dynamicRefineFvMesh.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  |
-------------------------------------------------------------------------------
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 "dynamicRefineFvMesh.H"
#include "addToRunTimeSelectionTable.H"
#include "surfaceInterpolate.H"
#include "volFields.H"
#include "polyTopoChange.H"
#include "surfaceFields.H"
#include "syncTools.H"
#include "pointFields.H"
#include "sigFpe.H"
#include "cellSet.H"
 
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
namespace Foam
{
    defineTypeNameAndDebug(dynamicRefineFvMesh, 0);
    addToRunTimeSelectionTable(dynamicFvMesh, dynamicRefineFvMesh, IOobject);
}
 
// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
// the PackedBoolList::count method would probably be faster
// since we are only checking for 'true' anyhow
Foam::label Foam::dynamicRefineFvMesh::count
(
    const PackedBoolList& l,
    const unsigned int val
)
{
    label n = 0;
    forAll(l, i)
    {
        if (l.get(i) == val)
        {
            n++;
        }
 
        // debug also serves to get-around Clang compiler trying to optimsie
        // out this forAll loop under O3 optimisation
        if (debug)
        {
            Info<< "n=" << n << endl;
        }
    }
 
    return n;
}
 
 
void Foam::dynamicRefineFvMesh::calculateProtectedCells
(
    PackedBoolList& unrefineableCell
) const
{
    if (protectedCell_.empty())
    {
        unrefineableCell.clear();
        return;
    }
 
    const labelList& cellLevel = meshCutter_.cellLevel();
 
    unrefineableCell = protectedCell_;
 
    // Get neighbouring cell level
    labelList neiLevel(nFaces()-nInternalFaces());
 
    for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
    {
        neiLevel[faceI-nInternalFaces()] = cellLevel[faceOwner()[faceI]];
    }
    syncTools::swapBoundaryFaceList(*this, neiLevel);
 
 
    while (true)
    {
        // Pick up faces on border of protected cells
        boolList seedFace(nFaces(), false);
 
        forAll(faceNeighbour(), faceI)
        {
            label own = faceOwner()[faceI];
            bool ownProtected = unrefineableCell.get(own);
            label nei = faceNeighbour()[faceI];
            bool neiProtected = unrefineableCell.get(nei);
 
            if (ownProtected && (cellLevel[nei] > cellLevel[own]))
            {
                seedFace[faceI] = true;
            }
            else if (neiProtected && (cellLevel[own] > cellLevel[nei]))
            {
                seedFace[faceI] = true;
            }
        }
        for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
        {
            label own = faceOwner()[faceI];
            bool ownProtected = unrefineableCell.get(own);
            if
            (
                ownProtected
             && (neiLevel[faceI-nInternalFaces()] > cellLevel[own])
            )
            {
                seedFace[faceI] = true;
            }
        }
 
        syncTools::syncFaceList(*this, seedFace, orEqOp<bool>());
 
 
        // Extend unrefineableCell
        bool hasExtended = false;
 
        for (label faceI = 0; faceI < nInternalFaces(); faceI++)
        {
            if (seedFace[faceI])
            {
                label own = faceOwner()[faceI];
                if (unrefineableCell.get(own) == 0)
                {
                    unrefineableCell.set(own, 1);
                    hasExtended = true;
                }
 
                label nei = faceNeighbour()[faceI];
                if (unrefineableCell.get(nei) == 0)
                {
                    unrefineableCell.set(nei, 1);
                    hasExtended = true;
                }
            }
        }
        for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
        {
            if (seedFace[faceI])
            {
                label own = faceOwner()[faceI];
                if (unrefineableCell.get(own) == 0)
                {
                    unrefineableCell.set(own, 1);
                    hasExtended = true;
                }
            }
        }
 
        if (!returnReduce(hasExtended, orOp<bool>()))
        {
            break;
        }
    }
}
 
 
void Foam::dynamicRefineFvMesh::readDict()
{
    dictionary refineDict
    (
        IOdictionary
        (
            IOobject
            (
                "dynamicMeshDict",
                time().constant(),
                *this,
                IOobject::MUST_READ_IF_MODIFIED,
                IOobject::NO_WRITE,
                false
            )
        ).subDict(typeName + "Coeffs")
    );
 
    List<Pair<word> > fluxVelocities = List<Pair<word> >
    (
        refineDict.lookup("correctFluxes")
    );
    // Rework into hashtable.
    correctFluxes_.resize(fluxVelocities.size());
    forAll(fluxVelocities, i)
    {
        correctFluxes_.insert(fluxVelocities[i][0], fluxVelocities[i][1]);
    }
 
    dumpLevel_ = Switch(refineDict.lookup("dumpLevel"));
}
 
 
// Refines cells, maps fields and recalculates (an approximate) flux
Foam::autoPtr<Foam::mapPolyMesh>
Foam::dynamicRefineFvMesh::refine
(
    const labelList& cellsToRefine
)
{
    // Mesh changing engine.
    polyTopoChange meshMod(*this);
 
    // Play refinement commands into mesh changer.
    meshCutter_.setRefinement(cellsToRefine, meshMod);
 
    // Create mesh (with inflation), return map from old to new mesh.
    //autoPtr<mapPolyMesh> map = meshMod.changeMesh(*this, true);
    autoPtr<mapPolyMesh> map = meshMod.changeMesh(*this, false);
 
    Info<< "Refined from "
        << returnReduce(map().nOldCells(), sumOp<label>())
        << " to " << globalData().nTotalCells() << " cells." << endl;
 
    if (debug)
    {
        // Check map.
        for (label faceI = 0; faceI < nInternalFaces(); faceI++)
        {
            label oldFaceI = map().faceMap()[faceI];
 
            if (oldFaceI >= nInternalFaces())
            {
                FatalErrorInFunction
                    << "New internal face:" << faceI
                    << " fc:" << faceCentres()[faceI]
                    << " originates from boundary oldFace:" << oldFaceI
                    << abort(FatalError);
            }
        }
    }
 
//    // Remove the stored tet base points
//    tetBasePtIsPtr_.clear();
//    // Remove the cell tree
//    cellTreePtr_.clear();
 
    // Update fields
    updateMesh(map);
 
 
    // Move mesh
    /*
    pointField newPoints;
    if (map().hasMotionPoints())
    {
        newPoints = map().preMotionPoints();
    }
    else
    {
        newPoints = points();
    }
    movePoints(newPoints);
    */
 
    // Correct the flux for modified/added faces. All the faces which only
    // have been renumbered will already have been handled by the mapping.
    {
        const labelList& faceMap = map().faceMap();
        const labelList& reverseFaceMap = map().reverseFaceMap();
 
        // Storage for any master faces. These will be the original faces
        // on the coarse cell that get split into four (or rather the
        // master face gets modified and three faces get added from the master)
        labelHashSet masterFaces(4*cellsToRefine.size());
 
        forAll(faceMap, faceI)
        {
            label oldFaceI = faceMap[faceI];
 
            if (oldFaceI >= 0)
            {
                label masterFaceI = reverseFaceMap[oldFaceI];
 
                if (masterFaceI < 0)
                {
                    FatalErrorInFunction
                        << "Problem: should not have removed faces"
                        << " when refining."
                        << nl << "face:" << faceI << abort(FatalError);
                }
                else if (masterFaceI != faceI)
                {
                    masterFaces.insert(masterFaceI);
                }
            }
        }
        if (debug)
        {
            Pout<< "Found " << masterFaces.size() << " split faces " << endl;
        }
 
        HashTable<surfaceScalarField*> fluxes
        (
            lookupClass<surfaceScalarField>()
        );
        forAllIter(HashTable<surfaceScalarField*>, fluxes, iter)
        {
            if (!correctFluxes_.found(iter.key()))
            {
                WarningInFunction
                    << "Cannot find surfaceScalarField " << iter.key()
                    << " in user-provided flux mapping table "
                    << correctFluxes_ << endl
                    << "    The flux mapping table is used to recreate the"
                    << " flux on newly created faces." << endl
                    << "    Either add the entry if it is a flux or use ("
                    << iter.key() << " none) to suppress this warning."
                    << endl;
                continue;
            }
 
            const word& UName = correctFluxes_[iter.key()];
 
            if (UName == "none")
            {
                continue;
            }
 
            if (UName == "NaN")
            {
                Pout<< "Setting surfaceScalarField " << iter.key()
                    << " to NaN" << endl;
 
                surfaceScalarField& phi = *iter();
 
                sigFpe::fillNan(phi.internalField());
 
                continue;
            }
 
            if (debug)
            {
                Pout<< "Mapping flux " << iter.key()
                    << " using interpolated flux " << UName
                    << endl;
            }
 
            surfaceScalarField& phi = *iter();
            const surfaceScalarField phiU
            (
                fvc::interpolate
                (
                    lookupObject<volVectorField>(UName)
                )
              & Sf()
            );
 
            // Recalculate new internal faces.
            for (label faceI = 0; faceI < nInternalFaces(); faceI++)
            {
                label oldFaceI = faceMap[faceI];
 
                if (oldFaceI == -1)
                {
                    // Inflated/appended
                    phi[faceI] = phiU[faceI];
                }
                else if (reverseFaceMap[oldFaceI] != faceI)
                {
                    // face-from-masterface
                    phi[faceI] = phiU[faceI];
                }
            }
 
            // Recalculate new boundary faces.
            surfaceScalarField::GeometricBoundaryField& bphi =
                phi.boundaryField();
            forAll(bphi, patchI)
            {
                fvsPatchScalarField& patchPhi = bphi[patchI];
                const fvsPatchScalarField& patchPhiU =
                    phiU.boundaryField()[patchI];
 
                label faceI = patchPhi.patch().start();
 
                forAll(patchPhi, i)
                {
                    label oldFaceI = faceMap[faceI];
 
                    if (oldFaceI == -1)
                    {
                        // Inflated/appended
                        patchPhi[i] = patchPhiU[i];
                    }
                    else if (reverseFaceMap[oldFaceI] != faceI)
                    {
                        // face-from-masterface
                        patchPhi[i] = patchPhiU[i];
                    }
 
                    faceI++;
                }
            }
 
            // Update master faces
            forAllConstIter(labelHashSet, masterFaces, iter)
            {
                label faceI = iter.key();
 
                if (isInternalFace(faceI))
                {
                    phi[faceI] = phiU[faceI];
                }
                else
                {
                    label patchI = boundaryMesh().whichPatch(faceI);
                    label i = faceI - boundaryMesh()[patchI].start();
 
                    const fvsPatchScalarField& patchPhiU =
                        phiU.boundaryField()[patchI];
 
                    fvsPatchScalarField& patchPhi = bphi[patchI];
 
                    patchPhi[i] = patchPhiU[i];
                }
            }
        }
    }
 
 
 
    // Update numbering of cells/vertices.
    meshCutter_.updateMesh(map);
 
    // Update numbering of protectedCell_
    if (protectedCell_.size())
    {
        PackedBoolList newProtectedCell(nCells());
 
        forAll(newProtectedCell, cellI)
        {
            label oldCellI = map().cellMap()[cellI];
            newProtectedCell.set(cellI, protectedCell_.get(oldCellI));
        }
        protectedCell_.transfer(newProtectedCell);
    }
 
    // Debug: Check refinement levels (across faces only)
    meshCutter_.checkRefinementLevels(-1, labelList(0));
 
    return map;
}
 
 
// Combines previously split cells, maps fields and recalculates
// (an approximate) flux
Foam::autoPtr<Foam::mapPolyMesh>
Foam::dynamicRefineFvMesh::unrefine
(
    const labelList& splitPoints
)
{
    polyTopoChange meshMod(*this);
 
    // Play refinement commands into mesh changer.
    meshCutter_.setUnrefinement(splitPoints, meshMod);
 
 
    // Save information on faces that will be combined
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
    // Find the faceMidPoints on cells to be combined.
    // for each face resulting of split of face into four store the
    // midpoint
    Map<label> faceToSplitPoint(3*splitPoints.size());
 
    {
        forAll(splitPoints, i)
        {
            label pointI = splitPoints[i];
 
            const labelList& pEdges = pointEdges()[pointI];
 
            forAll(pEdges, j)
            {
                label otherPointI = edges()[pEdges[j]].otherVertex(pointI);
 
                const labelList& pFaces = pointFaces()[otherPointI];
 
                forAll(pFaces, pFaceI)
                {
                    faceToSplitPoint.insert(pFaces[pFaceI], otherPointI);
                }
            }
        }
    }
 
 
    // Change mesh and generate map.
    //autoPtr<mapPolyMesh> map = meshMod.changeMesh(*this, true);
    autoPtr<mapPolyMesh> map = meshMod.changeMesh(*this, false);
 
    Info<< "Unrefined from "
        << returnReduce(map().nOldCells(), sumOp<label>())
        << " to " << globalData().nTotalCells() << " cells."
        << endl;
 
    // Update fields
    updateMesh(map);
 
 
    // Move mesh
    /*
    pointField newPoints;
    if (map().hasMotionPoints())
    {
        newPoints = map().preMotionPoints();
    }
    else
    {
        newPoints = points();
    }
    movePoints(newPoints);
    */
 
    // Correct the flux for modified faces.
    {
        const labelList& reversePointMap = map().reversePointMap();
        const labelList& reverseFaceMap = map().reverseFaceMap();
 
        HashTable<surfaceScalarField*> fluxes
        (
            lookupClass<surfaceScalarField>()
        );
        forAllIter(HashTable<surfaceScalarField*>, fluxes, iter)
        {
            if (!correctFluxes_.found(iter.key()))
            {
                WarningInFunction
                    << "Cannot find surfaceScalarField " << iter.key()
                    << " in user-provided flux mapping table "
                    << correctFluxes_ << endl
                    << "    The flux mapping table is used to recreate the"
                    << " flux on newly created faces." << endl
                    << "    Either add the entry if it is a flux or use ("
                    << iter.key() << " none) to suppress this warning."
                    << endl;
                continue;
            }
 
            const word& UName = correctFluxes_[iter.key()];
 
            if (UName == "none")
            {
                continue;
            }
 
            if (debug)
            {
                Info<< "Mapping flux " << iter.key()
                    << " using interpolated flux " << UName
                    << endl;
            }
 
            surfaceScalarField& phi = *iter();
            surfaceScalarField::GeometricBoundaryField& bphi =
                phi.boundaryField();
 
            const surfaceScalarField phiU
            (
                fvc::interpolate
                (
                    lookupObject<volVectorField>(UName)
                )
              & Sf()
            );
 
 
            forAllConstIter(Map<label>, faceToSplitPoint, iter)
            {
                label oldFaceI = iter.key();
                label oldPointI = iter();
 
                if (reversePointMap[oldPointI] < 0)
                {
                    // midpoint was removed. See if face still exists.
                    label faceI = reverseFaceMap[oldFaceI];
 
                    if (faceI >= 0)
                    {
                        if (isInternalFace(faceI))
                        {
                            phi[faceI] = phiU[faceI];
                        }
                        else
                        {
                            label patchI = boundaryMesh().whichPatch(faceI);
                            label i = faceI - boundaryMesh()[patchI].start();
 
                            const fvsPatchScalarField& patchPhiU =
                                phiU.boundaryField()[patchI];
                            fvsPatchScalarField& patchPhi = bphi[patchI];
                            patchPhi[i] = patchPhiU[i];
                        }
                    }
                }
            }
        }
    }
 
 
    // Update numbering of cells/vertices.
    meshCutter_.updateMesh(map);
 
    // Update numbering of protectedCell_
    if (protectedCell_.size())
    {
        PackedBoolList newProtectedCell(nCells());
 
        forAll(newProtectedCell, cellI)
        {
            label oldCellI = map().cellMap()[cellI];
            if (oldCellI >= 0)
            {
                newProtectedCell.set(cellI, protectedCell_.get(oldCellI));
            }
        }
        protectedCell_.transfer(newProtectedCell);
    }
 
    // Debug: Check refinement levels (across faces only)
    meshCutter_.checkRefinementLevels(-1, labelList(0));
 
    return map;
}
 
 
// Get max of connected point
Foam::scalarField
Foam::dynamicRefineFvMesh::maxPointField(const scalarField& pFld) const
{
    scalarField vFld(nCells(), -GREAT);
 
    forAll(pointCells(), pointI)
    {
        const labelList& pCells = pointCells()[pointI];
 
        forAll(pCells, i)
        {
            vFld[pCells[i]] = max(vFld[pCells[i]], pFld[pointI]);
        }
    }
    return vFld;
}
 
 
// Get max of connected cell
Foam::scalarField
Foam::dynamicRefineFvMesh::maxCellField(const volScalarField& vFld) const
{
    scalarField pFld(nPoints(), -GREAT);
 
    forAll(pointCells(), pointI)
    {
        const labelList& pCells = pointCells()[pointI];
 
        forAll(pCells, i)
        {
            pFld[pointI] = max(pFld[pointI], vFld[pCells[i]]);
        }
    }
    return pFld;
}
 
 
// Simple (non-parallel) interpolation by averaging.
Foam::scalarField
Foam::dynamicRefineFvMesh::cellToPoint(const scalarField& vFld) const
{
    scalarField pFld(nPoints());
 
    forAll(pointCells(), pointI)
    {
        const labelList& pCells = pointCells()[pointI];
 
        scalar sum = 0.0;
        forAll(pCells, i)
        {
            sum += vFld[pCells[i]];
        }
        pFld[pointI] = sum/pCells.size();
    }
    return pFld;
}
 
 
// Calculate error. Is < 0 or distance to minLevel, maxLevel
Foam::scalarField Foam::dynamicRefineFvMesh::error
(
    const scalarField& fld,
    const scalar minLevel,
    const scalar maxLevel
) const
{
    scalarField c(fld.size(), -1);
 
    forAll(fld, i)
    {
        scalar err = min(fld[i]-minLevel, maxLevel-fld[i]);
 
        if (err >= 0)
        {
            c[i] = err;
        }
    }
    return c;
}
 
 
void Foam::dynamicRefineFvMesh::selectRefineCandidates
(
    const scalar lowerRefineLevel,
    const scalar upperRefineLevel,
    const scalarField& vFld,
    PackedBoolList& candidateCell
) const
{
    // Get error per cell. Is -1 (not to be refined) to >0 (to be refined,
    // higher more desirable to be refined).
    scalarField cellError
    (
        maxPointField
        (
            error
            (
                cellToPoint(vFld),
                lowerRefineLevel,
                upperRefineLevel
            )
        )
    );
 
    // Mark cells that are candidates for refinement.
    forAll(cellError, cellI)
    {
        if (cellError[cellI] > 0)
        {
            candidateCell.set(cellI, 1);
        }
    }
}
 
 
Foam::labelList Foam::dynamicRefineFvMesh::selectRefineCells
(
    const label maxCells,
    const label maxRefinement,
    const PackedBoolList& candidateCell
) const
{
    // Every refined cell causes 7 extra cells
    label nTotToRefine = (maxCells - globalData().nTotalCells()) / 7;
 
    const labelList& cellLevel = meshCutter_.cellLevel();
 
    // Mark cells that cannot be refined since they would trigger refinement
    // of protected cells (since 2:1 cascade)
    PackedBoolList unrefineableCell;
    calculateProtectedCells(unrefineableCell);
 
    // Count current selection
    label nLocalCandidates = count(candidateCell, 1);
    label nCandidates = returnReduce(nLocalCandidates, sumOp<label>());
 
    // Collect all cells
    DynamicList<label> candidates(nLocalCandidates);
 
    if (nCandidates < nTotToRefine)
    {
        forAll(candidateCell, cellI)
        {
            if
            (
                cellLevel[cellI] < maxRefinement
             && candidateCell.get(cellI)
             && (
                    unrefineableCell.empty()
                 || !unrefineableCell.get(cellI)
                )
            )
            {
                candidates.append(cellI);
            }
        }
    }
    else
    {
        // Sort by error? For now just truncate.
        for (label level = 0; level < maxRefinement; level++)
        {
            forAll(candidateCell, cellI)
            {
                if
                (
                    cellLevel[cellI] == level
                 && candidateCell.get(cellI)
                 && (
                        unrefineableCell.empty()
                     || !unrefineableCell.get(cellI)
                    )
                )
                {
                    candidates.append(cellI);
                }
            }
 
            if (returnReduce(candidates.size(), sumOp<label>()) > nTotToRefine)
            {
                break;
            }
        }
    }
 
    // Guarantee 2:1 refinement after refinement
    labelList consistentSet
    (
        meshCutter_.consistentRefinement
        (
            candidates.shrink(),
            true               // Add to set to guarantee 2:1
        )
    );
 
    Info<< "Selected " << returnReduce(consistentSet.size(), sumOp<label>())
        << " cells for refinement out of " << globalData().nTotalCells()
        << "." << endl;
 
    return consistentSet;
}
 
 
Foam::labelList Foam::dynamicRefineFvMesh::selectUnrefinePoints
(
    const scalar unrefineLevel,
    const PackedBoolList& markedCell,
    const scalarField& pFld
) const
{
    // All points that can be unrefined
    const labelList splitPoints(meshCutter_.getSplitPoints());
 
 
    const labelListList& pointCells = this->pointCells();
 
    // If we have any protected cells make sure they also are not being
    // unrefined
 
    PackedBoolList protectedPoint(nPoints());
 
    if (protectedCell_.size())
    {
        // Get all points on a protected cell
        forAll(pointCells, pointI)
        {
            const labelList& pCells = pointCells[pointI];
 
            forAll(pCells, pCellI)
            {
                label cellI = pCells[pCellI];
 
                if (protectedCell_[cellI])
                {
                    protectedPoint[pointI] = true;
                    break;
                }
            }
        }
 
        syncTools::syncPointList
        (
            *this,
            protectedPoint,
            orEqOp<unsigned int>(),
            0U
        );
 
        if (debug)
        {
            Info<< "From "
                << returnReduce(protectedCell_.count(), sumOp<label>())
                << " protected cells found "
                << returnReduce(protectedPoint.count(), sumOp<label>())
                << " protected points." << endl;
        }
    }
 
 
    DynamicList<label> newSplitPoints(splitPoints.size());
 
    forAll(splitPoints, i)
    {
        label pointI = splitPoints[i];
 
        if (!protectedPoint[pointI] && pFld[pointI] < unrefineLevel)
        {
            // Check that all cells are not marked
            const labelList& pCells = pointCells[pointI];
 
            bool hasMarked = false;
 
            forAll(pCells, pCellI)
            {
                if (markedCell.get(pCells[pCellI]))
                {
                    hasMarked = true;
                    break;
                }
            }
 
            if (!hasMarked)
            {
                newSplitPoints.append(pointI);
            }
        }
    }
 
 
    newSplitPoints.shrink();
 
    // Guarantee 2:1 refinement after unrefinement
    labelList consistentSet
    (
        meshCutter_.consistentUnrefinement
        (
            newSplitPoints,
            false
        )
    );
    Info<< "Selected " << returnReduce(consistentSet.size(), sumOp<label>())
        << " split points out of a possible "
        << returnReduce(splitPoints.size(), sumOp<label>())
        << "." << endl;
 
    return consistentSet;
}
 
 
void Foam::dynamicRefineFvMesh::extendMarkedCells
(
    PackedBoolList& markedCell
) const
{
    // Mark faces using any marked cell
    boolList markedFace(nFaces(), false);
 
    forAll(markedCell, cellI)
    {
        if (markedCell.get(cellI))
        {
            const cell& cFaces = cells()[cellI];
 
            forAll(cFaces, i)
            {
                markedFace[cFaces[i]] = true;
            }
        }
    }
 
    syncTools::syncFaceList(*this, markedFace, orEqOp<bool>());
 
    // Update cells using any markedFace
    for (label faceI = 0; faceI < nInternalFaces(); faceI++)
    {
        if (markedFace[faceI])
        {
            markedCell.set(faceOwner()[faceI], 1);
            markedCell.set(faceNeighbour()[faceI], 1);
        }
    }
    for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
    {
        if (markedFace[faceI])
        {
            markedCell.set(faceOwner()[faceI], 1);
        }
    }
}
 
 
void Foam::dynamicRefineFvMesh::checkEightAnchorPoints
(
    PackedBoolList& protectedCell,
    label& nProtected
) const
{
    const labelList& cellLevel = meshCutter_.cellLevel();
    const labelList& pointLevel = meshCutter_.pointLevel();
 
    labelList nAnchorPoints(nCells(), 0);
 
    forAll(pointLevel, pointI)
    {
        const labelList& pCells = pointCells(pointI);
 
        forAll(pCells, pCellI)
        {
            label cellI = pCells[pCellI];
 
            if (pointLevel[pointI] <= cellLevel[cellI])
            {
                // Check if cell has already 8 anchor points -> protect cell
                if (nAnchorPoints[cellI] == 8)
                {
                    if (protectedCell.set(cellI, true))
                    {
                        nProtected++;
                    }
                }
 
                if (!protectedCell[cellI])
                {
                    nAnchorPoints[cellI]++;
                }
            }
        }
    }
 
 
    forAll(protectedCell, cellI)
    {
        if (!protectedCell[cellI] && nAnchorPoints[cellI] != 8)
        {
            protectedCell.set(cellI, true);
            nProtected++;
        }
    }
}
 
 
// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
Foam::dynamicRefineFvMesh::dynamicRefineFvMesh(const IOobject& io)
:
    dynamicFvMesh(io),
    meshCutter_(*this),
    dumpLevel_(false),
    nRefinementIterations_(0),
    protectedCell_(nCells(), 0)
{
    // Read static part of dictionary
    readDict();
 
 
    const labelList& cellLevel = meshCutter_.cellLevel();
    const labelList& pointLevel = meshCutter_.pointLevel();
 
    // Set cells that should not be refined.
    // This is currently any cell which does not have 8 anchor points or
    // uses any face which does not have 4 anchor points.
    // Note: do not use cellPoint addressing
 
    // Count number of points <= cellLevel
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
    labelList nAnchors(nCells(), 0);
 
    label nProtected = 0;
 
    forAll(pointCells(), pointI)
    {
        const labelList& pCells = pointCells()[pointI];
 
        forAll(pCells, i)
        {
            label cellI = pCells[i];
 
            if (!protectedCell_.get(cellI))
            {
                if (pointLevel[pointI] <= cellLevel[cellI])
                {
                    nAnchors[cellI]++;
 
                    if (nAnchors[cellI] > 8)
                    {
                        protectedCell_.set(cellI, 1);
                        nProtected++;
                    }
                }
            }
        }
    }
 
 
    // Count number of points <= faceLevel
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    // Bit tricky since proc face might be one more refined than the owner since
    // the coupled one is refined.
 
    {
        labelList neiLevel(nFaces());
 
        for (label faceI = 0; faceI < nInternalFaces(); faceI++)
        {
            neiLevel[faceI] = cellLevel[faceNeighbour()[faceI]];
        }
        for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
        {
            neiLevel[faceI] = cellLevel[faceOwner()[faceI]];
        }
        syncTools::swapFaceList(*this, neiLevel);
 
 
        boolList protectedFace(nFaces(), false);
 
        forAll(faceOwner(), faceI)
        {
            label faceLevel = max
            (
                cellLevel[faceOwner()[faceI]],
                neiLevel[faceI]
            );
 
            const face& f = faces()[faceI];
 
            label nAnchors = 0;
 
            forAll(f, fp)
            {
                if (pointLevel[f[fp]] <= faceLevel)
                {
                    nAnchors++;
 
                    if (nAnchors > 4)
                    {
                        protectedFace[faceI] = true;
                        break;
                    }
                }
            }
        }
 
        syncTools::syncFaceList(*this, protectedFace, orEqOp<bool>());
 
        for (label faceI = 0; faceI < nInternalFaces(); faceI++)
        {
            if (protectedFace[faceI])
            {
                protectedCell_.set(faceOwner()[faceI], 1);
                nProtected++;
                protectedCell_.set(faceNeighbour()[faceI], 1);
                nProtected++;
            }
        }
        for (label faceI = nInternalFaces(); faceI < nFaces(); faceI++)
        {
            if (protectedFace[faceI])
            {
                protectedCell_.set(faceOwner()[faceI], 1);
                nProtected++;
            }
        }
 
        // Also protect any cells that are less than hex
        forAll(cells(), cellI)
        {
            const cell& cFaces = cells()[cellI];
 
            if (cFaces.size() < 6)
            {
                if (protectedCell_.set(cellI, 1))
                {
                    nProtected++;
                }
            }
            else
            {
                forAll(cFaces, cFaceI)
                {
                    if (faces()[cFaces[cFaceI]].size() < 4)
                    {
                        if (protectedCell_.set(cellI, 1))
                        {
                            nProtected++;
                        }
                        break;
                    }
                }
            }
        }
 
        // Check cells for 8 corner points
        checkEightAnchorPoints(protectedCell_, nProtected);
    }
 
    if (returnReduce(nProtected, sumOp<label>()) == 0)
    {
        protectedCell_.clear();
    }
    else
    {
 
        cellSet protectedCells(*this, "protectedCells", nProtected);
        forAll(protectedCell_, cellI)
        {
            if (protectedCell_[cellI])
            {
                protectedCells.insert(cellI);
            }
        }
 
        Info<< "Detected " << returnReduce(nProtected, sumOp<label>())
            << " cells that are protected from refinement."
            << " Writing these to cellSet "
            << protectedCells.name()
            << "." << endl;
 
        protectedCells.write();
    }
}
 
 
// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
Foam::dynamicRefineFvMesh::~dynamicRefineFvMesh()
{}
 
 
// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
bool Foam::dynamicRefineFvMesh::update()
{
    // Re-read dictionary. Choosen since usually -small so trivial amount
    // of time compared to actual refinement. Also very useful to be able
    // to modify on-the-fly.
    dictionary refineDict
    (
        IOdictionary
        (
            IOobject
            (
                "dynamicMeshDict",
                time().constant(),
                *this,
                IOobject::MUST_READ_IF_MODIFIED,
                IOobject::NO_WRITE,
                false
            )
        ).subDict(typeName + "Coeffs")
    );
 
    label refineInterval = readLabel(refineDict.lookup("refineInterval"));
 
    bool hasChanged = false;
 
    if (refineInterval == 0)
    {
        topoChanging(hasChanged);
 
        return false;
    }
    else if (refineInterval < 0)
    {
        FatalErrorInFunction
            << "Illegal refineInterval " << refineInterval << nl
            << "The refineInterval setting in the dynamicMeshDict should"
            << " be >= 1." << nl
            << exit(FatalError);
    }
 
 
 
 
    // Note: cannot refine at time 0 since no V0 present since mesh not
    //       moved yet.
 
    if (time().timeIndex() > 0 && time().timeIndex() % refineInterval == 0)
    {
        label maxCells = readLabel(refineDict.lookup("maxCells"));
 
        if (maxCells <= 0)
        {
            FatalErrorInFunction
                << "Illegal maximum number of cells " << maxCells << nl
                << "The maxCells setting in the dynamicMeshDict should"
                << " be > 0." << nl
                << exit(FatalError);
        }
 
        label maxRefinement = readLabel(refineDict.lookup("maxRefinement"));
 
        if (maxRefinement <= 0)
        {
            FatalErrorInFunction
                << "Illegal maximum refinement level " << maxRefinement << nl
                << "The maxCells setting in the dynamicMeshDict should"
                << " be > 0." << nl
                << exit(FatalError);
        }
 
        const word fieldName(refineDict.lookup("field"));
 
        const volScalarField& vFld = lookupObject<volScalarField>(fieldName);
 
        const scalar lowerRefineLevel =
            readScalar(refineDict.lookup("lowerRefineLevel"));
        const scalar upperRefineLevel =
            readScalar(refineDict.lookup("upperRefineLevel"));
        const scalar unrefineLevel = refineDict.lookupOrDefault<scalar>
        (
            "unrefineLevel",
            GREAT
        );
        const label nBufferLayers =
            readLabel(refineDict.lookup("nBufferLayers"));
 
        // Cells marked for refinement or otherwise protected from unrefinement.
        PackedBoolList refineCell(nCells());
 
        // Determine candidates for refinement (looking at field only)
        selectRefineCandidates
        (
            lowerRefineLevel,
            upperRefineLevel,
            vFld,
            refineCell
        );
 
        if (globalData().nTotalCells() < maxCells)
        {
            // Select subset of candidates. Take into account max allowable
            // cells, refinement level, protected cells.
            labelList cellsToRefine
            (
                selectRefineCells
                (
                    maxCells,
                    maxRefinement,
                    refineCell
                )
            );
 
            label nCellsToRefine = returnReduce
            (
                cellsToRefine.size(), sumOp<label>()
            );
 
            if (nCellsToRefine > 0)
            {
                // Refine/update mesh and map fields
                autoPtr<mapPolyMesh> map = refine(cellsToRefine);
 
                // Update refineCell. Note that some of the marked ones have
                // not been refined due to constraints.
                {
                    const labelList& cellMap = map().cellMap();
                    const labelList& reverseCellMap = map().reverseCellMap();
 
                    PackedBoolList newRefineCell(cellMap.size());
 
                    forAll(cellMap, cellI)
                    {
                        label oldCellI = cellMap[cellI];
 
                        if (oldCellI < 0)
                        {
                            newRefineCell.set(cellI, 1);
                        }
                        else if (reverseCellMap[oldCellI] != cellI)
                        {
                            newRefineCell.set(cellI, 1);
                        }
                        else
                        {
                            newRefineCell.set(cellI, refineCell.get(oldCellI));
                        }
                    }
                    refineCell.transfer(newRefineCell);
                }
 
                // Extend with a buffer layer to prevent neighbouring points
                // being unrefined.
                for (label i = 0; i < nBufferLayers; i++)
                {
                    extendMarkedCells(refineCell);
                }
 
                hasChanged = true;
            }
        }
 
 
        {
            // Select unrefineable points that are not marked in refineCell
            labelList pointsToUnrefine
            (
                selectUnrefinePoints
                (
                    unrefineLevel,
                    refineCell,
                    maxCellField(vFld)
                )
            );
 
            label nSplitPoints = returnReduce
            (
                pointsToUnrefine.size(),
                sumOp<label>()
            );
 
            if (nSplitPoints > 0)
            {
                // Refine/update mesh
                unrefine(pointsToUnrefine);
 
                hasChanged = true;
            }
        }
 
 
        if ((nRefinementIterations_ % 10) == 0)
        {
            // Compact refinement history occassionally (how often?).
            // Unrefinement causes holes in the refinementHistory.
            const_cast<refinementHistory&>(meshCutter().history()).compact();
        }
        nRefinementIterations_++;
    }
 
    topoChanging(hasChanged);
    if (hasChanged)
    {
        // Reset moving flag (if any). If not using inflation we'll not move,
        // if are using inflation any follow on movePoints will set it.
        moving(false);
    }
 
    return hasChanged;
}
 
 
bool Foam::dynamicRefineFvMesh::writeObject
(
    IOstream::streamFormat fmt,
    IOstream::versionNumber ver,
    IOstream::compressionType cmp
) const
{
    // Force refinement data to go to the current time directory.
    const_cast<hexRef8&>(meshCutter_).setInstance(time().timeName());
 
    bool writeOk =
    (
        dynamicFvMesh::writeObjects(fmt, ver, cmp)
     && meshCutter_.write()
    );
 
    if (dumpLevel_)
    {
        volScalarField scalarCellLevel
        (
            IOobject
            (
                "cellLevel",
                time().timeName(),
                *this,
                IOobject::NO_READ,
                IOobject::AUTO_WRITE,
                false
            ),
            *this,
            dimensionedScalar("level", dimless, 0)
        );
 
        const labelList& cellLevel = meshCutter_.cellLevel();
 
        forAll(cellLevel, cellI)
        {
            scalarCellLevel[cellI] = cellLevel[cellI];
        }
 
        writeOk = writeOk && scalarCellLevel.write();
    }
 
    return writeOk;
}
 
 
// ************************************************************************* //