primitiveMeshCheck.C

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/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  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) 2019-2022 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 "pyramid.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
 
    solveVector sumClosed(Zero);
    solveScalar sumMagClosedBoundary(0);
 
    for (label facei = nInternalFaces(); facei < areas.size(); facei++)
    {
        if (!internalOrCoupledFaces.size() || !internalOrCoupledFaces[facei])
        {
            sumClosed += areas[facei];
            sumMagClosedBoundary += mag(areas[facei]);
        }
    }
 
    reduce(sumClosed, sumOp<solveVector>());
    reduce(sumMagClosedBoundary, sumOp<solveScalar>());
 
    solveVector 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)
    {
        const label neiSize = returnReduce(ortho.size(), 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 hasError = false;
    // Multiple faces detected?
    label nMultipleCells = 0;
 
    // 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])
        {
            hasError = 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)
            {
                hasError = true;
 
                if (setPtr)
                {
                    setPtr->insert(thisFace);
                }
            }
 
            prevCell = thisCell;
            prevFace = thisFace;
        }
 
        if (hasMultipleFaces)
        {
            nMultipleCells++;
        }
    }
 
    Pstream::reduceOr(hasError);
    reduce(nMultipleCells, sumOp<label>());
 
    if ((debug || report) && nMultipleCells > 0)
    {
        Info<< "  <<Found " << nMultipleCells
            << " neighbouring cells with multiple inbetween faces." << endl;
    }
 
    if (hasError)
    {
        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];
 
                forAll(cellEdges, cellEdgeI)
                {
                    if (cellEdges[cellEdgeI] == curEdge)
                    {
                        edgeUsage[cellEdgeI]++;
                        break;
                    }
                }
            }
        }
 
        edgeList singleEdges(cellEdges.size());
        label nSingleEdges = 0;
 
        forAll(edgeUsage, edgeI)
        {
            if (edgeUsage[edgeI] == 1)
            {
                singleEdges[nSingleEdges] = cellEdges[edgeI];
                nSingleEdges++;
            }
            else if (edgeUsage[edgeI] != 2)
            {
                if (setPtr)
                {
                    setPtr->insert(celli);
                }
            }
        }
 
        if (nSingleEdges > 0)
        {
            if (setPtr)
            {
                setPtr->insert(celli);
            }
 
            nOpenCells++;
        }
    }
 
    reduce(nOpenCells, sumOp<label>());
 
    if (nOpenCells > 0)
    {
        if (debug || report)
        {
            Info<< " ***Open cells found, number of cells: " << nOpenCells
                << ". This problem may be fixable using the zipUpMesh utility."
                << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "    Topological cell zip-up check OK." << endl;
    }
 
    return false;
}
 
 
bool Foam::primitiveMesh::checkFaceVertices
(
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face vertices" << endl;
 
    // Check that all vertex labels are valid
    const faceList& f = faces();
 
    label nErrorFaces = 0;
 
    forAll(f, fI)
    {
        const face& curFace = f[fI];
 
        if (min(curFace) < 0 || max(curFace) > nPoints())
        {
            if (setPtr)
            {
                setPtr->insert(fI);
            }
 
            nErrorFaces++;
        }
 
        // Uniqueness of vertices
        labelHashSet facePoints(2*curFace.size());
 
        forAll(curFace, fp)
        {
            bool inserted = facePoints.insert(curFace[fp]);
 
            if (!inserted)
            {
                if (setPtr)
                {
                    setPtr->insert(fI);
                }
 
                nErrorFaces++;
            }
        }
    }
 
    reduce(nErrorFaces, sumOp<label>());
 
    if (nErrorFaces > 0)
    {
        if (debug || report)
        {
            Info<< "    Faces with invalid vertex labels found, "
                << " number of faces: " << nErrorFaces << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "    Face vertices OK." << endl;
    }
 
    return false;
}
 
 
bool Foam::primitiveMesh::checkPoints
(
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking points" << endl;
 
    label nFaceErrors = 0;
    label nCellErrors = 0;
 
    const labelListList& pf = pointFaces();
 
    forAll(pf, pointi)
    {
        if (pf[pointi].empty())
        {
            if (setPtr)
            {
                setPtr->insert(pointi);
            }
 
            nFaceErrors++;
        }
    }
 
 
    forAll(pf, pointi)
    {
        const labelList& pc = pointCells(pointi);
 
        if (pc.empty())
        {
            if (setPtr)
            {
                setPtr->insert(pointi);
            }
 
            nCellErrors++;
        }
    }
 
    reduce(nFaceErrors, sumOp<label>());
    reduce(nCellErrors, sumOp<label>());
 
    if (nFaceErrors > 0 || nCellErrors > 0)
    {
        if (debug || report)
        {
            Info<< " ***Unused points found in the mesh, "
                   "number unused by faces: " << nFaceErrors
                << " number unused by cells: " << nCellErrors
                << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "    Point usage OK." << endl;
    }
 
    return false;
}
 
 
bool Foam::primitiveMesh::checkDuplicateFaces
(
    const label facei,
    const Map<label>& nCommonPoints,
    label& nBaffleFaces,
    labelHashSet* setPtr
) const
{
    bool error = false;
 
    forAllConstIters(nCommonPoints, iter)
    {
        label nbFacei = iter.key();
        label nCommon = iter();
 
        const face& curFace = faces()[facei];
        const face& nbFace = faces()[nbFacei];
 
        if (nCommon == nbFace.size() || nCommon == curFace.size())
        {
            if (nbFace.size() != curFace.size())
            {
                error = true;
            }
            else
            {
                nBaffleFaces++;
            }
 
            if (setPtr)
            {
                setPtr->insert(facei);
                setPtr->insert(nbFacei);
            }
        }
    }
 
    return error;
}
 
 
bool Foam::primitiveMesh::checkCommonOrder
(
    const label facei,
    const Map<label>& nCommonPoints,
    labelHashSet* setPtr
) const
{
    bool error = false;
 
    forAllConstIters(nCommonPoints, iter)
    {
        label nbFacei = iter.key();
        label nCommon = iter();
 
        const face& curFace = faces()[facei];
        const face& nbFace = faces()[nbFacei];
 
        if
        (
            nCommon >= 2
         && nCommon != nbFace.size()
         && nCommon != curFace.size()
        )
        {
            forAll(curFace, fp)
            {
                // Get the index in the neighbouring face shared with curFace
                label nb = nbFace.find(curFace[fp]);
 
                if (nb != -1)
                {
 
                    // Check the whole face from nb onwards for shared vertices
                    // with neighbouring face. Rule is that any shared vertices
                    // should be consecutive on both faces i.e. if they are
                    // vertices fp,fp+1,fp+2 on one face they should be
                    // vertices nb, nb+1, nb+2 (or nb+2, nb+1, nb) on the
                    // other face.
 
 
                    // Vertices before and after on curFace
                    label fpPlus1 = curFace.fcIndex(fp);
                    label fpMin1  = curFace.rcIndex(fp);
 
                    // Vertices before and after on nbFace
                    label nbPlus1 = nbFace.fcIndex(nb);
                    label nbMin1  = nbFace.rcIndex(nb);
 
                    // Find order of walking by comparing next points on both
                    // faces.
                    label curInc = labelMax;
                    label nbInc = labelMax;
 
                    if (nbFace[nbPlus1] == curFace[fpPlus1])
                    {
                        curInc = 1;
                        nbInc = 1;
                    }
                    else if (nbFace[nbPlus1] == curFace[fpMin1])
                    {
                        curInc = -1;
                        nbInc = 1;
                    }
                    else if (nbFace[nbMin1] == curFace[fpMin1])
                    {
                        curInc = -1;
                        nbInc = -1;
                    }
                    else
                    {
                        curInc = 1;
                        nbInc = -1;
                    }
 
 
                    // Pass1: loop until start of common vertices found.
                    label curNb = nb;
                    label curFp = fp;
 
                    do
                    {
                        curFp += curInc;
 
                        if (curFp >= curFace.size())
                        {
                            curFp = 0;
                        }
                        else if (curFp < 0)
                        {
                            curFp = curFace.size()-1;
                        }
 
                        curNb += nbInc;
 
                        if (curNb >= nbFace.size())
                        {
                            curNb = 0;
                        }
                        else if (curNb < 0)
                        {
                            curNb = nbFace.size()-1;
                        }
                    } while (curFace[curFp] == nbFace[curNb]);
 
 
                    // Pass2: check equality walking from curFp, curNb
                    // in opposite order.
 
                    curInc = -curInc;
                    nbInc = -nbInc;
 
                    for (label commonI = 0; commonI < nCommon; commonI++)
                    {
                        curFp += curInc;
 
                        if (curFp >= curFace.size())
                        {
                            curFp = 0;
                        }
                        else if (curFp < 0)
                        {
                            curFp = curFace.size()-1;
                        }
 
                        curNb += nbInc;
 
                        if (curNb >= nbFace.size())
                        {
                            curNb = 0;
                        }
                        else if (curNb < 0)
                        {
                            curNb = nbFace.size()-1;
                        }
 
                        if (curFace[curFp] != nbFace[curNb])
                        {
                            if (setPtr)
                            {
                                setPtr->insert(facei);
                                setPtr->insert(nbFacei);
                            }
 
                            error = true;
 
                            break;
                        }
                    }
 
 
                    // Done the curFace - nbFace combination.
                    break;
                }
            }
        }
    }
 
    return error;
}
 
 
bool Foam::primitiveMesh::checkFaceFaces
(
    const bool report,
    labelHashSet* setPtr
) const
{
    DebugInFunction << "Checking face-face connectivity" << endl;
 
    const labelListList& pf = pointFaces();
 
    label nBaffleFaces = 0;
    label nErrorDuplicate = 0;
    label nErrorOrder = 0;
    Map<label> nCommonPoints;
 
    for (label facei = 0; facei < nFaces(); facei++)
    {
        const face& curFace = faces()[facei];
 
        // Calculate number of common points between current facei and
        // neighbouring face. Store on map.
        nCommonPoints.clear();
 
        forAll(curFace, fp)
        {
            label pointi = curFace[fp];
 
            const labelList& nbs = pf[pointi];
 
            forAll(nbs, nbI)
            {
                label nbFacei = nbs[nbI];
 
                if (facei < nbFacei)
                {
                    // Only check once for each combination of two faces.
                    ++(nCommonPoints(nbFacei, 0));
                }
            }
        }
 
        // Perform various checks on common points
 
        // Check all vertices shared (duplicate point)
        if (checkDuplicateFaces(facei, nCommonPoints, nBaffleFaces, setPtr))
        {
            nErrorDuplicate++;
        }
 
        // Check common vertices are consecutive on both faces
        if (checkCommonOrder(facei, nCommonPoints, setPtr))
        {
            nErrorOrder++;
        }
    }
 
    reduce(nBaffleFaces, sumOp<label>());
    reduce(nErrorDuplicate, sumOp<label>());
    reduce(nErrorOrder, sumOp<label>());
 
    if (nBaffleFaces)
    {
        Info<< "    Number of identical duplicate faces (baffle faces): "
            << nBaffleFaces << endl;
    }
 
    if (nErrorDuplicate > 0 || nErrorOrder > 0)
    {
        // These are actually warnings, not errors.
        if (nErrorDuplicate > 0)
        {
            Info<< "  <<Number of duplicate (not baffle) faces found: "
                << nErrorDuplicate
                << ". This might indicate a problem." << endl;
        }
 
        if (nErrorOrder > 0)
        {
            Info<< "  <<Number of faces with non-consecutive shared points: "
                << nErrorOrder << ". This might indicate a problem." << endl;
        }
 
        return false;   //return true;
    }
 
    if (debug || report)
    {
        Info<< "    Face-face connectivity OK." << endl;
    }
 
    return false;
}
 
 
// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
bool Foam::primitiveMesh::checkClosedBoundary(const bool report) const
{
    return checkClosedBoundary(faceAreas(), report, bitSet());
}
 
 
bool Foam::primitiveMesh::checkClosedCells
(
    const bool report,
    labelHashSet* setPtr,
    labelHashSet* aspectSetPtr,
    const Vector<label>& solutionD
) const
{
    return checkClosedCells
    (
        faceAreas(),
        cellVolumes(),
        report,
        setPtr,
        aspectSetPtr,
        solutionD
    );
}
 
 
bool Foam::primitiveMesh::checkFaceAreas
(
    const bool report,
    labelHashSet* setPtr
) const
{
    return checkFaceAreas
    (
        faceAreas(),
        report,
        false,  // detailedReport,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkCellVolumes
(
    const bool report,
    labelHashSet* setPtr
) const
{
    return checkCellVolumes
    (
        cellVolumes(),
        report,
        false,  // detailedReport,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkFaceOrthogonality
(
    const bool report,
    labelHashSet* setPtr
) const
{
    return checkFaceOrthogonality
    (
        faceAreas(),
        cellCentres(),
        report,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkFacePyramids
(
    const bool report,
    const scalar minPyrVol,
    labelHashSet* setPtr
) const
{
    return checkFacePyramids
    (
        points(),
        cellCentres(),
        report,
        false,  // detailedReport,
        minPyrVol,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkFaceSkewness
(
    const bool report,
    labelHashSet* setPtr
) const
{
    return checkFaceSkewness
    (
        points(),
        faceCentres(),
        faceAreas(),
        cellCentres(),
        report,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkFaceAngles
(
    const bool report,
    const scalar maxDeg,
    labelHashSet* setPtr
) const
{
    return checkFaceAngles
    (
        points(),
        faceAreas(),
        report,
        maxDeg,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkFaceFlatness
(
    const bool report,
    const scalar warnFlatness,
    labelHashSet* setPtr
) const
{
    return checkFaceFlatness
    (
        points(),
        faceCentres(),
        faceAreas(),
        report,
        warnFlatness,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkConcaveCells
(
    const bool report,
    labelHashSet* setPtr
) const
{
    return checkConcaveCells
    (
        faceAreas(),
        faceCentres(),
        report,
        setPtr
    );
}
 
 
bool Foam::primitiveMesh::checkTopology(const bool report) const
{
    label nFailedChecks = 0;
 
    if (checkPoints(report)) ++nFailedChecks;
    if (checkUpperTriangular(report)) ++nFailedChecks;
    if (checkCellsZipUp(report)) ++nFailedChecks;
    if (checkFaceVertices(report)) ++nFailedChecks;
    if (checkFaceFaces(report)) ++nFailedChecks;
 
    if (nFailedChecks)
    {
        if (debug || report)
        {
            Info<< "    Failed " << nFailedChecks
                << " mesh topology checks." << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "    Mesh topology OK." << endl;
    }
 
    return false;
}
 
 
bool Foam::primitiveMesh::checkGeometry(const bool report) const
{
    label nFailedChecks = 0;
 
    if (checkClosedBoundary(report)) ++nFailedChecks;
    if (checkClosedCells(report)) ++nFailedChecks;
    if (checkFaceAreas(report)) ++nFailedChecks;
    if (checkCellVolumes(report)) ++nFailedChecks;
    if (checkFaceOrthogonality(report)) ++nFailedChecks;
    if (checkFacePyramids(report)) ++nFailedChecks;
    if (checkFaceSkewness(report)) ++nFailedChecks;
 
    if (nFailedChecks)
    {
        if (debug || report)
        {
            Info<< "    Failed " << nFailedChecks
                << " mesh geometry checks." << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "    Mesh geometry OK." << endl;
    }
 
    return false;
}
 
 
bool Foam::primitiveMesh::checkMesh(const bool report) const
{
    DebugInFunction << "Checking primitiveMesh" << endl;
 
    label nFailedChecks = checkTopology(report) + checkGeometry(report);
 
    if (nFailedChecks)
    {
        if (debug || report)
        {
            Info<< "    Failed " << nFailedChecks
                << " mesh checks." << endl;
        }
 
        return true;
    }
 
    if (debug || report)
    {
        Info<< "Mesh OK." << endl;
    }
 
    return false;
}
 
 
Foam::scalar Foam::primitiveMesh::setClosedThreshold(const scalar val)
{
    scalar prev = closedThreshold_;
    closedThreshold_ = val;
 
    return prev;
}
 
 
Foam::scalar Foam::primitiveMesh::setAspectThreshold(const scalar val)
{
    scalar prev = aspectThreshold_;
    aspectThreshold_ = val;
 
    return prev;
}
 
 
Foam::scalar Foam::primitiveMesh::setNonOrthThreshold(const scalar val)
{
    scalar prev = nonOrthThreshold_;
    nonOrthThreshold_ = val;
 
    return prev;
}
 
 
Foam::scalar Foam::primitiveMesh::setSkewThreshold(const scalar val)
{
    scalar prev = skewThreshold_;
    skewThreshold_ = val;
 
    return prev;
}
 
 
// ************************************************************************* //