label meshOptimizer::findLowQualityFaces
(
    labelHashSet& badFaces,
    const boolList& changedFace
) const
{
    badFaces.clear();

    polyMeshGenChecks::checkFaceDotProduct
    (
        mesh_,
        false,
        70.0,
        &badFaces
    );

    polyMeshGenChecks::checkFaceSkewness
    (
        mesh_,
        false,
        2.0,
        &badFaces
    );

    const label nBadFaces = returnReduce(badFaces.size(), sumOp<label>());

    return nBadFaces;
}
label meshOptimizer::findBadFaces
(
    labelHashSet& badFaces,
    const boolList& changedFace
) const
{
    badFaces.clear();

    polyMeshGenChecks::checkFacePyramids
    (
        mesh_,
        false,
        VSMALL,
        &badFaces,
        &changedFace
    );

    polyMeshGenChecks::checkFaceFlatness
    (
        mesh_,
        false,
        0.8,
        &badFaces,
        &changedFace
    );

    polyMeshGenChecks::checkCellPartTetrahedra
    (
        mesh_,
        false,
        VSMALL,
        &badFaces,
        &changedFace
    );

    polyMeshGenChecks::checkFaceAreas
    (
        mesh_,
        false,
        VSMALL,
        &badFaces,
        &changedFace
    );

    const label nBadFaces = returnReduce(badFaces.size(), sumOp<label>());

    return nBadFaces;
}
int main(int argc, char *argv[])
{
    #include "addOverwriteOption.H"
    argList::noParallel();
    argList::validArgs.append("patches");
    argList::validArgs.append("edgeFraction");

    argList::addOption
    (
        "useSet",
        "name",
        "restrict cells to refine based on specified cellSet name"
    );


    #include "setRootCase.H"
    #include "createTime.H"
    runTime.functionObjects().off();

    #include "createPolyMesh.H"
    const word oldInstance = mesh.pointsInstance();

    // Find set of patches from the list of regular expressions provided
    const wordReList patches((IStringStream(args[1])()));
    const labelHashSet patchSet(mesh.boundaryMesh().patchSet(patches));

    const scalar weight  = args.argRead<scalar>(2);
    const bool overwrite = args.optionFound("overwrite");

    if (!patchSet.size())
    {
        FatalErrorInFunction
            << "Cannot find any patches in set " << patches << endl
            << "Valid patches are " << mesh.boundaryMesh().names()
            << exit(FatalError);
    }

    label nPatchFaces = 0;
    label nPatchEdges = 0;

    forAllConstIter(labelHashSet, patchSet, iter)
    {
        nPatchFaces += mesh.boundaryMesh()[iter.key()].size();
        nPatchEdges += mesh.boundaryMesh()[iter.key()].nEdges();
    }
bool Foam::motionSmootherAlgo::checkMesh
(
    const bool report,
    const polyMesh& mesh,
    const dictionary& dict,
    const labelList& checkFaces,
    const List<labelPair>& baffles,
    labelHashSet& wrongFaces
)
{
    const scalar maxNonOrtho
    (
        readScalar(dict.lookup("maxNonOrtho", true))
    );
    const scalar minVol
    (
        readScalar(dict.lookup("minVol", true))
    );
    const scalar minTetQuality
    (
        readScalar(dict.lookup("minTetQuality", true))
    );
    const scalar maxConcave
    (
        readScalar(dict.lookup("maxConcave", true))
    );
    const scalar minArea
    (
        readScalar(dict.lookup("minArea", true))
    );
    const scalar maxIntSkew
    (
        readScalar(dict.lookup("maxInternalSkewness", true))
    );
    const scalar maxBounSkew
    (
        readScalar(dict.lookup("maxBoundarySkewness", true))
    );
    const scalar minWeight
    (
        readScalar(dict.lookup("minFaceWeight", true))
    );
    const scalar minVolRatio
    (
        readScalar(dict.lookup("minVolRatio", true))
    );
    const scalar minTwist
    (
        readScalar(dict.lookup("minTwist", true))
    );
    const scalar minTriangleTwist
    (
        readScalar(dict.lookup("minTriangleTwist", true))
    );
    scalar minFaceFlatness = -1.0;
    dict.readIfPresent("minFaceFlatness", minFaceFlatness, true);
    const scalar minDet
    (
        readScalar(dict.lookup("minDeterminant", true))
    );
    label nWrongFaces = 0;

    Info<< "Checking faces in error :" << endl;
    //Pout.setf(ios_base::left);

    if (maxNonOrtho < 180.0-SMALL)
    {
        polyMeshGeometry::checkFaceDotProduct
        (
            report,
            maxNonOrtho,
            mesh,
            mesh.cellCentres(),
            mesh.faceAreas(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    non-orthogonality > "
            << setw(3) << maxNonOrtho
            << " degrees                        : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minVol > -GREAT)
    {
        polyMeshGeometry::checkFacePyramids
        (
            report,
            minVol,
            mesh,
            mesh.cellCentres(),
            mesh.points(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with face pyramid volume < "
            << setw(5) << minVol << "                 : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minTetQuality > -GREAT)
    {
        polyMeshGeometry::checkFaceTets
        (
            report,
            minTetQuality,
            mesh,
            mesh.cellCentres(),
            mesh.faceCentres(),
            mesh.points(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with face-decomposition tet quality < "
            << setw(5) << minTetQuality << "      : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (maxConcave < 180.0-SMALL)
    {
        polyMeshGeometry::checkFaceAngles
        (
            report,
            maxConcave,
            mesh,
            mesh.faceAreas(),
            mesh.points(),
            checkFaces,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with concavity > "
            << setw(3) << maxConcave
            << " degrees                     : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minArea > -SMALL)
    {
        polyMeshGeometry::checkFaceArea
        (
            report,
            minArea,
            mesh,
            mesh.faceAreas(),
            checkFaces,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with area < "
            << setw(5) << minArea
            << " m^2                            : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (maxIntSkew > 0 || maxBounSkew > 0)
    {
        polyMeshGeometry::checkFaceSkewness
        (
            report,
            maxIntSkew,
            maxBounSkew,
            mesh,
            mesh.points(),
            mesh.cellCentres(),
            mesh.faceCentres(),
            mesh.faceAreas(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with skewness > "
            << setw(3) << maxIntSkew
            << " (internal) or " << setw(3) << maxBounSkew
            << " (boundary) : " << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minWeight >= 0 && minWeight < 1)
    {
        polyMeshGeometry::checkFaceWeights
        (
            report,
            minWeight,
            mesh,
            mesh.cellCentres(),
            mesh.faceCentres(),
            mesh.faceAreas(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with interpolation weights (0..1)  < "
            << setw(5) << minWeight
            << "       : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minVolRatio >= 0)
    {
        polyMeshGeometry::checkVolRatio
        (
            report,
            minVolRatio,
            mesh,
            mesh.cellVolumes(),
            checkFaces,
            baffles,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with volume ratio of neighbour cells < "
            << setw(5) << minVolRatio
            << "     : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minTwist > -1)
    {
        //Pout<< "Checking face twist: dot product of face normal "
        //    << "with face triangle normals" << endl;
        polyMeshGeometry::checkFaceTwist
        (
            report,
            minTwist,
            mesh,
            mesh.cellCentres(),
            mesh.faceAreas(),
            mesh.faceCentres(),
            mesh.points(),
            checkFaces,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with face twist < "
            << setw(5) << minTwist
            << "                          : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minTriangleTwist > -1)
    {
        //Pout<< "Checking triangle twist: dot product of consecutive triangle"
        //    << " normals resulting from face-centre decomposition" << endl;
        polyMeshGeometry::checkTriangleTwist
        (
            report,
            minTriangleTwist,
            mesh,
            mesh.faceAreas(),
            mesh.faceCentres(),
            mesh.points(),
            checkFaces,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with triangle twist < "
            << setw(5) << minTriangleTwist
            << "                      : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minFaceFlatness > -SMALL)
    {
        polyMeshGeometry::checkFaceFlatness
        (
            report,
            minFaceFlatness,
            mesh,
            mesh.faceAreas(),
            mesh.faceCentres(),
            mesh.points(),
            checkFaces,
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces with flatness < "
            << setw(5) << minFaceFlatness
            << "                      : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    if (minDet > -1)
    {
        polyMeshGeometry::checkCellDeterminant
        (
            report,
            minDet,
            mesh,
            mesh.faceAreas(),
            checkFaces,
            polyMeshGeometry::affectedCells(mesh, checkFaces),
            &wrongFaces
        );

        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());

        Info<< "    faces on cells with determinant < "
            << setw(5) << minDet << "                : "
            << nNewWrongFaces-nWrongFaces << endl;

        nWrongFaces = nNewWrongFaces;
    }

    //Pout.setf(ios_base::right);

    return nWrongFaces > 0;
}
// Same check as snapMesh
void checkSnapMesh
(
    const Time& runTime,
    const polyMesh& mesh,
    labelHashSet& wrongFaces
)
{
    IOdictionary snapDict
    (
        IOobject
        (
            "snapMeshDict",
            runTime.system(),
            mesh,
            IOobject::MUST_READ,
            IOobject::NO_WRITE
        )
    );

    // Max nonorthogonality allowed
    scalar maxNonOrtho(readScalar(snapDict.lookup("maxNonOrtho")));
    primitiveMesh::nonOrthThreshold_ = maxNonOrtho;

    // Max concaveness allowed.
    scalar maxConcave(readScalar(snapDict.lookup("maxConcave")));
    primitiveMesh::faceAngleThreshold_ = maxConcave;

    // Min volume allowed (factor of minimum cellVolume)
    scalar relMinVol(readScalar(snapDict.lookup("minVol")));
    const scalar minCellVol = min(mesh.cellVolumes());
    const scalar minPyrVol = relMinVol*minCellVol;

    // Min area
    scalar minArea(readScalar(snapDict.lookup("minArea")));

    if (maxNonOrtho < 180.0 - SMALL)
    {
        Pout<< "Checking non orthogonality" << endl;

        label nOldSize = wrongFaces.size();
        mesh.checkFaceOrthogonality(false, &wrongFaces);

        Pout<< "Detected " << wrongFaces.size() - nOldSize
            << " faces with non-orthogonality > " << maxNonOrtho << " degrees"
            << endl;
    }

    if (minPyrVol > -GREAT)
    {
        Pout<< "Checking face pyramids" << endl;

        label nOldSize = wrongFaces.size();
        mesh.checkFacePyramids(false, minPyrVol, &wrongFaces);
        Pout<< "Detected additional " << wrongFaces.size() - nOldSize
            << " faces with illegal face pyramids" << endl;
    }

    if (maxConcave < 180.0 - SMALL)
    {
        Pout<< "Checking face angles" << endl;

        label nOldSize = wrongFaces.size();
        mesh.checkFaceAngles(false, &wrongFaces);

        Pout<< "Detected additional " << wrongFaces.size() - nOldSize
            << " faces with concavity > " << maxConcave << " degrees"
            << endl;
    }

    if (minArea > -SMALL)
    {
        Pout<< "Checking face areas" << endl;

        label nOldSize = wrongFaces.size();

        const scalarField magFaceAreas = mag(mesh.faceAreas());

        forAll(magFaceAreas, faceI)
        {
            if (magFaceAreas[faceI] < minArea)
            {
                wrongFaces.insert(faceI);
            }
        }

        Pout<< "Detected additional " << wrongFaces.size() - nOldSize
            << " faces with area < " << minArea << " m^2" << endl;
    }