checkTopology.C

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/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Copyright (C) 2011-2018 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 "checkTopology.H"
#include "polyMesh.H"
#include "Time.H"
#include "regionSplit.H"
#include "cellSet.H"
#include "faceSet.H"
#include "pointSet.H"
#include "IOmanip.H"
#include "emptyPolyPatch.H"
#include "processorPolyPatch.H"
#include "surfaceWriter.H"
#include "checkTools.H"

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

Foam::label Foam::checkTopology
(
    const polyMesh& mesh,
    const bool allTopology,
    const bool allGeometry,
    const autoPtr<surfaceWriter>& surfWriter,
    const autoPtr<writer<scalar>>& setWriter
)
{
    label noFailedChecks = 0;

    Info<< "Checking topology..." << endl;

    // Check if the boundary definition is unique
    mesh.boundaryMesh().checkDefinition(true);

    // Check that empty patches cover all sides of the mesh
    {
        label nEmpty = 0;
        forAll(mesh.boundaryMesh(), patchi)
        {
            if (isA<emptyPolyPatch>(mesh.boundaryMesh()[patchi]))
            {
                nEmpty += mesh.boundaryMesh()[patchi].size();
            }
        }
        reduce(nEmpty, sumOp<label>());
        label nTotCells = returnReduce(mesh.cells().size(), sumOp<label>());

        // These are actually warnings, not errors.
        if (nTotCells && (nEmpty % nTotCells))
        {
            Info<< " ***Total number of faces on empty patches"
                << " is not divisible by the number of cells in the mesh."
                << " Hence this mesh is not 1D or 2D."
                << endl;
        }
    }

    // Check if the boundary processor patches are correct
    mesh.boundaryMesh().checkParallelSync(true);

    // Check names of zones are equal
    mesh.cellZones().checkDefinition(true);
    if (mesh.cellZones().checkParallelSync(true))
    {
        noFailedChecks++;
    }
    mesh.faceZones().checkDefinition(true);
    if (mesh.faceZones().checkParallelSync(true))
    {
        noFailedChecks++;
    }
    mesh.pointZones().checkDefinition(true);
    if (mesh.pointZones().checkParallelSync(true))
    {
        noFailedChecks++;
    }


    {
        cellSet cells(mesh, "illegalCells", mesh.nCells()/100);

        forAll(mesh.cells(), celli)
        {
            const cell& cFaces = mesh.cells()[celli];

            if (cFaces.size() <= 3)
            {
                cells.insert(celli);
            }
            forAll(cFaces, i)
            {
                if (cFaces[i] < 0 || cFaces[i] >= mesh.nFaces())
                {
                    cells.insert(celli);
                    break;
                }
            }
        }
        label nCells = returnReduce(cells.size(), sumOp<label>());

        if (nCells > 0)
        {
            Info<< "    Illegal cells (less than 4 faces or out of range faces)"
                << " found,  number of cells: " << nCells << endl;
            noFailedChecks++;

            Info<< "  <<Writing " << nCells
                << " illegal cells to set " << cells.name() << endl;
            cells.instance() = mesh.pointsInstance();
            cells.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), cells);
            }

        }
        else
        {
            Info<< "    Cell to face addressing OK." << endl;
        }
    }


    {
        pointSet points(mesh, "unusedPoints", mesh.nPoints()/100);
        if (mesh.checkPoints(true, &points))
        {
            noFailedChecks++;

            label nPoints = returnReduce(points.size(), sumOp<label>());

            Info<< "  <<Writing " << nPoints
                << " unused points to set " << points.name() << endl;
            points.instance() = mesh.pointsInstance();
            points.write();
            if (setWriter.valid())
            {
                mergeAndWrite(setWriter, points);
            }
        }
    }

    {
        faceSet faces(mesh, "upperTriangularFace", mesh.nFaces()/100);
        if (mesh.checkUpperTriangular(true, &faces))
        {
            noFailedChecks++;
        }

        label nFaces = returnReduce(faces.size(), sumOp<label>());

        if (nFaces > 0)
        {
            Info<< "  <<Writing " << nFaces
                << " unordered faces to set " << faces.name() << endl;
            faces.instance() = mesh.pointsInstance();
            faces.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), faces);
            }
        }
    }

    {
        faceSet faces(mesh, "outOfRangeFaces", mesh.nFaces()/100);
        if (mesh.checkFaceVertices(true, &faces))
        {
            noFailedChecks++;

            label nFaces = returnReduce(faces.size(), sumOp<label>());

            Info<< "  <<Writing " << nFaces
                << " faces with out-of-range or duplicate vertices to set "
                << faces.name() << endl;
            faces.instance() = mesh.pointsInstance();
            faces.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), faces);
            }
        }
    }

    if (allTopology)
    {
        cellSet cells(mesh, "zipUpCells", mesh.nCells()/100);
        if (mesh.checkCellsZipUp(true, &cells))
        {
            noFailedChecks++;

            label nCells = returnReduce(cells.size(), sumOp<label>());

            Info<< "  <<Writing " << nCells
                << " cells with over used edges to set " << cells.name()
                << endl;
            cells.instance() = mesh.pointsInstance();
            cells.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), cells);
            }

        }
    }

    if (allTopology)
    {
        faceSet faces(mesh, "edgeFaces", mesh.nFaces()/100);
        if (mesh.checkFaceFaces(true, &faces))
        {
            noFailedChecks++;
        }

        label nFaces = returnReduce(faces.size(), sumOp<label>());
        if (nFaces > 0)
        {
            Info<< "  <<Writing " << nFaces
                << " faces with non-standard edge connectivity to set "
                << faces.name() << endl;
            faces.instance() = mesh.pointsInstance();
            faces.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), faces);
            }
        }
    }

    if (allTopology)
    {
        labelList nInternalFaces(mesh.nCells(), 0);

        for (label facei = 0; facei < mesh.nInternalFaces(); facei++)
        {
            nInternalFaces[mesh.faceOwner()[facei]]++;
            nInternalFaces[mesh.faceNeighbour()[facei]]++;
        }
        const polyBoundaryMesh& patches = mesh.boundaryMesh();
        forAll(patches, patchi)
        {
            if (patches[patchi].coupled())
            {
                const labelUList& owners = patches[patchi].faceCells();

                forAll(owners, i)
                {
                    nInternalFaces[owners[i]]++;
                }
            }
        }

        cellSet oneCells(mesh, "oneInternalFaceCells", mesh.nCells()/100);
        cellSet twoCells(mesh, "twoInternalFacesCells", mesh.nCells()/100);

        forAll(nInternalFaces, celli)
        {
            if (nInternalFaces[celli] <= 1)
            {
                oneCells.insert(celli);
            }
            else if (nInternalFaces[celli] == 2)
            {
                twoCells.insert(celli);
            }
        }

        label nOneCells = returnReduce(oneCells.size(), sumOp<label>());

        if (nOneCells > 0)
        {
            Info<< "  <<Writing " << nOneCells
                << " cells with zero or one non-boundary face to set "
                << oneCells.name()
                << endl;
            oneCells.instance() = mesh.pointsInstance();
            oneCells.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), oneCells);
            }
        }

        label nTwoCells = returnReduce(twoCells.size(), sumOp<label>());

        if (nTwoCells > 0)
        {
            Info<< "  <<Writing " << nTwoCells
                << " cells with two non-boundary faces to set "
                << twoCells.name()
                << endl;
            twoCells.instance() = mesh.pointsInstance();
            twoCells.write();
            if (surfWriter.valid())
            {
                mergeAndWrite(surfWriter(), twoCells);
            }
        }
    }

    {
        regionSplit rs(mesh);

        if (rs.nRegions() <= 1)
        {
            Info<< "    Number of regions: " << rs.nRegions() << " (OK)."
                << endl;

        }
        else
        {
            Info<< "   *Number of regions: " << rs.nRegions() << endl;

            Info<< "    The mesh has multiple regions which are not connected "
                   "by any face." << endl
                << "  <<Writing region information to "
                << mesh.time().timeName()/"cellToRegion"
                << endl;

            labelIOList ctr
            (
                IOobject
                (
                    "cellToRegion",
                    mesh.time().timeName(),
                    mesh,
                    IOobject::NO_READ,
                    IOobject::NO_WRITE
                ),
                rs
            );
            ctr.write();


            // Points in multiple regions
            pointSet points
            (
                mesh,
                "multiRegionPoints",
                mesh.nPoints()/1000
            );

            // Is region disconnected
            boolList regionDisconnected(rs.nRegions(), true);
            if (allTopology)
            {
                // -1   : not assigned
                // -2   : multiple regions
                // >= 0 : single region
                labelList pointToRegion(mesh.nPoints(), -1);

                for
                (
                    label faceI = mesh.nInternalFaces();
                    faceI < mesh.nFaces();
                    faceI++
                )
                {
                    label regionI = rs[mesh.faceOwner()[faceI]];
                    const face& f = mesh.faces()[faceI];
                    forAll(f, fp)
                    {
                        label& pRegion = pointToRegion[f[fp]];
                        if (pRegion == -1)
                        {
                            pRegion = regionI;
                        }
                        else if (pRegion == -2)
                        {
                            // Already marked
                            regionDisconnected[regionI] = false;
                        }
                        else if (pRegion != regionI)
                        {
                            // Multiple regions
                            regionDisconnected[regionI] = false;
                            regionDisconnected[pRegion] = false;
                            pRegion = -2;
                            points.insert(f[fp]);
                        }
                    }
                }

                Pstream::listCombineGather(regionDisconnected, andEqOp<bool>());
                Pstream::listCombineScatter(regionDisconnected);
            }



            // write cellSet for each region
            PtrList<cellSet> cellRegions(rs.nRegions());
            for (label i = 0; i < rs.nRegions(); i++)
            {
                cellRegions.set
                (
                    i,
                    new cellSet
                    (
                        mesh,
                        "region" + Foam::name(i),
                        mesh.nCells()/100
                    )
                );
            }

            forAll(rs, i)
            {
                cellRegions[rs[i]].insert(i);
            }

            for (label i = 0; i < rs.nRegions(); i++)
            {
                Info<< "  <<Writing region " << i;
                if (allTopology)
                {
                    if (regionDisconnected[i])
                    {
                        Info<< " (fully disconnected)";
                    }
                    else
                    {
                        Info<< " (point connected)";
                    }
                }
                Info<< " with "
                    << returnReduce(cellRegions[i].size(), sumOp<scalar>())
                    << " cells to cellSet " << cellRegions[i].name() << endl;

                cellRegions[i].write();
            }

            label nPoints = returnReduce(points.size(), sumOp<label>());
            if (nPoints)
            {
                Info<< "  <<Writing " << nPoints
                    << " points that are in multiple regions to set "
                    << points.name() << endl;
                points.write();
                if (setWriter.valid())
                {
                    mergeAndWrite(setWriter, points);
                }
            }
        }
    }


    {
        if (!Pstream::parRun())
        {
            Info<< "\nChecking patch topology for multiply connected"
                << " surfaces..." << endl;
        }
        else
        {
            Info<< "\nChecking basic patch addressing..." << endl;
        }


        const polyBoundaryMesh& patches = mesh.boundaryMesh();

        // Non-manifold points
        pointSet points
        (
            mesh,
            "nonManifoldPoints",
            mesh.nPoints()/1000
        );

        Pout.setf(ios_base::left);

        Info<< "    "
            << setw(20) << "Patch"
            << setw(9) << "Faces"
            << setw(9) << "Points";
        if (!Pstream::parRun())
        {
            Info<< setw(34) << "Surface topology";
        }
        if (allGeometry)
        {
            Info<< " Bounding box";
        }
        Info<< endl;

        forAll(patches, patchi)
        {
            const polyPatch& pp = patches[patchi];

            if (!isA<processorPolyPatch>(pp))
            {
                Info<< "    "
                    << setw(20) << pp.name()
                    << setw(9) << returnReduce(pp.size(), sumOp<label>())
                    << setw(9) << returnReduce(pp.nPoints(), sumOp<label>());

                if (!Pstream::parRun())
                {
                    primitivePatch::surfaceTopo pTyp = pp.surfaceType();

                    if (pp.empty())
                    {
                        Info<< setw(34) << "ok (empty)";
                    }
                    else if (pTyp == primitivePatch::MANIFOLD)
                    {
                        if (pp.checkPointManifold(true, &points))
                        {
                            Info<< setw(34)
                                << "multiply connected (shared point)";
                        }
                        else
                        {
                            Info<< setw(34) << "ok (closed singly connected)";
                        }

                        // Add points on non-manifold edges to make set complete
                        pp.checkTopology(false, &points);
                    }
                    else
                    {
                        pp.checkTopology(false, &points);

                        if (pTyp == primitivePatch::OPEN)
                        {
                            Info<< setw(34)
                                << "ok (non-closed singly connected)";
                        }
                        else
                        {
                            Info<< setw(34)
                                << "multiply connected (shared edge)";
                        }
                    }
                }

                if (allGeometry)
                {
                    const pointField& pts = pp.points();
                    const labelList& mp = pp.meshPoints();

                    if (returnReduce(mp.size(), sumOp<label>()) > 0)
                    {
                        boundBox bb(point::max, point::min);
                        forAll(mp, i)
                        {
                            bb.min() = min(bb.min(), pts[mp[i]]);
                            bb.max() = max(bb.max(), pts[mp[i]]);
                        }
                        reduce(bb.min(), minOp<vector>());
                        reduce(bb.max(), maxOp<vector>());
                        Info<< ' ' << bb;
                    }
                }
                Info<< endl;
            }
        }

        if (points.size())
        {
            Info<< "  <<Writing " << returnReduce(points.size(), sumOp<label>())
                << " conflicting points to set "
                << points.name() << endl;

            points.instance() = mesh.pointsInstance();
            points.write();
        }

        // Info.setf(ios_base::right);
    }

    // Force creation of all addressing if requested.
    // Errors will be reported as required
    if (allTopology)
    {
        mesh.cells();
        mesh.faces();
        mesh.edges();
        mesh.points();
        mesh.faceOwner();
        mesh.faceNeighbour();
        mesh.cellCells();
        mesh.edgeCells();
        mesh.pointCells();
        mesh.edgeFaces();
        mesh.pointFaces();
        mesh.cellEdges();
        mesh.faceEdges();
        mesh.pointEdges();
    }

    return noFailedChecks;
}


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