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openfoam/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
Mark Olesen bac943e6fc ENH: new bitSet class and improved PackedList class (closes #751) 
- The bitSet class replaces the old PackedBoolList class.
  The redesign provides better block-wise access and reduced method
  calls. This helps both in cases where the bitSet may be relatively
  sparse, and in cases where advantage of contiguous operations can be
  made. This makes it easier to work with a bitSet as top-level object.

  In addition to the previously available count() method to determine
  if a bitSet is being used, now have simpler queries:

    - all()  - true if all bits in the addressable range are empty
    - any()  - true if any bits are set at all.
    - none() - true if no bits are set.

  These are faster than count() and allow early termination.

  The new test() method tests the value of a single bit position and
  returns a bool without any ambiguity caused by the return type
  (like the get() method), nor the const/non-const access (like
  operator[] has). The name corresponds to what std::bitset uses.

  The new find_first(), find_last(), find_next() methods provide a faster
  means of searching for bits that are set.

  This can be especially useful when using a bitSet to control an
  conditional:

  OLD (with macro):

      forAll(selected, celli)
      {
          if (selected[celli])
          {
              sumVol += mesh_.cellVolumes()[celli];
          }
      }

  NEW (with const_iterator):

      for (const label celli : selected)
      {
          sumVol += mesh_.cellVolumes()[celli];
      }

      or manually

      for
      (
          label celli = selected.find_first();
          celli != -1;
          celli = selected.find_next()
      )
      {
          sumVol += mesh_.cellVolumes()[celli];
      }

- When marking up contiguous parts of a bitset, an interval can be
  represented more efficiently as a labelRange of start/size.
  For example,

  OLD:

      if (isA<processorPolyPatch>(pp))
      {
          forAll(pp, i)
          {
              ignoreFaces.set(i);
          }
      }

  NEW:

      if (isA<processorPolyPatch>(pp))
      {
          ignoreFaces.set(pp.range());
      }
2018-03-07 11:21:48 +01:00

727 lines
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/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2017 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 "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"
#include "treeBoundBox.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
template<class PatchType>
void Foam::checkPatch
(
const bool allGeometry,
const word& name,
const PatchType& pp,
pointSet& points
)
{
Info<< " "
<< setw(20) << name
<< setw(9) << returnReduce(pp.size(), sumOp<label>())
<< setw(9) << returnReduce(pp.nPoints(), sumOp<label>());
if (!Pstream::parRun())
{
typedef typename PatchType::surfaceTopo TopoType;
TopoType pTyp = pp.surfaceType();
if (pp.empty())
{
Info<< setw(34) << "ok (empty)";
}
else if (pTyp == TopoType::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 == TopoType::OPEN)
{
Info<< setw(34)
<< "ok (non-closed singly connected)";
}
else
{
Info<< setw(34)
<< "multiply connected (shared edge)";
}
}
}
if (allGeometry)
{
const labelList& mp = pp.meshPoints();
if (returnReduce(mp.size(), sumOp<label>()) > 0)
{
boundBox bb(pp.points(), mp, true); // reduce
Info<< ' ' << bb;
}
}
}
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);
}
for (const label facei : cFaces)
{
if (facei < 0 || facei >= mesh.nFaces())
{
cells.insert(celli);
break;
}
}
}
const 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++;
}
const 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++;
const 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++;
const 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++;
}
const 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();
for (const label facei : owners)
{
nInternalFaces[facei]++;
}
}
}
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
)
{
const label regioni = rs[mesh.faceOwner()[facei]];
const face& f = mesh.faces()[facei];
for (const label verti : f)
{
label& pRegion = pointToRegion[verti];
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(verti);
}
}
}
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);
}
}
}
}
// Non-manifold points
pointSet points
(
mesh,
"nonManifoldPoints",
mesh.nPoints()/1000
);
{
if (!Pstream::parRun())
{
Info<< "\nChecking patch topology for multiply connected"
<< " surfaces..." << endl;
}
else
{
Info<< "\nChecking basic patch addressing..." << endl;
}
const polyBoundaryMesh& patches = mesh.boundaryMesh();
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))
{
checkPatch(allGeometry, pp.name(), pp, points);
Info<< endl;
}
}
//Info.setf(ios_base::right);
}
{
if (!Pstream::parRun())
{
Info<< "\nChecking faceZone topology for multiply connected"
<< " surfaces..." << endl;
}
else
{
Info<< "\nChecking basic faceZone addressing..." << endl;
}
Pout.setf(ios_base::left);
const faceZoneMesh& faceZones = mesh.faceZones();
if (faceZones.size())
{
Info<< " "
<< setw(20) << "FaceZone"
<< setw(9) << "Faces"
<< setw(9) << "Points";
if (!Pstream::parRun())
{
Info<< setw(34) << "Surface topology";
}
if (allGeometry)
{
Info<< " Bounding box";
}
Info<< endl;
for (const faceZone& fz : faceZones)
{
checkPatch(allGeometry, fz.name(), fz(), points);
Info<< endl;
}
}
else
{
Info<< " No faceZones found."<<endl;
}
}
const label nPoints = returnReduce(points.size(), sumOp<label>());
if (nPoints)
{
Info<< " <<Writing " << nPoints
<< " conflicting points to set " << points.name() << endl;
points.instance() = mesh.pointsInstance();
points.write();
if (setWriter.valid())
{
mergeAndWrite(setWriter(), points);
}
}
{
Info<< "\nChecking basic cellZone addressing..." << endl;
Pout.setf(ios_base::left);
const cellZoneMesh& cellZones = mesh.cellZones();
if (cellZones.size())
{
Info<< " "
<< setw(20) << "CellZone"
<< setw(13) << "Cells"
<< setw(13) << "Points"
<< ' ' << "BoundingBox" <<endl;
const cellList& cells = mesh.cells();
const faceList& faces = mesh.faces();
bitSet isZonePoint(mesh.nPoints());
for (const cellZone& cZone : cellZones)
{
boundBox bb;
isZonePoint.reset(); // clears all bits (reset count)
for (const label celli : cZone)
{
for (const label facei : cells[celli])
{
const face& f = faces[facei];
for (const label verti : f)
{
if (isZonePoint.set(verti))
{
bb.add(mesh.points()[verti]);
}
}
}
}
bb.reduce(); // Global min/max
Info<< " "
<< setw(20) << cZone.name()
<< ' ' << setw(12)
<< returnReduce(cZone.size(), sumOp<label>())
<< ' ' << setw(12)
<< returnReduce(isZonePoint.count(), sumOp<label>())
<< ' ' << bb << endl;
}
}
else
{
Info<< " No cellZones found."<<endl;
}
}
// 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;
}
// ************************************************************************* //
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