void Foam::simpleTwoStroke::addZonesAndModifiers()
{
    // Add the zones and mesh modifiers to operate piston motion

    if
    (
        pointZones().size() > 0
        || faceZones().size() > 0
        || cellZones().size() > 0
    )
    {
        Info<< "Time = " << engTime().theta() << endl;
        Info<< "void simpleTwoStroke::addZonesAndModifiers() : "
            << "Zones and modifiers already present.  Skipping."
            << endl;

        if (topoChanger_.size() == 0)
        {
            FatalErrorIn
            (
                "void simpleTwoStroke::addZonesAndModifiers()"
            )   << "Mesh modifiers not read properly"
                << abort(FatalError);
        }

        setVirtualPistonPosition();
        checkAndCalculate();

        return;


    }

    Info << "checkAndCalculate()" << endl;
    checkAndCalculate();

    Info<< "Time = " << engTime().theta() << endl
        << "Adding zones to the engine mesh" << endl;


    //fz = 4: virtual piston, outSidePort, insidePort, cutFaceZone
    //pz = 2: piston points, cutPointZone
    //cz = 1: moving mask

    List<pointZone*> pz(3);
    List<faceZone*> fz(4);
    List<cellZone*> cz(1);

    label nPointZones = 0;
    label nFaceZones = 0;
    label nCellZones = 0;

    // Add the piston zone
    if (piston().patchID().active())
    {

        // Piston position

        Info << "Adding face zone for piston layer addition/removal" << endl;

        label pistonPatchID = piston().patchID().index();

        scalar zPist =
            max(boundary()[pistonPatchID].patch().localPoints()).z();

        scalar zPistV = zPist + offSet();

        labelList zone1(faceCentres().size());
        boolList flipZone1(faceCentres().size(), false);
        label nZoneFaces1 = 0;

        bool foundAtLeastOne = false;
        scalar zHigher = GREAT;
        scalar dh = GREAT;
        scalar dl = GREAT;

        forAll (faceCentres(), faceI)
        {
            // The points have to be in the cylinder and not in the ports....

            scalar zc = faceCentres()[faceI].z();

            scalar xc = faceCentres()[faceI].x();
            scalar yc = faceCentres()[faceI].y();

            vector n = faceAreas()[faceI]/mag(faceAreas()[faceI]);
            scalar dd = n & vector(0,0,1);

            if(sqrt(sqr(xc)+sqr(yc)) <  0.5 * engTime().bore().value())
            {
                if (dd > 0.1)
                {
                    if (zPistV - zc > 0 && zPistV - zc < dl)
                    {
                        dl = zPistV - zc;
                    }

                    if (zc - zPistV > 0 && zc - zPistV < dh)
                    {
                        zHigher = zc;
                        dh = zc - zHigher;
                    }

                    if
                    (
                        zc > zPistV - delta()
                        && zc < zPistV + delta()
                    )
                    {
                        foundAtLeastOne = true;
                        if ((faceAreas()[faceI] & vector(0,0,1)) < 0)
                        {
                            flipZone1[nZoneFaces1] = true;
                        }

                        zone1[nZoneFaces1] = faceI;
                        nZoneFaces1++;
                    }
                }
            }
        }
void Foam::layerAR::addZonesAndModifiers()
{
    // Add the zones and mesh modifiers to operate piston motion

    if
    (
        pointZones().size() > 0
     || faceZones().size() > 0
     || cellZones().size() > 0
    )
    {
        Info<< "void layerAR::addZonesAndModifiers() : "
            << "Zones and modifiers already present.  Skipping."
            << endl;

        if (topoChanger_.size() == 0)
        {
            FatalErrorIn
            (
                "void layerAR::addZonesAndModifiers()"
            )   << "Mesh modifiers not read properly"
                << abort(FatalError);
        }

        setVirtualPistonPosition();
        checkAndCalculate();

        return;
    }

    checkAndCalculate();

    Info<< "Time = " << engTime().theta() << endl
        << "Adding zones to the engine mesh" << endl;

    //fz = 1: faces where layer are added/removed
    //pz = 2: points below the virtual piston faces and head points

    List<pointZone*> pz(2);
    List<faceZone*> fz(1);
    List<cellZone*> cz(0);

    label nPointZones = 0;
    label nFaceZones = 0;

    // Add the piston zone
    if (piston().patchID().active() && offSet() > SMALL)
    {

        // Piston position

        label pistonPatchID = piston().patchID().index();

        scalar zPist = max(boundary()[pistonPatchID].patch().localPoints()).z();

        scalar zPistV = zPist + offSet();

        labelList zone1(faceCentres().size());
        boolList flipZone1(faceCentres().size(), false);
        label nZoneFaces1 = 0;

        bool foundAtLeastOne = false;
        scalar zHigher = GREAT;
        scalar dh = GREAT;
        scalar dl = GREAT;

        forAll (faceCentres(), faceI)
        {
            scalar zc = faceCentres()[faceI].z();
            vector n = faceAreas()[faceI]/mag(faceAreas()[faceI]);
            scalar dd = n & vector(0,0,1);

            if (dd > 0.1)
            {
                if (zPistV - zc > 0 && zPistV - zc < dl)
                {
                    dl = zPistV - zc;
                }

                if (zc - zPistV > 0 && zc - zPistV < dh)
                {
                    zHigher = zc;
                    dh = zc - zHigher;
                }

                if
                (
                    zc > zPistV - delta()
                    && zc < zPistV + delta()
                )
                {
                    foundAtLeastOne = true;
                    if ((faceAreas()[faceI] & vector(0,0,1)) < 0)
                    {
                        flipZone1[nZoneFaces1] = true;
                    }

                    zone1[nZoneFaces1] = faceI;
                    nZoneFaces1++;
                }
            }
        }
void Foam::movingConeTopoFvMesh::addZonesAndModifiers()
{
    // Add zones and modifiers for motion action

    if
    (
        pointZones().size()
     || faceZones().size()
     || cellZones().size()
     || topoChanger_.size()
    )
    {
        Info<< "void movingConeTopoFvMesh::addZonesAndModifiers() : "
            << "Zones and modifiers already present.  Skipping."
            << endl;

        return;
    }

    Info<< "Time = " << time().timeName() << endl
        << "Adding zones and modifiers to the mesh" << endl;

    const vectorField& fc = faceCentres();
    const vectorField& fa = faceAreas();

    labelList zone1(fc.size());
    boolList flipZone1(fc.size(), false);
    label nZoneFaces1 = 0;

    labelList zone2(fc.size());
    boolList flipZone2(fc.size(), false);
    label nZoneFaces2 = 0;

    forAll(fc, faceI)
    {
        if
        (
            fc[faceI].x() > -0.003501
         && fc[faceI].x() < -0.003499
        )
        {
            if ((fa[faceI] & vector(1, 0, 0)) < 0)
            {
                flipZone1[nZoneFaces1] = true;
            }

            zone1[nZoneFaces1] = faceI;
            Info<< "face " << faceI << " for zone 1.  Flip: "
                << flipZone1[nZoneFaces1] << endl;
            nZoneFaces1++;
        }
        else if
        (
            fc[faceI].x() > -0.00701
         && fc[faceI].x() < -0.00699
        )
        {
            zone2[nZoneFaces2] = faceI;

            if ((fa[faceI] & vector(1, 0, 0)) > 0)
            {
                flipZone2[nZoneFaces2] = true;
            }

            Info<< "face " << faceI << " for zone 2.  Flip: "
                << flipZone2[nZoneFaces2] << endl;
            nZoneFaces2++;
        }
    }

    zone1.setSize(nZoneFaces1);
    flipZone1.setSize(nZoneFaces1);

    zone2.setSize(nZoneFaces2);
    flipZone2.setSize(nZoneFaces2);

    Info<< "zone: " << zone1 << endl;
    Info<< "zone: " << zone2 << endl;

    List<pointZone*> pz(0);
    List<faceZone*> fz(2);
    List<cellZone*> cz(0);

    label nFz = 0;

    fz[nFz] =
        new faceZone
        (
            "rightExtrusionFaces",
            zone1,
            flipZone1,
            nFz,
            faceZones()
        );
    nFz++;

    fz[nFz] =
        new faceZone
        (
            "leftExtrusionFaces",
            zone2,
            flipZone2,
            nFz,
            faceZones()
        );
    nFz++;

    fz.setSize(nFz);

    Info<< "Adding mesh zones." << endl;
    addZones(pz, fz, cz);


    // Add layer addition/removal interfaces

    List<polyMeshModifier*> tm(2);
    label nMods = 0;

    tm[nMods] =
        new layerAdditionRemoval
        (
            "right",
            nMods,
            topoChanger_,
            "rightExtrusionFaces",
            readScalar
            (
                motionDict_.subDict("right").lookup("minThickness")
            ),
            readScalar
            (
                motionDict_.subDict("right").lookup("maxThickness")
            )
        );
    nMods++;

    tm[nMods] = new layerAdditionRemoval
    (
        "left",
        nMods,
        topoChanger_,
        "leftExtrusionFaces",
        readScalar
        (
            motionDict_.subDict("left").lookup("minThickness")
        ),
        readScalar
        (
            motionDict_.subDict("left").lookup("maxThickness")
        )
    );
    nMods++;
    tm.setSize(nMods);

    Info<< "Adding " << nMods << " mesh modifiers" << endl;
    topoChanger_.addTopologyModifiers(tm);

    write();
}