BUGFIX: Uninitialised member variables

[foam-extend-3.2.git] / applications / utilities / surface / surfaceToPatch / boundaryMesh.C

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | Copyright held by original author
     \\/     M anipulation  |
-------------------------------------------------------------------------------
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 2 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, write to the Free Software Foundation,
    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

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

#include "boundaryMesh.H"
#include "objectRegistry.H"
#include "Time.H"
#include "polyMesh.H"
#include "repatchPolyTopoChanger.H"
#include "faceList.H"
#include "indexedOctree.H"
#include "treeDataPrimitivePatch.H"
#include "triSurface.H"
#include "SortableList.H"
#include "OFstream.H"
#include "uindirectPrimitivePatch.H"

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

defineTypeNameAndDebug(Foam::boundaryMesh, 0);

// Normal along which to divide faces into categories (used in getNearest)
const Foam::vector Foam::boundaryMesh::splitNormal_(3, 2, 1);

// Distance to face tolerance for getNearest
const Foam::scalar Foam::boundaryMesh::distanceTol_ = 1E-2;


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

// Returns number of feature edges connected to pointI
Foam::label Foam::boundaryMesh::nFeatureEdges(label pointI) const
{
    label nFeats = 0;

    const labelList& pEdges = mesh().pointEdges()[pointI];

    forAll(pEdges, pEdgeI)
    {
        label edgeI = pEdges[pEdgeI];

        if (edgeToFeature_[edgeI] != -1)
        {
            nFeats++;
        }
    }
    return nFeats;
}


// Returns next feature edge connected to pointI
Foam::label Foam::boundaryMesh::nextFeatureEdge
(
    const label edgeI,
    const label vertI
) const
{
    const labelList& pEdges = mesh().pointEdges()[vertI];

    forAll(pEdges, pEdgeI)
    {
        label nbrEdgeI = pEdges[pEdgeI];

        if (nbrEdgeI != edgeI)
        {
            label featI = edgeToFeature_[nbrEdgeI];

            if (featI != -1)
            {
                return nbrEdgeI;
            }
        }
    }

    return -1;
}


// Finds connected feature edges, starting from startPointI and returns
// feature labels (not edge labels). Marks feature edges handled in
// featVisited.
Foam::labelList Foam::boundaryMesh::collectSegment
(
    const boolList& isFeaturePoint,
    const label startEdgeI,
    boolList& featVisited
) const
{
    // Find starting feature point on edge.

    label edgeI = startEdgeI;

    const edge& e = mesh().edges()[edgeI];

    label vertI = e.start();

    while (!isFeaturePoint[vertI])
    {
        // Step to next feature edge

        edgeI = nextFeatureEdge(edgeI, vertI);

        if ((edgeI == -1) || (edgeI == startEdgeI))
        {
            break;
        }

        // Step to next vertex on edge

        const edge& e = mesh().edges()[edgeI];

        vertI = e.otherVertex(vertI);
    }

    //
    // Now we have:
    //    edgeI : first edge on this segment
    //    vertI : one of the endpoints of this segment
    //
    // Start walking other way and storing edges as we go along.
    //

    // Untrimmed storage for current segment
    labelList featLabels(featureEdges_.size());

    label featLabelI = 0;

    label initEdgeI = edgeI;

    do
    {
        // Mark edge as visited
        label featI = edgeToFeature_[edgeI];

        if (featI == -1)
        {
            FatalErrorIn("boundaryMesh::collectSegment")
                << "Problem" << abort(FatalError);
        }
        featLabels[featLabelI++] = featI;

        featVisited[featI] = true;

        // Step to next vertex on edge

        const edge& e = mesh().edges()[edgeI];

        vertI = e.otherVertex(vertI);

        // Step to next feature edge

        edgeI = nextFeatureEdge(edgeI, vertI);

        if ((edgeI == -1) || (edgeI == initEdgeI))
        {
            break;
        }
    }
    while (!isFeaturePoint[vertI]);


    // Trim to size
    featLabels.setSize(featLabelI);

    return featLabels;
}


void Foam::boundaryMesh::markEdges
(
    const label maxDistance,
    const label edgeI,
    const label distance,
    labelList& minDistance,
    DynamicList<label>& visited
) const
{
    if (distance < maxDistance)
    {
        // Don't do anything if reached beyond maxDistance.

        if (minDistance[edgeI] == -1)
        {
            // First visit of edge. Store edge label.
            visited.append(edgeI);
        }
        else if (minDistance[edgeI] <= distance)
        {
            // Already done this edge
            return;
        }

        minDistance[edgeI] = distance;

        const edge& e = mesh().edges()[edgeI];

        // Do edges connected to e.start
        const labelList& startEdges = mesh().pointEdges()[e.start()];

        forAll(startEdges, pEdgeI)
        {
            markEdges
            (
                maxDistance,
                startEdges[pEdgeI],
                distance+1,
                minDistance,
                visited
            );
        }

        // Do edges connected to e.end
        const labelList& endEdges = mesh().pointEdges()[e.end()];

        forAll(endEdges, pEdgeI)
        {
            markEdges
            (
                maxDistance,
                endEdges[pEdgeI],
                distance+1,
                minDistance,
                visited
            );
        }
    }
}


Foam::label Foam::boundaryMesh::findPatchID
(
    const polyPatchList& patches,
    const word& patchName
) const
{
    forAll(patches, patchI)
    {
        if (patches[patchI].name() == patchName)
        {
            return patchI;
        }
    }

    return -1;
}


Foam::wordList Foam::boundaryMesh::patchNames() const
{
    wordList names(patches_.size());

    forAll(patches_, patchI)
    {
        names[patchI] = patches_[patchI].name();
    }
    return names;
}


Foam::label Foam::boundaryMesh::whichPatch
(
    const polyPatchList& patches,
    const label faceI
) const
{
    forAll(patches, patchI)
    {
        const polyPatch& pp = patches[patchI];

        if ((faceI >= pp.start()) && (faceI < (pp.start() + pp.size())))
        {
            return patchI;
        }
    }
    return -1;
}


// Gets labels of changed faces and propagates them to the edges. Returns
// labels of edges changed.
Foam::labelList Foam::boundaryMesh::faceToEdge
(
    const boolList& regionEdge,
    const label region,
    const labelList& changedFaces,
    labelList& edgeRegion
) const
{
    labelList changedEdges(mesh().nEdges(), -1);
    label changedI = 0;

    forAll(changedFaces, i)
    {
        label faceI = changedFaces[i];

        const labelList& fEdges = mesh().faceEdges()[faceI];

        forAll(fEdges, fEdgeI)
        {
            label edgeI = fEdges[fEdgeI];

            if (!regionEdge[edgeI] && (edgeRegion[edgeI] == -1))
            {
                edgeRegion[edgeI] = region;

                changedEdges[changedI++] = edgeI;
            }
        }
    }

    changedEdges.setSize(changedI);

    return changedEdges;
}


// Reverse of faceToEdge: gets edges and returns faces
Foam::labelList Foam::boundaryMesh::edgeToFace
(
    const label region,
    const labelList& changedEdges,
    labelList& faceRegion
) const
{
    labelList changedFaces(mesh().size(), -1);
    label changedI = 0;

    forAll(changedEdges, i)
    {
        label edgeI = changedEdges[i];

        const labelList& eFaces = mesh().edgeFaces()[edgeI];

        forAll(eFaces, eFaceI)
        {
            label faceI = eFaces[eFaceI];

            if (faceRegion[faceI] == -1)
            {
                faceRegion[faceI] = region;

                changedFaces[changedI++] = faceI;
            }
        }
    }

    changedFaces.setSize(changedI);

    return changedFaces;
}


// Finds area, starting at faceI, delimited by borderEdge
void Foam::boundaryMesh::markZone
(
    const boolList& borderEdge,
    label faceI,
    label currentZone,
    labelList& faceZone
) const
{
    faceZone[faceI] = currentZone;

    // List of faces whose faceZone has been set.
    labelList changedFaces(1, faceI);
    // List of edges whose faceZone has been set.
    labelList changedEdges;

    // Zones on all edges.
    labelList edgeZone(mesh().nEdges(), -1);

    while(1)
    {
        changedEdges = faceToEdge
        (
            borderEdge,
            currentZone,
            changedFaces,
            edgeZone
        );

        if (debug)
        {
            Pout<< "From changedFaces:" << changedFaces.size()
                << " to changedEdges:" << changedEdges.size()
                << endl;
        }

        if (changedEdges.empty())
        {
            break;
        }

        changedFaces = edgeToFace(currentZone, changedEdges, faceZone);

        if (debug)
        {
            Pout<< "From changedEdges:" << changedEdges.size()
                << " to changedFaces:" << changedFaces.size()
                << endl;
        }

        if (changedFaces.empty())
        {
            break;
        }
    }
}


// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //

// Null constructor
Foam::boundaryMesh::boundaryMesh()
:
    meshPtr_(NULL),
    patches_(),
    meshFace_(),
    featurePoints_(),
    featureEdges_(),
    featureToEdge_(),
    edgeToFeature_(),
    featureSegments_(),
    extraEdges_()
{}


// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //

Foam::boundaryMesh::~boundaryMesh()
{
    clearOut();
}


void Foam::boundaryMesh::clearOut()
{
    if (meshPtr_)
    {
        delete meshPtr_;

        meshPtr_ = NULL;
    }
}


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

void Foam::boundaryMesh::read(const polyMesh& mesh)
{
    patches_.clear();

    patches_.setSize(mesh.boundaryMesh().size());

    // Number of boundary faces
    label nBFaces = mesh.nFaces() - mesh.nInternalFaces();

    faceList bFaces(nBFaces);

    meshFace_.setSize(nBFaces);

    label bFaceI = 0;

    // Collect all boundary faces.
    forAll(mesh.boundaryMesh(), patchI)
    {
        const polyPatch& pp = mesh.boundaryMesh()[patchI];

        patches_.set
        (
            patchI,
            new boundaryPatch
            (
                pp.name(),
                patchI,
                pp.size(),
                bFaceI,
                pp.type()
            )
        );

        // Collect all faces in global numbering.
        forAll(pp, patchFaceI)
        {
            meshFace_[bFaceI] = pp.start() + patchFaceI;

            bFaces[bFaceI] = pp[patchFaceI];

            bFaceI++;
        }
    }


    if (debug)
    {
        Pout<< "read : patches now:" << endl;

        forAll(patches_, patchI)
        {
            const boundaryPatch& bp = patches_[patchI];

            Pout<< "    name  : " << bp.name() << endl
                << "    size  : " << bp.size() << endl
                << "    start : " << bp.start() << endl
                << "    type  : " << bp.physicalType() << endl
                << endl;
        }
    }

    //
    // Construct single patch for all of boundary
    //

    // Temporary primitivePatch to calculate compact points & faces.
    PrimitivePatch<face, List, const pointField&> globalPatch
    (
        bFaces,
        mesh.points()
    );

    // Store in local(compact) addressing
    clearOut();

    meshPtr_ = new bMesh(globalPatch.localFaces(), globalPatch.localPoints());


    if (debug & 2)
    {
        const bMesh& msh = *meshPtr_;

        Pout<< "** Start of Faces **" << endl;

        forAll(msh, faceI)
        {
            const face& f = msh[faceI];

            point ctr(vector::zero);

            forAll(f, fp)
            {
                ctr += msh.points()[f[fp]];
            }
            ctr /= f.size();

            Pout<< "    " << faceI
                << " ctr:" << ctr
                << " verts:" << f
                << endl;
        }

        Pout<< "** End of Faces **" << endl;

        Pout<< "** Start of Points **" << endl;

        forAll(msh.points(), pointI)
        {
            Pout<< "    " << pointI
                << " coord:" << msh.points()[pointI]
                << endl;
        }

        Pout<< "** End of Points **" << endl;
    }

    // Clear edge storage
    featurePoints_.setSize(0);
    featureEdges_.setSize(0);

    featureToEdge_.setSize(0);
    edgeToFeature_.setSize(meshPtr_->nEdges());
    edgeToFeature_ = -1;

    featureSegments_.setSize(0);

    extraEdges_.setSize(0);
}


void Foam::boundaryMesh::readTriSurface(const fileName& fName)
{
    triSurface surf(fName);

    if (surf.empty())
    {
        return;
    }

    // Sort according to region
    SortableList<label> regions(surf.size());

    forAll(surf, triI)
    {
        regions[triI] = surf[triI].region();
    }
    regions.sort();

    // Determine region mapping.
    Map<label> regionToBoundaryPatch;

    label oldRegion = -1111;
    label boundPatch = 0;

    forAll(regions, i)
    {
        if (regions[i] != oldRegion)
        {
            regionToBoundaryPatch.insert(regions[i], boundPatch);

            oldRegion = regions[i];
            boundPatch++;
        }
    }

    const geometricSurfacePatchList& surfPatches = surf.patches();

    patches_.clear();

    if (surfPatches.size() == regionToBoundaryPatch.size())
    {
        // There are as many surface patches as region numbers in triangles
        // so use the surface patches

        patches_.setSize(surfPatches.size());

        // Take over patches, setting size to 0 for now.
        forAll(surfPatches, patchI)
        {
            const geometricSurfacePatch& surfPatch = surfPatches[patchI];

            patches_.set
            (
                patchI,
                new boundaryPatch
                (
                    surfPatch.name(),
                    patchI,
                    0,
                    0,
                    surfPatch.geometricType()
                )
            );
        }
    }
    else
    {
        // There are not enough surface patches. Make up my own.

        patches_.setSize(regionToBoundaryPatch.size());

        forAll(patches_, patchI)
        {
            patches_.set
            (
                patchI,
                new boundaryPatch
                (
                    "patch" + name(patchI),
                    patchI,
                    0,
                    0,
                    "empty"
                )
            );
        }
    }

    //
    // Copy according into bFaces according to regions
    //

    const labelList& indices = regions.indices();

    faceList bFaces(surf.size());

    meshFace_.setSize(surf.size());

    label bFaceI = 0;

    // Current region number
    label surfRegion = regions[0];
    label foamRegion = regionToBoundaryPatch[surfRegion];

    Pout<< "Surface region " << surfRegion << " becomes boundary patch "
        << foamRegion << " with name " << patches_[foamRegion].name() << endl;


    // Index in bFaces of start of current patch
    label startFaceI = 0;

    forAll(indices, indexI)
    {
        label triI = indices[indexI];

        const labelledTri& tri = surf.localFaces()[triI];

        if (tri.region() != surfRegion)
        {
            // Change of region. We now know the size of the previous one.
            boundaryPatch& bp = patches_[foamRegion];

            bp.size() = bFaceI - startFaceI;
            bp.start() = startFaceI;

            surfRegion = tri.region();
            foamRegion = regionToBoundaryPatch[surfRegion];

            Pout<< "Surface region " << surfRegion << " becomes boundary patch "
                << foamRegion << " with name " << patches_[foamRegion].name()
                << endl;

            startFaceI = bFaceI;
        }

        meshFace_[bFaceI] = triI;

        bFaces[bFaceI++] = face(tri);
    }

    // Final region
    boundaryPatch& bp = patches_[foamRegion];

    bp.size() = bFaceI - startFaceI;
    bp.start() = startFaceI;

    //
    // Construct single primitivePatch for all of boundary
    //

    clearOut();

    // Store compact.
    meshPtr_ = new bMesh(bFaces, surf.localPoints());

    // Clear edge storage
    featurePoints_.setSize(0);
    featureEdges_.setSize(0);

    featureToEdge_.setSize(0);
    edgeToFeature_.setSize(meshPtr_->nEdges());
    edgeToFeature_ = -1;

    featureSegments_.setSize(0);

    extraEdges_.setSize(0);
}


void Foam::boundaryMesh::writeTriSurface(const fileName& fName) const
{
    geometricSurfacePatchList surfPatches(patches_.size());

    forAll(patches_, patchI)
    {
        const boundaryPatch& bp = patches_[patchI];

        surfPatches[patchI] =
            geometricSurfacePatch
            (
                bp.physicalType(),
                bp.name(),
                patchI
            );
    }

    //
    // Simple triangulation.
    //

    // Get number of triangles per face
    labelList nTris(mesh().size());

    label totalNTris = getNTris(0, mesh().size(), nTris);

    // Determine per face the starting triangle.
    labelList startTri(mesh().size());

    label triI = 0;

    forAll(mesh(), faceI)
    {
        startTri[faceI] = triI;

        triI += nTris[faceI];
    }

    // Triangulate
    labelList triVerts(3*totalNTris);

    triangulate(0, mesh().size(), totalNTris, triVerts);

    // Convert to labelledTri

    List<labelledTri> tris(totalNTris);

    triI = 0;

    forAll(patches_, patchI)
    {
        const boundaryPatch& bp = patches_[patchI];

        forAll(bp, patchFaceI)
        {
            label faceI = bp.start() + patchFaceI;

            label triVertI = 3*startTri[faceI];

            for (label faceTriI = 0; faceTriI < nTris[faceI]; faceTriI++)
            {
                label v0 = triVerts[triVertI++];
                label v1 = triVerts[triVertI++];
                label v2 = triVerts[triVertI++];

                tris[triI++] = labelledTri(v0, v1, v2, patchI);
            }
        }
    }

    triSurface surf(tris, surfPatches, mesh().points());

    OFstream surfStream(fName);

    surf.write(surfStream);
}


// Get index in this (boundaryMesh) of face nearest to each boundary face in
// pMesh.
// Origininally all triangles/faces of boundaryMesh would be bunged into
// one big octree. Problem was that faces on top of each other, differing
// only in sign of normal, could not be found separately. It would always
// find only one. We could detect that it was probably finding the wrong one
// (based on normal) but could not 'tell' the octree to retrieve the other
// one (since they occupy exactly the same space)
// So now faces get put into different octrees depending on normal.
// !It still will not be possible to differentiate between two faces on top
// of each other having the same normal
Foam::labelList Foam::boundaryMesh::getNearest
(
    const primitiveMesh& pMesh,
    const vector& searchSpan
) const
{

    // Divide faces into two bins acc. to normal
    // - left of splitNormal
    // - right ,,
    DynamicList<label> leftFaces(mesh().size()/2);
    DynamicList<label> rightFaces(mesh().size()/2);

    forAll(mesh(), bFaceI)
    {
        scalar sign = mesh().faceNormals()[bFaceI] & splitNormal_;

        if (sign > -1E-5)
        {
            rightFaces.append(bFaceI);
        }
        if (sign < 1E-5)
        {
            leftFaces.append(bFaceI);
        }
    }

    leftFaces.shrink();
    rightFaces.shrink();

    if (debug)
    {
        Pout<< "getNearest :"
            << " rightBin:" << rightFaces.size()
            << " leftBin:" << leftFaces.size()
            << endl;
    }

    uindirectPrimitivePatch leftPatch
    (
        UIndirectList<face>(mesh(), leftFaces),
        mesh().points()
    );
    uindirectPrimitivePatch rightPatch
    (
        UIndirectList<face>(mesh(), rightFaces),
        mesh().points()
    );


    // Overall bb
    treeBoundBox overallBb(mesh().localPoints());

    // Extend domain slightly (also makes it 3D if was 2D)
    // Note asymmetry to avoid having faces align with octree cubes.
    scalar tol = 1E-6 * overallBb.avgDim();

    point& bbMin = overallBb.min();
    bbMin.x() -= tol;
    bbMin.y() -= tol;
    bbMin.z() -= tol;

    point& bbMax = overallBb.max();
    bbMax.x() += 2*tol;
    bbMax.y() += 2*tol;
    bbMax.z() += 2*tol;

    // Create the octrees
    indexedOctree
    <
        treeDataPrimitivePatch<face, UIndirectList, const pointField&>
    > leftTree
    (
        treeDataPrimitivePatch<face, UIndirectList, const pointField&>
        (
            false,          // cacheBb
            leftPatch
        ),
        overallBb,
        10, // maxLevel
        10, // leafSize
        3.0 // duplicity
    );
    indexedOctree
    <
        treeDataPrimitivePatch<face, UIndirectList, const pointField&>
    > rightTree
    (
        treeDataPrimitivePatch<face, UIndirectList, const pointField&>
        (
            false,          // cacheBb
            rightPatch
        ),
        overallBb,
        10, // maxLevel
        10, // leafSize
        3.0 // duplicity
    );

    if (debug)
    {
        Pout<< "getNearest : built trees" << endl;
    }


    const vectorField& ns = mesh().faceNormals();


    //
    // Search nearest triangle centre for every polyMesh boundary face
    //

    labelList nearestBFaceI(pMesh.nFaces() - pMesh.nInternalFaces());

    treeBoundBox tightest;

    const scalar searchDimSqr = magSqr(searchSpan);

    forAll(nearestBFaceI, patchFaceI)
    {
        label meshFaceI = pMesh.nInternalFaces() + patchFaceI;

        const point& ctr = pMesh.faceCentres()[meshFaceI];

        if (debug && (patchFaceI % 1000) == 0)
        {
            Pout<< "getNearest : patchFace:" << patchFaceI
                << " meshFaceI:" << meshFaceI << " ctr:" << ctr << endl;
        }


        // Get normal from area vector
        vector n = pMesh.faceAreas()[meshFaceI];
        scalar area = mag(n);
        n /= area;

        scalar typDim = -GREAT;
        const face& f = pMesh.faces()[meshFaceI];

        forAll(f, fp)
        {
            typDim = max(typDim, mag(pMesh.points()[f[fp]] - ctr));
        }

        // Search right tree
        pointIndexHit rightInfo = rightTree.findNearest(ctr, searchDimSqr);

        // Search left tree. Note: could start from rightDist bounding box
        // instead of starting from top.
        pointIndexHit leftInfo = leftTree.findNearest(ctr, searchDimSqr);

        if (rightInfo.hit())
        {
            if (leftInfo.hit())
            {
                // Found in both trees. Compare normals.
                label rightFaceI = rightFaces[rightInfo.index()];
                label leftFaceI = leftFaces[leftInfo.index()];

                label rightDist = mag(rightInfo.hitPoint()-ctr);
                label leftDist = mag(leftInfo.hitPoint()-ctr);

                scalar rightSign = n & ns[rightFaceI];
                scalar leftSign = n & ns[leftFaceI];

                if
                (
                    (rightSign > 0 && leftSign > 0)
                 || (rightSign < 0 && leftSign < 0)
                )
                {
                    // Both same sign. Choose nearest.
                    if (rightDist < leftDist)
                    {
                        nearestBFaceI[patchFaceI] = rightFaceI;
                    }
                    else
                    {
                        nearestBFaceI[patchFaceI] = leftFaceI;
                    }
                }
                else
                {
                    // Differing sign.
                    // - if both near enough choose one with correct sign
                    // - otherwise choose nearest.

                    // Get local dimension as max of distance between ctr and
                    // any face vertex.

                    typDim *= distanceTol_;

                    if (rightDist < typDim && leftDist < typDim)
                    {
                        // Different sign and nearby. Choosing matching normal
                        if (rightSign > 0)
                        {
                            nearestBFaceI[patchFaceI] = rightFaceI;
                        }
                        else
                        {
                            nearestBFaceI[patchFaceI] = leftFaceI;
                        }
                    }
                    else
                    {
                        // Different sign but faraway. Choosing nearest.
                        if (rightDist < leftDist)
                        {
                            nearestBFaceI[patchFaceI] = rightFaceI;
                        }
                        else
                        {
                            nearestBFaceI[patchFaceI] = leftFaceI;
                        }
                    }
                }
            }
            else
            {
                // Found in right but not in left. Choose right regardless if
                // correct sign. Note: do we want this?
                label rightFaceI = rightFaces[rightInfo.index()];
                nearestBFaceI[patchFaceI] = rightFaceI;
            }
        }
        else
        {
            // No face found in right tree.

            if (leftInfo.hit())
            {
                // Found in left but not in right. Choose left regardless if
                // correct sign. Note: do we want this?
                nearestBFaceI[patchFaceI] = leftFaces[leftInfo.index()];
            }
            else
            {
                // No face found in left tree.
                nearestBFaceI[patchFaceI] = -1;
            }
        }
    }

    return nearestBFaceI;
}


void Foam::boundaryMesh::patchify
(
    const labelList& nearest,
    const polyBoundaryMesh& oldPatches,
    polyMesh& newMesh
) const
{

    // 2 cases to be handled:
    // A- patches in boundaryMesh patches_
    // B- patches not in boundaryMesh patches_ but in polyMesh

    // Create maps from patch name to new patch index.
    HashTable<label> nameToIndex(2*patches_.size());

    Map<word> indexToName(2*patches_.size());


    label nNewPatches = patches_.size();

    forAll(oldPatches, oldPatchI)
    {
        const polyPatch& patch = oldPatches[oldPatchI];

        label newPatchI = findPatchID(patch.name());

        if (newPatchI != -1)
        {
            nameToIndex.insert(patch.name(), newPatchI);

            indexToName.insert(newPatchI, patch.name());
        }
    }

    // Include all boundaryPatches not yet in nameToIndex (i.e. not in old
    // patches)
    forAll(patches_, bPatchI)
    {
        const boundaryPatch& bp = patches_[bPatchI];

        if (!nameToIndex.found(bp.name()))
        {
            nameToIndex.insert(bp.name(), bPatchI);

            indexToName.insert(bPatchI, bp.name());
        }
    }

    // Pass1:
    // Copy names&type of patches (with zero size) from old mesh as far as
    // possible. First patch created gets all boundary faces; all others get
    // zero faces (repatched later on). Exception is coupled patches which
    // keep their size.

    List<polyPatch*> newPatchPtrList(nNewPatches);

    label meshFaceI = newMesh.nInternalFaces();

    // First patch gets all non-coupled faces
    label facesToBeDone = newMesh.nFaces() - newMesh.nInternalFaces();

    forAll(patches_, bPatchI)
    {
        const boundaryPatch& bp = patches_[bPatchI];

        label newPatchI = nameToIndex[bp.name()];

        // Find corresponding patch in polyMesh
        label oldPatchI = findPatchID(oldPatches, bp.name());

        if (oldPatchI == -1)
        {
            // Newly created patch. Gets all or zero faces.
            if (debug)
            {
                Pout<< "patchify : Creating new polyPatch:" << bp.name()
                    << " type:" << bp.physicalType() << endl;
            }

            newPatchPtrList[newPatchI] = polyPatch::New
            (
                bp.physicalType(),
                bp.name(),
                facesToBeDone,
                meshFaceI,
                newPatchI,
                newMesh.boundaryMesh()
            ).ptr();

            meshFaceI += facesToBeDone;

            // first patch gets all boundary faces; all others get 0.
            facesToBeDone = 0;
        }
        else
        {
            // Existing patch. Gets all or zero faces.
            const polyPatch& oldPatch = oldPatches[oldPatchI];

            if (debug)
            {
                Pout<< "patchify : Cloning existing polyPatch:"
                    << oldPatch.name() << endl;
            }

            newPatchPtrList[newPatchI] = oldPatch.clone
            (
                newMesh.boundaryMesh(),
                newPatchI,
                facesToBeDone,
                meshFaceI
            ).ptr();

            meshFaceI += facesToBeDone;

            // first patch gets all boundary faces; all others get 0.
            facesToBeDone = 0;
        }
    }


    if (debug)
    {
        Pout<< "Patchify : new polyPatch list:" << endl;

        forAll(newPatchPtrList, patchI)
        {
            const polyPatch& newPatch = *newPatchPtrList[patchI];

            if (debug)
            {
                Pout<< "polyPatch:" << newPatch.name() << endl
                    << "    type :" << newPatch.typeName << endl
                    << "    size :" << newPatch.size() << endl
                    << "    start:" << newPatch.start() << endl
                    << "    index:" << patchI << endl;
            }
        }
    }

    // Actually add new list of patches
    repatchPolyTopoChanger polyMeshRepatcher(newMesh);
    polyMeshRepatcher.changePatches(newPatchPtrList);


    // Pass2:
    // Change patch type for face

    if (newPatchPtrList.size())
    {
        List<DynamicList<label> > patchFaces(nNewPatches);

        // Give reasonable estimate for size of patches
        label nAvgFaces =
            (newMesh.nFaces() - newMesh.nInternalFaces())
          / nNewPatches;

        forAll(patchFaces, newPatchI)
        {
            patchFaces[newPatchI].setCapacity(nAvgFaces);
        }

        //
        // Sort faces acc. to new patch index. Can loop over all old patches
        // since will contain all faces.
        //

        forAll(oldPatches, oldPatchI)
        {
            const polyPatch& patch = oldPatches[oldPatchI];

            forAll(patch, patchFaceI)
            {
                // Put face into region given by nearest boundary face

                label meshFaceI = patch.start() + patchFaceI;

                label bFaceI = meshFaceI - newMesh.nInternalFaces();

                patchFaces[whichPatch(nearest[bFaceI])].append(meshFaceI);
            }
        }

        forAll(patchFaces, newPatchI)
        {
            patchFaces[newPatchI].shrink();
        }


        // Change patch > 0. (since above we put all faces into the zeroth
        // patch)

        for (label newPatchI = 1; newPatchI < patchFaces.size(); newPatchI++)
        {
            const labelList& pFaces = patchFaces[newPatchI];

            forAll(pFaces, pFaceI)
            {
                polyMeshRepatcher.changePatchID(pFaces[pFaceI], newPatchI);
            }
        }

        polyMeshRepatcher.repatch();
    }
}


void Foam::boundaryMesh::setFeatureEdges(const scalar minCos)
{
    edgeToFeature_.setSize(mesh().nEdges());

    edgeToFeature_ = -1;

    // 1. Mark feature edges

    // Storage for edge labels that are features. Trim later.
    featureToEdge_.setSize(mesh().nEdges());

    label featureI = 0;

    if (minCos >= 0.9999)
    {
        // Select everything
        forAll(mesh().edges(), edgeI)
        {
            edgeToFeature_[edgeI] = featureI;
            featureToEdge_[featureI++] = edgeI;
        }
    }
    else
    {
        forAll(mesh().edges(), edgeI)
        {
            const labelList& eFaces = mesh().edgeFaces()[edgeI];

            if (eFaces.size() == 2)
            {
                label face0I = eFaces[0];

                label face1I = eFaces[1];

                ////- Uncomment below code if you want to include patch
                ////  boundaries in feature edges.
                //if (whichPatch(face0I) != whichPatch(face1I))
                //{
                //    edgeToFeature_[edgeI] = featureI;
                //    featureToEdge_[featureI++] = edgeI;
                //}
                //else
                {
                    const vector& n0 = mesh().faceNormals()[face0I];

                    const vector& n1 = mesh().faceNormals()[face1I];

                    float cosAng = n0 & n1;

                    if (cosAng < minCos)
                    {
                        edgeToFeature_[edgeI] = featureI;
                        featureToEdge_[featureI++] = edgeI;
                    }
                }
            }
            else
            {
                //Should not occur: 0 or more than two faces
                edgeToFeature_[edgeI] = featureI;
                featureToEdge_[featureI++] = edgeI;
            }
        }
    }

    // Trim featureToEdge_ to actual number of edges.
    featureToEdge_.setSize(featureI);

    //
    // Compact edges i.e. relabel vertices.
    //

    featureEdges_.setSize(featureI);
    featurePoints_.setSize(mesh().nPoints());

    labelList featToMeshPoint(mesh().nPoints(), -1);

    label featPtI = 0;

    forAll(featureToEdge_, fEdgeI)
    {
        label edgeI = featureToEdge_[fEdgeI];

        const edge& e = mesh().edges()[edgeI];

        label start = featToMeshPoint[e.start()];

        if (start == -1)
        {
            featToMeshPoint[e.start()] = featPtI;

            featurePoints_[featPtI] = mesh().points()[e.start()];

            start = featPtI;

            featPtI++;
        }

        label end = featToMeshPoint[e.end()];

        if (end == -1)
        {
            featToMeshPoint[e.end()] = featPtI;

            featurePoints_[featPtI] = mesh().points()[e.end()];

            end = featPtI;

            featPtI++;
        }

        // Store with renumbered vertices.
        featureEdges_[fEdgeI] = edge(start, end);
    }

    // Compact points
    featurePoints_.setSize(featPtI);


    //
    // 2. Mark endpoints of feature segments. These are points with
    // != 2 feature edges connected.
    // Note: can add geometric constraint here as well that if 2 feature
    // edges the angle between them should be less than xxx.
    //

    boolList isFeaturePoint(mesh().nPoints(), false);

    forAll(featureToEdge_, featI)
    {
        label edgeI = featureToEdge_[featI];

        const edge& e = mesh().edges()[edgeI];

        if (nFeatureEdges(e.start()) != 2)
        {
            isFeaturePoint[e.start()] = true;
        }

        if (nFeatureEdges(e.end()) != 2)
        {
            isFeaturePoint[e.end()] = true;
        }
    }


    //
    // 3: Split feature edges into segments:
    // find point with not 2 feature edges -> start of feature segment
    //

    DynamicList<labelList> segments;


    boolList featVisited(featureToEdge_.size(), false);

    do
    {
        label startFeatI = -1;

        forAll(featVisited, featI)
        {
            if (!featVisited[featI])
            {
                startFeatI = featI;

                break;
            }
        }

        if (startFeatI == -1)
        {
            // No feature lines left.
            break;
        }

        segments.append
        (
            collectSegment
            (
                isFeaturePoint,
                featureToEdge_[startFeatI],
                featVisited
            )
        );
    }
    while (true);


    //
    // Store in *this
    //
    featureSegments_.setSize(segments.size());

    forAll(featureSegments_, segmentI)
    {
        featureSegments_[segmentI] = segments[segmentI];
    }
}


void Foam::boundaryMesh::setExtraEdges(const label edgeI)
{
    labelList minDistance(mesh().nEdges(), -1);

    // All edge labels encountered
    DynamicList<label> visitedEdges;

    // Floodfill from edgeI starting from distance 0. Stop at distance.
    markEdges(8, edgeI, 0, minDistance, visitedEdges);

    // Set edge labels to display
    extraEdges_.transfer(visitedEdges);
}


Foam::label Foam::boundaryMesh::whichPatch(const label faceI) const
{
    forAll(patches_, patchI)
    {
        const boundaryPatch& bp = patches_[patchI];

        if ((faceI >= bp.start()) && (faceI < (bp.start() + bp.size())))
        {
            return patchI;
        }
    }

    FatalErrorIn("boundaryMesh::whichPatch(const label)")
        << "Cannot find face " << faceI << " in list of boundaryPatches "
        << patches_
        << abort(FatalError);

    return -1;
}


Foam::label Foam::boundaryMesh::findPatchID(const word& patchName) const
{
    forAll(patches_, patchI)
    {
        if (patches_[patchI].name() == patchName)
        {
            return patchI;
        }
    }

    return -1;
}


void Foam::boundaryMesh::addPatch(const word& patchName)
{
    patches_.setSize(patches_.size() + 1);

    // Add empty patch at end of patch list.

    label patchI = patches_.size()-1;

    boundaryPatch* bpPtr = new boundaryPatch
    (
        patchName,
        patchI,
        0,
        mesh().size(),
        "empty"
    );

    patches_.set(patchI, bpPtr);

    if (debug)
    {
        Pout<< "addPatch : patches now:" << endl;

        forAll(patches_, patchI)
        {
            const boundaryPatch& bp = patches_[patchI];

            Pout<< "    name  : " << bp.name() << endl
                << "    size  : " << bp.size() << endl
                << "    start : " << bp.start() << endl
                << "    type  : " << bp.physicalType() << endl
                << endl;
        }
    }
}


void Foam::boundaryMesh::deletePatch(const word& patchName)
{
    label delPatchI = findPatchID(patchName);

    if (delPatchI == -1)
    {
        FatalErrorIn("boundaryMesh::deletePatch(const word&")
            << "Can't find patch named " << patchName
            << abort(FatalError);
    }

    if (patches_[delPatchI].size())
    {
        FatalErrorIn("boundaryMesh::deletePatch(const word&")
            << "Trying to delete non-empty patch " << patchName
            << endl << "Current size:" << patches_[delPatchI].size()
            << abort(FatalError);
    }

    PtrList<boundaryPatch> newPatches(patches_.size() - 1);

    for (label patchI = 0; patchI < delPatchI; patchI++)
    {
        newPatches.set(patchI, patches_[patchI].clone());
    }

    // Move patches down, starting from delPatchI.

    for (label patchI = delPatchI + 1; patchI < patches_.size(); patchI++)
    {
        newPatches.set(patchI - 1, patches_[patchI].clone());
    }

    patches_.clear();

    patches_ = newPatches;

    if (debug)
    {
        Pout<< "deletePatch : patches now:" << endl;

        forAll(patches_, patchI)
        {
            const boundaryPatch& bp = patches_[patchI];

            Pout<< "    name  : " << bp.name() << endl
                << "    size  : " << bp.size() << endl
                << "    start : " << bp.start() << endl
                << "    type  : " << bp.physicalType() << endl
                << endl;
        }
    }
}


void Foam::boundaryMesh::changePatchType
(
    const word& patchName,
    const word& patchType
)
{
    label changeI = findPatchID(patchName);

    if (changeI == -1)
    {
        FatalErrorIn("boundaryMesh::changePatchType(const word&, const word&)")
            << "Can't find patch named " << patchName
            << abort(FatalError);
    }


    // Cause we can't reassign to individual PtrList elems ;-(
    // work on copy


    PtrList<boundaryPatch> newPatches(patches_.size());

    forAll(patches_, patchI)
    {
        if (patchI == changeI)
        {
            // Create copy but for type
            const boundaryPatch& oldBp = patches_[patchI];

            boundaryPatch* bpPtr = new boundaryPatch
            (
                oldBp.name(),
                oldBp.index(),
                oldBp.size(),
                oldBp.start(),
                patchType
            );

            newPatches.set(patchI, bpPtr);
        }
        else
        {
            // Create copy
            newPatches.set(patchI, patches_[patchI].clone());
        }
    }

    patches_ = newPatches;
}


void Foam::boundaryMesh::changeFaces
(
    const labelList& patchIDs,
    labelList& oldToNew
)
{
    if (patchIDs.size() != mesh().size())
    {
        FatalErrorIn("boundaryMesh::changeFaces(const labelList& patchIDs)")
            << "List of patchIDs not equal to number of faces." << endl
            << "PatchIDs size:" << patchIDs.size()
            << " nFaces::" << mesh().size()
            << abort(FatalError);
    }

    // Count number of faces for each patch

    labelList nFaces(patches_.size(), 0);

    forAll(patchIDs, faceI)
    {
        label patchID = patchIDs[faceI];

        if (patchID < 0 || patchID >= patches_.size())
        {
            FatalErrorIn("boundaryMesh::changeFaces(const labelList&)")
                << "PatchID " << patchID << " out of range"
                << abort(FatalError);
        }
        nFaces[patchID]++;
    }


    // Determine position in faces_ for each patch

    labelList startFace(patches_.size());

    startFace[0] = 0;

    for (label patchI = 1; patchI < patches_.size(); patchI++)
    {
        startFace[patchI] = startFace[patchI-1] + nFaces[patchI-1];
    }

    // Update patch info
    PtrList<boundaryPatch> newPatches(patches_.size());

    forAll(patches_, patchI)
    {
        const boundaryPatch& bp = patches_[patchI];

        newPatches.set
        (
            patchI,
            new boundaryPatch
            (
                bp.name(),
                patchI,
                nFaces[patchI],
                startFace[patchI],
                bp.physicalType()
            )
        );
    }
    patches_ = newPatches;

    if (debug)
    {
        Pout<< "changeFaces : patches now:" << endl;

        forAll(patches_, patchI)
        {
            const boundaryPatch& bp = patches_[patchI];

            Pout<< "    name  : " << bp.name() << endl
                << "    size  : " << bp.size() << endl
                << "    start : " << bp.start() << endl
                << "    type  : " << bp.physicalType() << endl
                << endl;
        }
    }


    // Construct face mapping array
    oldToNew.setSize(patchIDs.size());

    forAll(patchIDs, faceI)
    {
        int patchID = patchIDs[faceI];

        oldToNew[faceI] = startFace[patchID]++;
    }

    // Copy faces into correct position and maintain label of original face
    faceList newFaces(mesh().size());

    labelList newMeshFace(mesh().size());

    forAll(oldToNew, faceI)
    {
        newFaces[oldToNew[faceI]] = mesh()[faceI];
        newMeshFace[oldToNew[faceI]] = meshFace_[faceI];
    }

    // Reconstruct 'mesh' from new faces and (copy of) existing points.
    bMesh* newMeshPtr_ = new bMesh(newFaces, mesh().points());

    // Reset meshFace_ to new ordering.
    meshFace_.transfer(newMeshFace);


    // Remove old PrimitivePatch on meshPtr_.
    clearOut();

    // And insert new 'mesh'.
    meshPtr_ = newMeshPtr_;
}


Foam::label Foam::boundaryMesh::getNTris(const label faceI) const
{
    const face& f = mesh()[faceI];

    return f.nTriangles(mesh().points());
}


Foam::label Foam::boundaryMesh::getNTris
(
    const label startFaceI,
    const label nFaces,
    labelList& nTris
) const
{
    label totalNTris = 0;

    nTris.setSize(nFaces);

    for (label i = 0; i < nFaces; i++)
    {
        label faceNTris = getNTris(startFaceI + i);

        nTris[i] = faceNTris;

        totalNTris += faceNTris;
    }
    return totalNTris;
}


// Simple triangulation of face subset. Stores vertices in tris[] as three
// consecutive vertices per triangle.
void Foam::boundaryMesh::triangulate
(
    const label startFaceI,
    const label nFaces,
    const label totalNTris,
    labelList& triVerts
) const
{
    // Triangulate faces.
    triVerts.setSize(3*totalNTris);

    label vertI = 0;

    for (label i = 0; i < nFaces; i++)
    {
        label faceI = startFaceI + i;

        const face& f = mesh()[faceI];

        // Have face triangulate itself (results in faceList)
        faceList triFaces(f.nTriangles(mesh().points()));

        label nTri = 0;

        f.triangles(mesh().points(), nTri, triFaces);

        // Copy into triVerts

        forAll(triFaces, triFaceI)
        {
            const face& triF = triFaces[triFaceI];

            triVerts[vertI++] = triF[0];
            triVerts[vertI++] = triF[1];
            triVerts[vertI++] = triF[2];
        }
    }
}


// Number of local points in subset.
Foam::label Foam::boundaryMesh::getNPoints
(
    const label startFaceI,
    const label nFaces
) const
{
    SubList<face> patchFaces(mesh(), nFaces, startFaceI);

    primitivePatch patch(patchFaces, mesh().points());

    return patch.nPoints();
}


// Triangulation of face subset in local coords.
void Foam::boundaryMesh::triangulateLocal
(
    const label startFaceI,
    const label nFaces,
    const label totalNTris,
    labelList& triVerts,
    labelList& localToGlobal
) const
{
    SubList<face> patchFaces(mesh(), nFaces, startFaceI);

    primitivePatch patch(patchFaces, mesh().points());

    // Map from local to mesh().points() addressing
    localToGlobal = patch.meshPoints();

    // Triangulate patch faces.
    triVerts.setSize(3*totalNTris);

    label vertI = 0;

    for (label i = 0; i < nFaces; i++)
    {
        // Local face
        const face& f = patch.localFaces()[i];

        // Have face triangulate itself (results in faceList)
        faceList triFaces(f.nTriangles(patch.localPoints()));

        label nTri = 0;

        f.triangles(patch.localPoints(), nTri, triFaces);

        // Copy into triVerts

        forAll(triFaces, triFaceI)
        {
            const face& triF = triFaces[triFaceI];

            triVerts[vertI++] = triF[0];
            triVerts[vertI++] = triF[1];
            triVerts[vertI++] = triF[2];
        }
    }
}


void Foam::boundaryMesh::markFaces
(
    const labelList& protectedEdges,
    const label seedFaceI,
    boolList& visited
) const
{
    boolList protectedEdge(mesh().nEdges(), false);

    forAll(protectedEdges, i)
    {
        protectedEdge[protectedEdges[i]] = true;
    }


    // Initialize zone for all faces to -1
    labelList currentZone(mesh().size(), -1);

    // Mark with 0 all faces reachable from seedFaceI
    markZone(protectedEdge, seedFaceI, 0, currentZone);

    // Set in visited all reached ones.
    visited.setSize(mesh().size());

    forAll(currentZone, faceI)
    {
        if (currentZone[faceI] == 0)
        {
            visited[faceI] = true;
        }
        else
        {
            visited[faceI] = false;
        }
    }
}


// ************************************************************************* //