,
    const pointField& fCentres,
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking for concave cells" << endl;

    const cellList& c = cells();
    const labelList& fOwner = faceOwner();

    label nConcaveCells = 0;

    forAll(c, celli)
    {
        const cell& cFaces = c[celli];

        bool concave = false;

        forAll(cFaces, i)
        {
            if (concave)
            {
                break;
            }

            label fI = cFaces[i];

            const point& fC = fCentres[fI];

            vector fN = fAreas[fI];

            fN /= max(mag(fN), VSMALL);

            // Flip normal if required so that it is always pointing out of
            // the cell
            if (fOwner[fI] != celli)
            {
                fN *= -1;
            }

            // Is the centre of any other face of the cell on the
            // wrong side of the plane of this face?

            forAll(cFaces, j)
            {
                if (j != i)
                {
                    label fJ = cFaces[j];

                    const point& pt = fCentres[fJ];

                    // If the cell is concave, the point will be on the
                    // positive normal side of the plane of f, defined by
                    // its centre and normal, and the angle between (pt -
                    // fC) and fN will be less than 90 degrees, so the dot
                    // product will be positive.

                    vector pC = (pt - fC);

                    pC /= max(mag(pC), VSMALL);

                    if ((pC & fN) > -planarCosAngle_)
                    {
                        // Concave or planar face

                        concave = true;

                        if (setPtr)
                        {
                            setPtr->insert(celli);
                        }

                        nConcaveCells++;

                        break;
                    }
                }
            }
        }
    }

    reduce(nConcaveCells, sumOp<label>());

    if (nConcaveCells > 0)
    {
        if (debug || report)
        {
            Info<< " ***Concave cells (using face planes) found,"
                << " number of cells: " << nConcaveCells << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Concave cell check OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkUpperTriangular
(
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face ordering" << endl;

    // Check whether internal faces are ordered in the upper triangular order
    const labelList& own = faceOwner();
    const labelList& nei = faceNeighbour();

    const cellList& c = cells();

    label internal = nInternalFaces();

    // Has error occurred?
    bool error = false;
    // Have multiple faces been detected?
    label nMultipleCells = false;

    // Loop through faceCells once more and make sure that for internal cell
    // the first label is smaller
    for (label facei = 0; facei < internal; facei++)
    {
        if (own[facei] >= nei[facei])
        {
            error  = true;

            if (setPtr)
            {
                setPtr->insert(facei);
            }
        }
    }

    // Loop through all cells. For each cell, find the face that is internal
    // and add it to the check list (upper triangular order).
    // Once the list is completed, check it against the faceCell list

    forAll(c, celli)
    {
        const labelList& curFaces = c[celli];

        // Neighbouring cells
        SortableList<label> nbr(curFaces.size());

        forAll(curFaces, i)
        {
            label facei = curFaces[i];

            if (facei >= nInternalFaces())
            {
                // Sort last
                nbr[i] = labelMax;
            }
            else
            {
                label nbrCelli = nei[facei];

                if (nbrCelli == celli)
                {
                    nbrCelli = own[facei];
                }

                if (celli < nbrCelli)
                {
                    // celli is master
                    nbr[i] = nbrCelli;
                }
                else
                {
                    // nbrCell is master. Let it handle this face.
                    nbr[i] = labelMax;
                }
            }
        }

        nbr.sort();

        // Now nbr holds the cellCells in incremental order. Check:
        // - neighbouring cells appear only once. Since nbr is sorted this
        //   is simple check on consecutive elements
        // - faces indexed in same order as nbr are incrementing as well.

        label prevCell = nbr[0];
        label prevFace = curFaces[nbr.indices()[0]];

        bool hasMultipleFaces = false;

        for (label i = 1; i < nbr.size(); i++)
        {
            label thisCell = nbr[i];
            label thisFace = curFaces[nbr.indices()[i]];

            if (thisCell == labelMax)
            {
                break;
            }

            if (thisCell == prevCell)
            {
                hasMultipleFaces = true;

                if (setPtr)
                {
                    setPtr->insert(prevFace);
                    setPtr->insert(thisFace);
                }
            }
            else if (thisFace < prevFace)
            {
                error = true;

                if (setPtr)
                {
                    setPtr->insert(thisFace);
                }
            }

            prevCell = thisCell;
            prevFace = thisFace;
        }

        if (hasMultipleFaces)
        {
            nMultipleCells++;
        }
    }

    reduce(error, orOp<bool>());
    reduce(nMultipleCells, sumOp<label>());

    if ((debug || report) && nMultipleCells > 0)
    {
        Info<< "  <<Found " << nMultipleCells
            << " neighbouring cells with multiple inbetween faces." << endl;
    }

    if (error)
    {
        if (debug || report)
        {
            Info<< " ***Faces not in upper triangular order." << endl;
        }

        return true;
    }

    if (debug || report)
    {
        Info<< "    Upper triangular ordering OK." << endl;
    }

    return false;
}


bool Foam::primitiveMesh::checkCellsZipUp
(
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking topological cell openness" << endl;

    label nOpenCells = 0;

    const faceList& f = faces();
    const cellList& c = cells();

    forAll(c, celli)
    {
        const labelList& curFaces = c[celli];

        const edgeList cellEdges = c[celli].edges(f);

        labelList edgeUsage(cellEdges.size(), Zero);

        forAll(curFaces, facei)
        {
            edgeList curFaceEdges = f[curFaces[facei]].edges();

            forAll(curFaceEdges, faceEdgeI)
            {
                const edge& curEdge = curFaceEdges[faceEdgeI];