isoSurface.C

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/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
     \\/     M anipulation  | Copyright (C) 2015 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 "isoSurface.H"
#include "fvMesh.H"
#include "mergePoints.H"
#include "addToRunTimeSelectionTable.H"
#include "slicedVolFields.H"
#include "volFields.H"
#include "surfaceFields.H"
#include "OFstream.H"
#include "meshTools.H"
#include "triSurfaceSearch.H"
#include "surfaceIntersection.H"
#include "intersectedSurface.H"
#include "searchableBox.H"
#include "triSurfaceMesh.H"
#include "triPoints.H"
 
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
namespace Foam
{
defineTypeNameAndDebug(isoSurface, 0);
 
// Helper class for slicing triangles
class storeOp
{
public:
    DynamicList<triPoints>& tris_;
 
    inline storeOp(DynamicList<triPoints>& tris)
    :
        tris_(tris)
    {}
 
    inline void operator()(const triPoints& tri)
    {
        tris_.append(tri);
    }
};
 
}
 
 
// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
bool Foam::isoSurface::noTransform(const tensor& tt) const
{
    return
        (mag(tt.xx()-1) < mergeDistance_)
     && (mag(tt.yy()-1) < mergeDistance_)
     && (mag(tt.zz()-1) < mergeDistance_)
     && (mag(tt.xy()) < mergeDistance_)
     && (mag(tt.xz()) < mergeDistance_)
     && (mag(tt.yx()) < mergeDistance_)
     && (mag(tt.yz()) < mergeDistance_)
     && (mag(tt.zx()) < mergeDistance_)
     && (mag(tt.zy()) < mergeDistance_);
}
 
 
// Calculates per face whether couple is collocated.
bool Foam::isoSurface::collocatedPatch(const polyPatch& pp)
{
    const coupledPolyPatch& cpp = refCast<const coupledPolyPatch>(pp);
    return cpp.parallel() && !cpp.separated();
}
 
 
// Calculates per face whether couple is collocated.
Foam::PackedBoolList Foam::isoSurface::collocatedFaces
(
    const coupledPolyPatch& pp
) const
{
    // Initialise to false
    PackedBoolList collocated(pp.size());
 
    if (isA<processorPolyPatch>(pp))
    {
        if (collocatedPatch(pp))
        {
            forAll(pp, i)
            {
                collocated[i] = 1u;
            }
        }
    }
    else if (isA<cyclicPolyPatch>(pp))
    {
        if (collocatedPatch(pp))
        {
            forAll(pp, i)
            {
                collocated[i] = 1u;
            }
        }
    }
    else
    {
        FatalErrorInFunction
            << "Unhandled coupledPolyPatch type " << pp.type()
            << abort(FatalError);
    }
    return collocated;
}
 
 
void Foam::isoSurface::syncUnseparatedPoints
(
    pointField& pointValues,
    const point& nullValue
) const
{
    // Until syncPointList handles separated coupled patches with multiple
    // transforms do our own synchronisation of non-separated patches only
    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
 
    if (Pstream::parRun())
    {
        // Send
        forAll(patches, patchI)
        {
            if
            (
                isA<processorPolyPatch>(patches[patchI])
             && patches[patchI].nPoints() > 0
             && collocatedPatch(patches[patchI])
            )
            {
                const processorPolyPatch& pp =
                    refCast<const processorPolyPatch>(patches[patchI]);
 
                const labelList& meshPts = pp.meshPoints();
                const labelList& nbrPts = pp.neighbPoints();
 
                pointField patchInfo(meshPts.size());
 
                forAll(nbrPts, pointI)
                {
                    label nbrPointI = nbrPts[pointI];
                    patchInfo[nbrPointI] = pointValues[meshPts[pointI]];
                }
 
                OPstream toNbr(Pstream::blocking, pp.neighbProcNo());
                toNbr << patchInfo;
            }
        }
 
        // Receive and combine.
 
        forAll(patches, patchI)
        {
            if
            (
                isA<processorPolyPatch>(patches[patchI])
             && patches[patchI].nPoints() > 0
             && collocatedPatch(patches[patchI])
            )
            {
                const processorPolyPatch& pp =
                    refCast<const processorPolyPatch>(patches[patchI]);
 
                pointField nbrPatchInfo(pp.nPoints());
                {
                    // We do not know the number of points on the other side
                    // so cannot use Pstream::read.
                    IPstream fromNbr(Pstream::blocking, pp.neighbProcNo());
                    fromNbr >> nbrPatchInfo;
                }
 
                const labelList& meshPts = pp.meshPoints();
 
                forAll(meshPts, pointI)
                {
                    label meshPointI = meshPts[pointI];
                    minEqOp<point>()
                    (
                        pointValues[meshPointI],
                        nbrPatchInfo[pointI]
                    );
                }
            }
        }
    }
 
    // Do the cyclics.
    forAll(patches, patchI)
    {
        if (isA<cyclicPolyPatch>(patches[patchI]))
        {
            const cyclicPolyPatch& cycPatch =
                refCast<const cyclicPolyPatch>(patches[patchI]);
 
            if (cycPatch.owner() && collocatedPatch(cycPatch))
            {
                // Owner does all.
 
                const edgeList& coupledPoints = cycPatch.coupledPoints();
                const labelList& meshPts = cycPatch.meshPoints();
                const cyclicPolyPatch& nbrPatch = cycPatch.neighbPatch();
                const labelList& nbrMeshPoints = nbrPatch.meshPoints();
 
                pointField half0Values(coupledPoints.size());
                pointField half1Values(coupledPoints.size());
 
                forAll(coupledPoints, i)
                {
                    const edge& e = coupledPoints[i];
                    half0Values[i] = pointValues[meshPts[e[0]]];
                    half1Values[i] = pointValues[nbrMeshPoints[e[1]]];
                }
 
                forAll(coupledPoints, i)
                {
                    const edge& e = coupledPoints[i];
                    label p0 = meshPts[e[0]];
                    label p1 = nbrMeshPoints[e[1]];
 
                    minEqOp<point>()(pointValues[p0], half1Values[i]);
                    minEqOp<point>()(pointValues[p1], half0Values[i]);
                }
            }
        }
    }
 
    // Synchronize multiple shared points.
    const globalMeshData& pd = mesh_.globalData();
 
    if (pd.nGlobalPoints() > 0)
    {
        // Values on shared points.
        pointField sharedPts(pd.nGlobalPoints(), nullValue);
 
        forAll(pd.sharedPointLabels(), i)
        {
            label meshPointI = pd.sharedPointLabels()[i];
            // Fill my entries in the shared points
            sharedPts[pd.sharedPointAddr()[i]] = pointValues[meshPointI];
        }
 
        // Combine on master.
        Pstream::listCombineGather(sharedPts, minEqOp<point>());
        Pstream::listCombineScatter(sharedPts);
 
        // Now we will all have the same information. Merge it back with
        // my local information.
        forAll(pd.sharedPointLabels(), i)
        {
            label meshPointI = pd.sharedPointLabels()[i];
            pointValues[meshPointI] = sharedPts[pd.sharedPointAddr()[i]];
        }
    }
}
 
 
Foam::scalar Foam::isoSurface::isoFraction
(
    const scalar s0,
    const scalar s1
) const
{
    scalar d = s1-s0;
 
    if (mag(d) > VSMALL)
    {
        return (iso_-s0)/d;
    }
    else
    {
        return -1.0;
    }
}
 
 
bool Foam::isoSurface::isEdgeOfFaceCut
(
    const scalarField& pVals,
    const face& f,
    const bool ownLower,
    const bool neiLower
) const
{
    forAll(f, fp)
    {
        bool fpLower = (pVals[f[fp]] < iso_);
        if
        (
            (fpLower != ownLower)
         || (fpLower != neiLower)
         || (fpLower != (pVals[f[f.fcIndex(fp)]] < iso_))
        )
        {
            return true;
        }
    }
    return false;
}
 
 
// Get neighbour value and position.
void Foam::isoSurface::getNeighbour
(
    const labelList& boundaryRegion,
    const volVectorField& meshC,
    const volScalarField& cVals,
    const label cellI,
    const label faceI,
    scalar& nbrValue,
    point& nbrPoint
) const
{
    const labelList& own = mesh_.faceOwner();
    const labelList& nei = mesh_.faceNeighbour();
 
    if (mesh_.isInternalFace(faceI))
    {
        label nbr = (own[faceI] == cellI ? nei[faceI] : own[faceI]);
        nbrValue = cVals[nbr];
        nbrPoint = meshC[nbr];
    }
    else
    {
        label bFaceI = faceI-mesh_.nInternalFaces();
        label patchI = boundaryRegion[bFaceI];
        const polyPatch& pp = mesh_.boundaryMesh()[patchI];
        label patchFaceI = faceI-pp.start();
 
        nbrValue = cVals.boundaryField()[patchI][patchFaceI];
        nbrPoint = meshC.boundaryField()[patchI][patchFaceI];
    }
}
 
 
// Determine for every face/cell whether it (possibly) generates triangles.
void Foam::isoSurface::calcCutTypes
(
    const labelList& boundaryRegion,
    const volVectorField& meshC,
    const volScalarField& cVals,
    const scalarField& pVals
)
{
    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
    const labelList& own = mesh_.faceOwner();
    const labelList& nei = mesh_.faceNeighbour();
 
    faceCutType_.setSize(mesh_.nFaces());
    faceCutType_ = NOTCUT;
 
    for (label faceI = 0; faceI < mesh_.nInternalFaces(); faceI++)
    {
        // CC edge.
        bool ownLower = (cVals[own[faceI]] < iso_);
 
        scalar nbrValue;
        point nbrPoint;
        getNeighbour
        (
            boundaryRegion,
            meshC,
            cVals,
            own[faceI],
            faceI,
            nbrValue,
            nbrPoint
        );
 
        bool neiLower = (nbrValue < iso_);
 
        if (ownLower != neiLower)
        {
            faceCutType_[faceI] = CUT;
        }
        else
        {
            // See if any mesh edge is cut by looping over all the edges of the
            // face.
            const face f = mesh_.faces()[faceI];
 
            if (isEdgeOfFaceCut(pVals, f, ownLower, neiLower))
            {
                faceCutType_[faceI] = CUT;
            }
        }
    }
 
    forAll(patches, patchI)
    {
        const polyPatch& pp = patches[patchI];
 
        label faceI = pp.start();
 
        forAll(pp, i)
        {
            bool ownLower = (cVals[own[faceI]] < iso_);
 
            scalar nbrValue;
            point nbrPoint;
            getNeighbour
            (
                boundaryRegion,
                meshC,
                cVals,
                own[faceI],
                faceI,
                nbrValue,
                nbrPoint
            );
 
            bool neiLower = (nbrValue < iso_);
 
            if (ownLower != neiLower)
            {
                faceCutType_[faceI] = CUT;
            }
            else
            {
                // Mesh edge.
                const face f = mesh_.faces()[faceI];
 
                if (isEdgeOfFaceCut(pVals, f, ownLower, neiLower))
                {
                    faceCutType_[faceI] = CUT;
                }
            }
 
            faceI++;
        }
    }
 
 
 
    nCutCells_ = 0;
    cellCutType_.setSize(mesh_.nCells());
    cellCutType_ = NOTCUT;
 
    for (label faceI = 0; faceI < mesh_.nInternalFaces(); faceI++)
    {
        if (faceCutType_[faceI] != NOTCUT)
        {
            if (cellCutType_[own[faceI]] == NOTCUT)
            {
                cellCutType_[own[faceI]] = CUT;
                nCutCells_++;
            }
            if (cellCutType_[nei[faceI]] == NOTCUT)
            {
                cellCutType_[nei[faceI]] = CUT;
                nCutCells_++;
            }
        }
    }
    for (label faceI = mesh_.nInternalFaces(); faceI < mesh_.nFaces(); faceI++)
    {
        if (faceCutType_[faceI] != NOTCUT)
        {
            if (cellCutType_[own[faceI]] == NOTCUT)
            {
                cellCutType_[own[faceI]] = CUT;
                nCutCells_++;
            }
        }
    }
 
    if (debug)
    {
        Pout<< "isoSurface : detected " << nCutCells_
            << " candidate cut cells (out of " << mesh_.nCells()
            << ")." << endl;
    }
}
 
 
// Caculate centre of surface.
Foam::point Foam::isoSurface::calcCentre(const triSurface& s)
{
    vector sum = vector::zero;
 
    forAll(s, i)
    {
        sum += s[i].centre(s.points());
    }
    return sum/s.size();
}
 
 
// Determine per cell centre whether all the intersections get collapsed
// to a single point
void Foam::isoSurface::calcSnappedCc
(
    const labelList& boundaryRegion,
    const volVectorField& meshC,
    const volScalarField& cVals,
    const scalarField& pVals,
 
    DynamicList<point>& snappedPoints,
    labelList& snappedCc
) const
{
    const pointField& pts = mesh_.points();
    const pointField& cc = mesh_.cellCentres();
 
    snappedCc.setSize(mesh_.nCells());
    snappedCc = -1;
 
    // Work arrays
    DynamicList<point, 64> localTriPoints(64);
 
    forAll(mesh_.cells(), cellI)
    {
        if (cellCutType_[cellI] == CUT)
        {
            scalar cVal = cVals[cellI];
 
            const cell& cFaces = mesh_.cells()[cellI];
 
            localTriPoints.clear();
            label nOther = 0;
            point otherPointSum = vector::zero;
 
            // Create points for all intersections close to cell centre
            // (i.e. from pyramid edges)
 
            forAll(cFaces, cFaceI)
            {
                label faceI = cFaces[cFaceI];
 
                scalar nbrValue;
                point nbrPoint;
                getNeighbour
                (
                    boundaryRegion,
                    meshC,
                    cVals,
                    cellI,
                    faceI,
                    nbrValue,
                    nbrPoint
                );
 
                // Calculate intersection points of edges to cell centre
                FixedList<scalar, 3> s;
                FixedList<point, 3> pt;
 
                // From cc to neighbour cc.
                s[2] = isoFraction(cVal, nbrValue);
                pt[2] = (1.0-s[2])*cc[cellI] + s[2]*nbrPoint;
 
                const face& f = mesh_.faces()[cFaces[cFaceI]];
 
                forAll(f, fp)
                {
                    // From cc to fp
                    label p0 = f[fp];
                    s[0] = isoFraction(cVal, pVals[p0]);
                    pt[0] = (1.0-s[0])*cc[cellI] + s[0]*pts[p0];
 
                    // From cc to fp+1
                    label p1 = f[f.fcIndex(fp)];
                    s[1] = isoFraction(cVal, pVals[p1]);
                    pt[1] = (1.0-s[1])*cc[cellI] + s[1]*pts[p1];
 
                    if
                    (
                        (s[0] >= 0.0 && s[0] <= 0.5)
                     && (s[1] >= 0.0 && s[1] <= 0.5)
                     && (s[2] >= 0.0 && s[2] <= 0.5)
                    )
                    {
                        localTriPoints.append(pt[0]);
                        localTriPoints.append(pt[1]);
                        localTriPoints.append(pt[2]);
                    }
                    else
                    {
                        // Get average of all other points
                        forAll(s, i)
                        {
                            if (s[i] >= 0.0 && s[i] <= 0.5)
                            {
                                otherPointSum += pt[i];
                                nOther++;
                            }
                        }
                    }
                }
            }
 
            if (localTriPoints.size() == 0)
            {
                // No complete triangles. Get average of all intersection
                // points.
                if (nOther > 0)
                {
                    snappedCc[cellI] = snappedPoints.size();
                    snappedPoints.append(otherPointSum/nOther);
 
                    //Pout<< "    point:" << pointI
                    //    << " replacing coord:" << mesh_.points()[pointI]
                    //    << " by average:" << collapsedPoint[pointI] << endl;
                }
            }
            else if (localTriPoints.size() == 3)
            {
                // Single triangle. No need for any analysis. Average points.
                pointField points;
                points.transfer(localTriPoints);
                snappedCc[cellI] = snappedPoints.size();
                snappedPoints.append(sum(points)/points.size());
 
                //Pout<< "    point:" << pointI
                //    << " replacing coord:" << mesh_.points()[pointI]
                //    << " by average:" << collapsedPoint[pointI] << endl;
            }
            else
            {
                // Convert points into triSurface.
 
                // Merge points and compact out non-valid triangles
                labelList triMap;               // merged to unmerged triangle
                labelList triPointReverseMap;   // unmerged to merged point
                triSurface surf
                (
                    stitchTriPoints
                    (
                        false,              // do not check for duplicate tris
                        localTriPoints,
                        triPointReverseMap,
                        triMap
                    )
                );
 
                labelList faceZone;
                label nZones = surf.markZones
                (
                    boolList(surf.nEdges(), false),
                    faceZone
                );
 
                if (nZones == 1)
                {
                    snappedCc[cellI] = snappedPoints.size();
                    snappedPoints.append(calcCentre(surf));
                    //Pout<< "    point:" << pointI << " nZones:" << nZones
                    //    << " replacing coord:" << mesh_.points()[pointI]
                    //    << " by average:" << collapsedPoint[pointI] << endl;
                }
            }
        }
    }
}
 
 
// Determine per meshpoint whether all the intersections get collapsed
// to a single point
void Foam::isoSurface::calcSnappedPoint
(
    const PackedBoolList& isBoundaryPoint,
    const labelList& boundaryRegion,
    const volVectorField& meshC,
    const volScalarField& cVals,
    const scalarField& pVals,
 
    DynamicList<point>& snappedPoints,
    labelList& snappedPoint
) const
{
    const pointField& pts = mesh_.points();
    const pointField& cc = mesh_.cellCentres();
 
    pointField collapsedPoint(mesh_.nPoints(), point::max);
 
 
    // Work arrays
    DynamicList<point, 64> localTriPoints(100);
 
    forAll(mesh_.pointFaces(), pointI)
    {
        if (isBoundaryPoint.get(pointI) == 1)
        {
            continue;
        }
 
        const labelList& pFaces = mesh_.pointFaces()[pointI];
 
        bool anyCut = false;
 
        forAll(pFaces, i)
        {
            label faceI = pFaces[i];
 
            if (faceCutType_[faceI] == CUT)
            {
                anyCut = true;
                break;
            }
        }
 
        if (!anyCut)
        {
            continue;
        }
 
 
        localTriPoints.clear();
        label nOther = 0;
        point otherPointSum = vector::zero;
 
        forAll(pFaces, pFaceI)
        {
            // Create points for all intersections close to point
            // (i.e. from pyramid edges)
 
            label faceI = pFaces[pFaceI];
            const face& f = mesh_.faces()[faceI];
            label own = mesh_.faceOwner()[faceI];
 
            // Get neighbour value
            scalar nbrValue;
            point nbrPoint;
            getNeighbour
            (
                boundaryRegion,
                meshC,
                cVals,
                own,
                faceI,
                nbrValue,
                nbrPoint
            );
 
            // Calculate intersection points of edges emanating from point
            FixedList<scalar, 4> s;
            FixedList<point, 4> pt;
 
            label fp = findIndex(f, pointI);
            s[0] = isoFraction(pVals[pointI], cVals[own]);
            pt[0] = (1.0-s[0])*pts[pointI] + s[0]*cc[own];
 
            s[1] = isoFraction(pVals[pointI], nbrValue);
            pt[1] = (1.0-s[1])*pts[pointI] + s[1]*nbrPoint;
 
            label nextPointI = f[f.fcIndex(fp)];
            s[2] = isoFraction(pVals[pointI], pVals[nextPointI]);
            pt[2] = (1.0-s[2])*pts[pointI] + s[2]*pts[nextPointI];
 
            label prevPointI = f[f.rcIndex(fp)];
            s[3] = isoFraction(pVals[pointI], pVals[prevPointI]);
            pt[3] = (1.0-s[3])*pts[pointI] + s[3]*pts[prevPointI];
 
            if
            (
                (s[0] >= 0.0 && s[0] <= 0.5)
             && (s[1] >= 0.0 && s[1] <= 0.5)
             && (s[2] >= 0.0 && s[2] <= 0.5)
            )
            {
                localTriPoints.append(pt[0]);
                localTriPoints.append(pt[1]);
                localTriPoints.append(pt[2]);
            }
            if
            (
                (s[0] >= 0.0 && s[0] <= 0.5)
             && (s[1] >= 0.0 && s[1] <= 0.5)
             && (s[3] >= 0.0 && s[3] <= 0.5)
            )
            {
                localTriPoints.append(pt[3]);
                localTriPoints.append(pt[0]);
                localTriPoints.append(pt[1]);
            }
 
            // Get average of points as fallback
            forAll(s, i)
            {
                if (s[i] >= 0.0 && s[i] <= 0.5)
                {
                    otherPointSum += pt[i];
                    nOther++;
                }
            }
        }
 
        if (localTriPoints.size() == 0)
        {
            // No complete triangles. Get average of all intersection
            // points.
            if (nOther > 0)
            {
                collapsedPoint[pointI] = otherPointSum/nOther;
            }
        }
        else if (localTriPoints.size() == 3)
        {
            // Single triangle. No need for any analysis. Average points.
            pointField points;
            points.transfer(localTriPoints);
            collapsedPoint[pointI] = sum(points)/points.size();
        }
        else
        {
            // Convert points into triSurface.
 
            // Merge points and compact out non-valid triangles
            labelList triMap;               // merged to unmerged triangle
            labelList triPointReverseMap;   // unmerged to merged point
            triSurface surf
            (
                stitchTriPoints
                (
                    false,                  // do not check for duplicate tris
                    localTriPoints,
                    triPointReverseMap,
                    triMap
                )
            );
 
            labelList faceZone;
            label nZones = surf.markZones
            (
                boolList(surf.nEdges(), false),
                faceZone
            );
 
            if (nZones == 1)
            {
                collapsedPoint[pointI] = calcCentre(surf);
            }
        }
    }
 
 
    // Synchronise snap location
    syncUnseparatedPoints(collapsedPoint, point::max);
 
 
    snappedPoint.setSize(mesh_.nPoints());
    snappedPoint = -1;
 
    forAll(collapsedPoint, pointI)
    {
        if (collapsedPoint[pointI] != point::max)
        {
            snappedPoint[pointI] = snappedPoints.size();
            snappedPoints.append(collapsedPoint[pointI]);
        }
    }
}
 
 
Foam::triSurface Foam::isoSurface::stitchTriPoints
(
    const bool checkDuplicates,
    const List<point>& triPoints,
    labelList& triPointReverseMap,  // unmerged to merged point
    labelList& triMap               // merged to unmerged triangle
) const
{
    label nTris = triPoints.size()/3;
 
    if ((triPoints.size() % 3) != 0)
    {
        FatalErrorInFunction
            << "Problem: number of points " << triPoints.size()
            << " not a multiple of 3." << abort(FatalError);
    }
 
    pointField newPoints;
    mergePoints
    (
        triPoints,
        mergeDistance_,
        false,
        triPointReverseMap,
        newPoints
    );
 
    // Check that enough merged.
    if (debug)
    {
        pointField newNewPoints;
        labelList oldToNew;
        bool hasMerged = mergePoints
        (
            newPoints,
            mergeDistance_,
            true,
            oldToNew,
            newNewPoints
        );
 
        if (hasMerged)
        {
            FatalErrorInFunction
                << "Merged points contain duplicates"
                << " when merging with distance " << mergeDistance_ << endl
                << "merged:" << newPoints.size() << " re-merged:"
                << newNewPoints.size()
                << abort(FatalError);
        }
    }
 
 
    List<labelledTri> tris;
    {
        DynamicList<labelledTri> dynTris(nTris);
        label rawPointI = 0;
        DynamicList<label> newToOldTri(nTris);
 
        for (label oldTriI = 0; oldTriI < nTris; oldTriI++)
        {
            labelledTri tri
            (
                triPointReverseMap[rawPointI],
                triPointReverseMap[rawPointI+1],
                triPointReverseMap[rawPointI+2],
                0
            );
            rawPointI += 3;
 
            if ((tri[0] != tri[1]) && (tri[0] != tri[2]) && (tri[1] != tri[2]))
            {
                newToOldTri.append(oldTriI);
                dynTris.append(tri);
            }
        }
 
        triMap.transfer(newToOldTri);
        tris.transfer(dynTris);
    }
 
 
 
    // Determine 'flat hole' situation (see RMT paper).
    // Two unconnected triangles get connected because (some of) the edges
    // separating them get collapsed. Below only checks for duplicate triangles,
    // not non-manifold edge connectivity.
    if (checkDuplicates)
    {
        labelListList pointFaces;
        invertManyToMany(newPoints.size(), tris, pointFaces);
 
        // Filter out duplicates.
        DynamicList<label> newToOldTri(tris.size());
 
        forAll(tris, triI)
        {
            const labelledTri& tri = tris[triI];
            const labelList& pFaces = pointFaces[tri[0]];
 
            // Find the maximum of any duplicates. Maximum since the tris
            // below triI
            // get overwritten so we cannot use them in a comparison.
            label dupTriI = -1;
            forAll(pFaces, i)
            {
                label nbrTriI = pFaces[i];
 
                if (nbrTriI > triI && (tris[nbrTriI] == tri))
                {
                    //Pout<< "Duplicate : " << triI << " verts:" << tri
                    //    << " to " << nbrTriI << " verts:" << tris[nbrTriI]
                    //    << endl;
                    dupTriI = nbrTriI;
                    break;
                }
            }
 
            if (dupTriI == -1)
            {
                // There is no (higher numbered) duplicate triangle
                label newTriI = newToOldTri.size();
                newToOldTri.append(triMap[triI]);
                tris[newTriI] = tris[triI];
            }
        }
 
        triMap.transfer(newToOldTri);
        tris.setSize(triMap.size());
 
        if (debug)
        {
            Pout<< "isoSurface : merged from " << nTris
                << " down to " << tris.size() << " unique triangles." << endl;
        }
 
 
        if (debug)
        {
            triSurface surf(tris, geometricSurfacePatchList(0), newPoints);
 
            forAll(surf, faceI)
            {
                const labelledTri& f = surf[faceI];
                const labelList& fFaces = surf.faceFaces()[faceI];
 
                forAll(fFaces, i)
                {
                    label nbrFaceI = fFaces[i];
 
                    if (nbrFaceI <= faceI)
                    {
                        // lower numbered faces already checked
                        continue;
                    }
 
                    const labelledTri& nbrF = surf[nbrFaceI];
 
                    if (f == nbrF)
                    {
                        FatalErrorInFunction
                            << "Check : "
                            << " triangle " << faceI << " vertices " << f
                            << " fc:" << f.centre(surf.points())
                            << " has the same vertices as triangle " << nbrFaceI
                            << " vertices " << nbrF
                            << " fc:" << nbrF.centre(surf.points())
                            << abort(FatalError);
                    }
                }
            }
        }
    }
 
    return triSurface(tris, geometricSurfacePatchList(0), newPoints, true);
}
 
 
void Foam::isoSurface::trimToPlanes
(
    const PtrList<plane>& planes,
    const triPointRef& tri,
    DynamicList<point>& newTriPoints
)
{
    // Buffer for generated triangles
    DynamicList<triPoints> insideTrisA;
    storeOp insideOpA(insideTrisA);
 
    // Buffer for generated triangles
    DynamicList<triPoints> insideTrisB;
    storeOp insideOpB(insideTrisB);
 
    triPointRef::dummyOp dop;
 
    // Store starting triangle in insideTrisA
    insideOpA(triPoints(tri.a(), tri.b(), tri.c()));
 
 
    bool useA = true;
 
    forAll(planes, faceI)
    {
        const plane& pl = planes[faceI];
 
        if (useA)
        {
            insideOpB.tris_.clear();
            forAll(insideOpA.tris_, i)
            {
                const triPoints& tri = insideOpA.tris_[i];
                triPointRef(tri).sliceWithPlane(pl, insideOpB, dop);
            }
        }
        else
        {
            insideOpA.tris_.clear();
            forAll(insideOpB.tris_, i)
            {
                const triPoints& tri = insideOpB.tris_[i];
                triPointRef(tri).sliceWithPlane(pl, insideOpA, dop);
            }
        }
        useA = !useA;
    }
 
 
    // Transfer
    if (useA)
    {
        forAll(insideOpA.tris_, i)
        {
            const triPoints& tri = insideOpA.tris_[i];
            newTriPoints.append(tri[0]);
            newTriPoints.append(tri[1]);
            newTriPoints.append(tri[2]);
        }
    }
    else
    {
        forAll(insideOpB.tris_, i)
        {
            const triPoints& tri = insideOpB.tris_[i];
            newTriPoints.append(tri[0]);
            newTriPoints.append(tri[1]);
            newTriPoints.append(tri[2]);
        }
    }
}
 
 
void Foam::isoSurface::trimToBox
(
    const treeBoundBox& bb,
    DynamicList<point>& triPoints,
    DynamicList<label>& triMap      // trimmed to original tris
)
{
    if (debug)
    {
        Pout<< "isoSurface : trimming to " << bb << endl;
    }
 
    // Generate inwards pointing planes
    PtrList<plane> planes(6);
    const pointField pts(bb.treeBoundBox::points());
    forAll(treeBoundBox::faces, faceI)
    {
        const face& f = treeBoundBox::faces[faceI];
        const vector& n = treeBoundBox::faceNormals[faceI];
        planes.set(faceI, new plane(pts[f[0]], -n));
    }
 
    label nTris = triPoints.size()/3;
 
    DynamicList<point> newTriPoints(triPoints.size()/16);
    triMap.setCapacity(nTris/16);
 
    label vertI = 0;
    for (label triI = 0; triI < nTris; triI++)
    {
        const point& p0 = triPoints[vertI++];
        const point& p1 = triPoints[vertI++];
        const point& p2 = triPoints[vertI++];
 
        label oldNPoints = newTriPoints.size();
        trimToPlanes
        (
            planes,
            triPointRef(p0, p1, p2),
            newTriPoints
        );
 
        label nCells = (newTriPoints.size()-oldNPoints)/3;
        for (label i = 0; i < nCells; i++)
        {
            triMap.append(triI);
        }
    }
 
    if (debug)
    {
        Pout<< "isoSurface : trimmed from " << nTris
            << " down to " << triMap.size()
            << " triangles." << endl;
    }
 
    triPoints.transfer(newTriPoints);
}
 
 
void Foam::isoSurface::trimToBox
(
    const treeBoundBox& bb,
    DynamicList<point>& triPoints,  // new points
    DynamicList<label>& triMap,     // map from (new) triangle to original
    labelList& triPointMap,         // map from (new) point to original
    labelList& interpolatedPoints,  // labels of newly introduced points
    List<FixedList<label, 3> >& interpolatedOldPoints,// and their interpolation
    List<FixedList<scalar, 3> >& interpolationWeights
)
{
    const List<point> oldTriPoints(triPoints);
 
    // Trim triPoints, return map
    trimToBox(bb, triPoints, triMap);
 
 
    // Find point correspondence:
    // - one-to-one for preserved original points (triPointMap)
    // - interpolation for newly introduced points
    //   (interpolatedOldPoints)
    label sz = oldTriPoints.size()/100;
    DynamicList<label> dynInterpolatedPoints(sz);
    DynamicList<FixedList<label, 3> > dynInterpolatedOldPoints(sz);
    DynamicList<FixedList<scalar, 3> > dynInterpolationWeights(sz);
 
 
    triPointMap.setSize(triPoints.size());
    forAll(triMap, triI)
    {
        label oldTriI = triMap[triI];
 
        // Find point correspondence. Assumes coordinate is bit-copy.
        for (label i = 0; i < 3; i++)
        {
            label pointI = 3*triI+i;
            const point& pt = triPoints[pointI];
 
            // Compare to old-triangle's points
            label matchPointI = -1;
            for (label j = 0; j < 3; j++)
            {
                label oldPointI = 3*oldTriI+j;
                if (pt == oldTriPoints[oldPointI])
                {
                    matchPointI = oldPointI;
                    break;
                }
            }
 
            triPointMap[pointI] = matchPointI;
 
            // If new point: calculate and store interpolation
            if (matchPointI == -1)
            {
                dynInterpolatedPoints.append(pointI);
 
                FixedList<label, 3> oldPoints;
                oldPoints[0] = 3*oldTriI;
                oldPoints[1] = 3*oldTriI+1;
                oldPoints[2] = 3*oldTriI+2;
                dynInterpolatedOldPoints.append(oldPoints);
 
                triPointRef tri(oldTriPoints, oldPoints);
                scalarList bary;
                tri.barycentric(pt, bary);
                FixedList<scalar, 3> weights;
                weights[0] = bary[0];
                weights[1] = bary[1];
                weights[2] = bary[2];
                dynInterpolationWeights.append(weights);
            }
        }
    }
 
    interpolatedPoints.transfer(dynInterpolatedPoints);
    interpolatedOldPoints.transfer(dynInterpolatedOldPoints);
    interpolationWeights.transfer(dynInterpolationWeights);
}
 
 
// Does face use valid vertices?
bool Foam::isoSurface::validTri(const triSurface& surf, const label faceI)
{
    // Simple check on indices ok.
 
    const labelledTri& f = surf[faceI];
 
    if
    (
        (f[0] < 0) || (f[0] >= surf.points().size())
     || (f[1] < 0) || (f[1] >= surf.points().size())
     || (f[2] < 0) || (f[2] >= surf.points().size())
    )
    {
        WarningInFunction
            << "triangle " << faceI << " vertices " << f
            << " uses point indices outside point range 0.."
            << surf.points().size()-1 << endl;
 
        return false;
    }
 
    if ((f[0] == f[1]) || (f[0] == f[2]) || (f[1] == f[2]))
    {
        WarningInFunction
            << "triangle " << faceI
            << " uses non-unique vertices " << f
            << endl;
        return false;
    }
 
    // duplicate triangle check
 
    const labelList& fFaces = surf.faceFaces()[faceI];
 
    // Check if faceNeighbours use same points as this face.
    // Note: discards normal information - sides of baffle are merged.
    forAll(fFaces, i)
    {
        label nbrFaceI = fFaces[i];
 
        if (nbrFaceI <= faceI)
        {
            // lower numbered faces already checked
            continue;
        }
 
        const labelledTri& nbrF = surf[nbrFaceI];
 
        if
        (
            ((f[0] == nbrF[0]) || (f[0] == nbrF[1]) || (f[0] == nbrF[2]))
         && ((f[1] == nbrF[0]) || (f[1] == nbrF[1]) || (f[1] == nbrF[2]))
         && ((f[2] == nbrF[0]) || (f[2] == nbrF[1]) || (f[2] == nbrF[2]))
        )
        {
            WarningInFunction
                << "triangle " << faceI << " vertices " << f
                << " fc:" << f.centre(surf.points())
                << " has the same vertices as triangle " << nbrFaceI
                << " vertices " << nbrF
                << " fc:" << nbrF.centre(surf.points())
                << endl;
 
            return false;
        }
    }
    return true;
}
 
 
Foam::triSurface Foam::isoSurface::subsetMesh
(
    const triSurface& s,
    const labelList& newToOldFaces,
    labelList& oldToNewPoints,
    labelList& newToOldPoints
)
{
    const boolList include
    (
        createWithValues<boolList>
        (
            s.size(),
            false,
            newToOldFaces,
            true
        )
    );
 
    newToOldPoints.setSize(s.points().size());
    oldToNewPoints.setSize(s.points().size());
    oldToNewPoints = -1;
    {
        label pointI = 0;
 
        forAll(include, oldFacei)
        {
            if (include[oldFacei])
            {
                // Renumber labels for triangle
                const labelledTri& tri = s[oldFacei];
 
                forAll(tri, fp)
                {
                    label oldPointI = tri[fp];
 
                    if (oldToNewPoints[oldPointI] == -1)
                    {
                        oldToNewPoints[oldPointI] = pointI;
                        newToOldPoints[pointI++] = oldPointI;
                    }
                }
            }
        }
        newToOldPoints.setSize(pointI);
    }
 
    // Extract points
    pointField newPoints(newToOldPoints.size());
    forAll(newToOldPoints, i)
    {
        newPoints[i] = s.points()[newToOldPoints[i]];
    }
    // Extract faces
    List<labelledTri> newTriangles(newToOldFaces.size());
 
    forAll(newToOldFaces, i)
    {
        // Get old vertex labels
        const labelledTri& tri = s[newToOldFaces[i]];
 
        newTriangles[i][0] = oldToNewPoints[tri[0]];
        newTriangles[i][1] = oldToNewPoints[tri[1]];
        newTriangles[i][2] = oldToNewPoints[tri[2]];
        newTriangles[i].region() = tri.region();
    }
 
    // Reuse storage.
    return triSurface(newTriangles, s.patches(), newPoints, true);
}
 
 
// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
Foam::isoSurface::isoSurface
(
    const volScalarField& cVals,
    const scalarField& pVals,
    const scalar iso,
    const bool regularise,
    const boundBox& bounds,
    const scalar mergeTol
)
:
    mesh_(cVals.mesh()),
    pVals_(pVals),
    iso_(iso),
    regularise_(regularise),
    bounds_(bounds),
    mergeDistance_(mergeTol*mesh_.bounds().mag())
{
    if (debug)
    {
        Pout<< "isoSurface:" << nl
            << "    isoField      : " << cVals.name() << nl
            << "    cell min/max  : "
            << min(cVals.internalField()) << " / "
            << max(cVals.internalField()) << nl
            << "    point min/max : "
            << min(pVals_) << " / "
            << max(pVals_) << nl
            << "    isoValue      : " << iso << nl
            << "    regularise    : " << regularise_ << nl
            << "    mergeTol      : " << mergeTol << nl
            << endl;
    }
 
    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
 
 
    // Rewrite input field
    // ~~~~~~~~~~~~~~~~~~~
    // Rewrite input volScalarField to have interpolated values
    // on separated patches.
 
    cValsPtr_.reset(adaptPatchFields(cVals).ptr());
 
 
    // Construct cell centres field consistent with cVals
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    // Generate field to interpolate. This is identical to the mesh.C()
    // except on separated coupled patches and on empty patches.
 
    slicedVolVectorField meshC
    (
        IOobject
        (
            "C",
            mesh_.pointsInstance(),
            mesh_.meshSubDir,
            mesh_,
            IOobject::NO_READ,
            IOobject::NO_WRITE,
            false
        ),
        mesh_,
        dimLength,
        mesh_.cellCentres(),
        mesh_.faceCentres()
    );
    forAll(patches, patchI)
    {
        const polyPatch& pp = patches[patchI];
 
        // Adapt separated coupled (proc and cyclic) patches
        if (pp.coupled())
        {
            fvPatchVectorField& pfld = const_cast<fvPatchVectorField&>
            (
                meshC.boundaryField()[patchI]
            );
 
            PackedBoolList isCollocated
            (
                collocatedFaces(refCast<const coupledPolyPatch>(pp))
            );
 
            forAll(isCollocated, i)
            {
                if (!isCollocated[i])
                {
                    pfld[i] = mesh_.faceCentres()[pp.start()+i];
                }
            }
        }
        else if (isA<emptyPolyPatch>(pp))
        {
            typedef slicedVolVectorField::GeometricBoundaryField bType;
 
            bType& bfld = const_cast<bType&>(meshC.boundaryField());
 
            // Clear old value. Cannot resize it since is a slice.
            bfld.set(patchI, NULL);
 
            // Set new value we can change
            bfld.set
            (
                patchI,
                new calculatedFvPatchField<vector>
                (
                    mesh_.boundary()[patchI],
                    meshC
                )
            );
 
            // Change to face centres
            bfld[patchI] = pp.patchSlice(mesh_.faceCentres());
        }
    }
 
 
 
    // Pre-calculate patch-per-face to avoid whichPatch call.
    labelList boundaryRegion(mesh_.nFaces()-mesh_.nInternalFaces());
 
    forAll(patches, patchI)
    {
        const polyPatch& pp = patches[patchI];
 
        label faceI = pp.start();
 
        forAll(pp, i)
        {
            boundaryRegion[faceI-mesh_.nInternalFaces()] = patchI;
            faceI++;
        }
    }
 
 
 
    // Determine if any cut through face/cell
    calcCutTypes(boundaryRegion, meshC, cValsPtr_(), pVals_);
 
 
    DynamicList<point> snappedPoints(nCutCells_);
 
    // Per cc -1 or a point inside snappedPoints.
    labelList snappedCc;
    if (regularise_)
    {
        calcSnappedCc
        (
            boundaryRegion,
            meshC,
            cValsPtr_(),
            pVals_,
 
            snappedPoints,
            snappedCc
        );
    }
    else
    {
        snappedCc.setSize(mesh_.nCells());
        snappedCc = -1;
    }
 
 
 
    if (debug)
    {
        Pout<< "isoSurface : shifted " << snappedPoints.size()
            << " cell centres to intersection." << endl;
    }
 
    label nCellSnaps = snappedPoints.size();
 
 
    // Per point -1 or a point inside snappedPoints.
    labelList snappedPoint;
    if (regularise_)
    {
        // Determine if point is on boundary.
        PackedBoolList isBoundaryPoint(mesh_.nPoints());
 
        forAll(patches, patchI)
        {
            // Mark all boundary points that are not physically coupled
            // (so anything but collocated coupled patches)
 
            if (patches[patchI].coupled())
            {
                const coupledPolyPatch& cpp =
                    refCast<const coupledPolyPatch>
                    (
                        patches[patchI]
                    );
 
                PackedBoolList isCollocated(collocatedFaces(cpp));
 
                forAll(isCollocated, i)
                {
                    if (!isCollocated[i])
                    {
                        const face& f = mesh_.faces()[cpp.start()+i];
 
                        forAll(f, fp)
                        {
                            isBoundaryPoint.set(f[fp], 1);
                        }
                    }
                }
            }
            else
            {
                const polyPatch& pp = patches[patchI];
 
                forAll(pp, i)
                {
                    const face& f = mesh_.faces()[pp.start()+i];
 
                    forAll(f, fp)
                    {
                        isBoundaryPoint.set(f[fp], 1);
                    }
                }
            }
        }
 
        calcSnappedPoint
        (
            isBoundaryPoint,
            boundaryRegion,
            meshC,
            cValsPtr_(),
            pVals_,
 
            snappedPoints,
            snappedPoint
        );
    }
    else
    {
        snappedPoint.setSize(mesh_.nPoints());
        snappedPoint = -1;
    }
 
    if (debug)
    {
        Pout<< "isoSurface : shifted " << snappedPoints.size()-nCellSnaps
            << " vertices to intersection." << endl;
    }
 
 
    {
        DynamicList<point> triPoints(3*nCutCells_);
        DynamicList<label> triMeshCells(nCutCells_);
 
        generateTriPoints
        (
            cValsPtr_(),
            pVals_,
 
            meshC,
            mesh_.points(),
 
            snappedPoints,
            snappedCc,
            snappedPoint,
 
            triPoints,      // 3 points of the triangle
            triMeshCells    // per triangle the originating cell
        );
 
        if (debug)
        {
            Pout<< "isoSurface : generated " << triMeshCells.size()
                << " unmerged triangles from " << triPoints.size()
                << " unmerged points." << endl;
        }
 
        label nOldPoints = triPoints.size();
 
        // Trimmed to original triangle
        DynamicList<label> trimTriMap;
        // Trimmed to original point
        labelList trimTriPointMap;
        if (bounds_ != boundBox::greatBox)
        {
            trimToBox
            (
                treeBoundBox(bounds_),
                triPoints,              // new points
                trimTriMap,             // map from (new) triangle to original
                trimTriPointMap,        // map from (new) point to original
                interpolatedPoints_,    // labels of newly introduced points
                interpolatedOldPoints_, // and their interpolation
                interpolationWeights_
            );
            triMeshCells = labelField(triMeshCells, trimTriMap);
        }
 
 
        // Merge points and compact out non-valid triangles
        labelList triMap;           // merged to unmerged triangle
        triSurface::operator=
        (
            stitchTriPoints
            (
                true,               // check for duplicate tris
                triPoints,
                triPointMergeMap_,  // unmerged to merged point
                triMap
            )
        );
 
        if (debug)
        {
            Pout<< "isoSurface : generated " << triMap.size()
                << " merged triangles." << endl;
        }
 
 
        if (bounds_ != boundBox::greatBox)
        {
            // Adjust interpolatedPoints_
            inplaceRenumber(triPointMergeMap_, interpolatedPoints_);
 
            // Adjust triPointMergeMap_
            labelList newTriPointMergeMap(nOldPoints, -1);
            forAll(trimTriPointMap, trimPointI)
            {
                label oldPointI = trimTriPointMap[trimPointI];
                if (oldPointI >= 0)
                {
                    label pointI = triPointMergeMap_[trimPointI];
                    if (pointI >= 0)
                    {
                        newTriPointMergeMap[oldPointI] = pointI;
                    }
                }
            }
            triPointMergeMap_.transfer(newTriPointMergeMap);
        }
 
        meshCells_.setSize(triMap.size());
        forAll(triMap, i)
        {
            meshCells_[i] = triMeshCells[triMap[i]];
        }
    }
 
    if (debug)
    {
        Pout<< "isoSurface : checking " << size()
            << " triangles for validity." << endl;
 
        forAll(*this, triI)
        {
            // Copied from surfaceCheck
            validTri(*this, triI);
        }
 
        fileName stlFile = mesh_.time().path() + ".stl";
        Pout<< "Dumping surface to " << stlFile << endl;
        triSurface::write(stlFile);
    }
}
 
 
// ************************************************************************* //