Files
OpenFOAM-12/applications/utilities/surface/surfaceCheck/surfaceCheck.C
Will Bainbridge 25a6d068f0 sampledSets, streamlines: Various improvements
Sampled sets and streamlines now write all their fields to the same
file. This prevents excessive duplication of the geometry and makes
post-processing tasks more convenient.

"axis" entries are now optional in sampled sets and streamlines. When
omitted, a default entry will be used, which is chosen appropriately for
the coordinate set and the write format. Some combinations are not
supported. For example, a scalar ("x", "y", "z" or "distance") axis
cannot be used to write in the vtk format, as vtk requires 3D locations
with which to associate data. Similarly, a point ("xyz") axis cannot be
used with the gnuplot format, as gnuplot needs a single scalar to
associate with the x-axis.

Streamlines can now write out fields of any type, not just scalars and
vectors, and there is no longer a strict requirement for velocity to be
one of the fields.

Streamlines now output to postProcessing/<functionName>/time/<file> in
the same way as other functions. The additional "sets" subdirectory has
been removed.

The raw set writer now aligns columns correctly.

The handling of segments in coordSet and sampledSet has been
fixed/completed. Segments mean that a coordinate set can represent a
number of contiguous lines, disconnected points, or some combination
thereof. This works in parallel; segments remain contiguous across
processor boundaries. Set writers now only need one write method, as the
previous "writeTracks" functionality is now handled by streamlines
providing the writer with the appropriate segment structure.

Coordinate sets and set writers now have a convenient programmatic
interface. To write a graph of A and B against some coordinate X, in
gnuplot format, we can call the following:

    setWriter::New("gnuplot")->write
    (
        directoryName,
        graphName,
        coordSet(true, "X", X), // <-- "true" indicates a contiguous
        "A",                    //     line, "false" would mean
        A,                      //     disconnected points
        "B",
        B
    );

This write function is variadic. It supports any number of
field-name-field pairs, and they can be of any primitive type.

Support for Jplot and Xmgrace formats has been removed. Raw, CSV,
Gnuplot, VTK and Ensight formats are all still available.

The old "graph" functionality has been removed from the code, with the
exception of the randomProcesses library and associated applications
(noise, DNSFoam and boxTurb). The intention is that these should also
eventually be converted to use the setWriters. For now, so that it is
clear that the "graph" functionality is not to be used elsewhere, it has
been moved into a subdirectory of the randomProcesses library.
2021-12-07 11:18:27 +00:00

795 lines
21 KiB
C++

/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2021 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/>.
Application
surfaceCheck
Description
Checks geometric and topological quality of a surface.
\*---------------------------------------------------------------------------*/
#include "triangle.H"
#include "triSurface.H"
#include "triSurfaceSearch.H"
#include "argList.H"
#include "OFstream.H"
#include "OBJstream.H"
#include "SortableList.H"
#include "PatchTools.H"
#include "vtkSurfaceWriter.H"
using namespace Foam;
// Does face use valid vertices?
bool validTri
(
const bool verbose,
const triSurface& surf,
const label facei
)
{
// Simple check on indices ok.
const labelledTri& f = surf[facei];
forAll(f, fp)
{
if (f[fp] < 0 || f[fp] >= 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
<< " coords:" << f.points(surf.points())
<< 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
<< " has the same vertices as triangle " << nbrFacei
<< " vertices " << nbrF
<< " coords:" << f.points(surf.points())
<< endl;
return false;
}
}
return true;
}
labelList countBins
(
const scalar min,
const scalar max,
const label nBins,
const scalarField& vals
)
{
scalar dist = nBins/(max - min);
labelList binCount(nBins, 0);
forAll(vals, i)
{
scalar val = vals[i];
label index = -1;
if (Foam::mag(val - min) < small)
{
index = 0;
}
else if (val >= max - small)
{
index = nBins - 1;
}
else
{
index = label((val - min)*dist);
if ((index < 0) || (index >= nBins))
{
WarningInFunction
<< "value " << val << " at index " << i
<< " outside range " << min << " .. " << max << endl;
if (index < 0)
{
index = 0;
}
else
{
index = nBins - 1;
}
}
}
binCount[index]++;
}
return binCount;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
int main(int argc, char *argv[])
{
#include "removeCaseOptions.H"
argList::validArgs.append("surface file");
argList::addBoolOption
(
"checkSelfIntersection",
"also check for self-intersection"
);
argList::addBoolOption
(
"splitNonManifold",
"split surface along non-manifold edges"
" (default split is fully disconnected)"
);
argList::addBoolOption
(
"verbose",
"verbose operation"
);
argList::addBoolOption
(
"blockMesh",
"write vertices/blocks for blockMeshDict"
);
argList args(argc, argv);
const fileName surfFileName = args[1];
const bool checkSelfIntersect = args.optionFound("checkSelfIntersection");
const bool verbose = args.optionFound("verbose");
const bool splitNonManifold = args.optionFound("splitNonManifold");
Info<< "Reading surface from " << surfFileName << " ..." << nl << endl;
// Read
// ~~~~
triSurface surf(surfFileName);
Info<< "Statistics:" << endl;
surf.writeStats(Info);
Info<< endl;
// write bounding box corners
if (args.optionFound("blockMesh"))
{
pointField cornerPts(boundBox(surf.points(), false).points());
Info<< "// blockMeshDict info" << nl << nl;
Info<< "vertices\n(" << nl;
forAll(cornerPts, ptI)
{
Info<< " " << cornerPts[ptI] << nl;
}
// number of divisions needs adjustment later
Info<< ");\n" << nl
<< "blocks\n"
<< "(\n"
<< " hex (0 1 2 3 4 5 6 7) (10 10 10) simpleGrading (1 1 1)\n"
<< ");\n" << nl;
Info<< "edges\n();" << nl
<< "patches\n();" << endl;
Info<< nl << "// end blockMeshDict info" << nl << endl;
}
// Region sizes
// ~~~~~~~~~~~~
{
labelList regionSize(surf.patches().size(), 0);
forAll(surf, facei)
{
label region = surf[facei].region();
if (region < 0 || region >= regionSize.size())
{
WarningInFunction
<< "Triangle " << facei << " vertices " << surf[facei]
<< " has region " << region << " which is outside the range"
<< " of regions 0.." << surf.patches().size()-1
<< endl;
}
else
{
regionSize[region]++;
}
}
Info<< "Region\tSize" << nl
<< "------\t----" << nl;
forAll(surf.patches(), patchi)
{
Info<< surf.patches()[patchi].name() << '\t'
<< regionSize[patchi] << nl;
}
Info<< nl << endl;
}
// Check triangles
// ~~~~~~~~~~~~~~~
{
DynamicList<label> illegalFaces(surf.size()/100 + 1);
forAll(surf, facei)
{
if (!validTri(verbose, surf, facei))
{
illegalFaces.append(facei);
}
}
if (illegalFaces.size())
{
Info<< "Surface has " << illegalFaces.size()
<< " illegal triangles." << endl;
OFstream str("illegalFaces");
Info<< "Dumping conflicting face labels to " << str.name() << endl
<< "Paste this into the input for surfaceSubset" << endl;
str << illegalFaces;
}
else
{
Info<< "Surface has no illegal triangles." << endl;
}
Info<< endl;
}
// Triangle quality
// ~~~~~~~~~~~~~~~~
{
scalarField triQ(surf.size(), 0);
forAll(surf, facei)
{
const labelledTri& f = surf[facei];
if (f[0] == f[1] || f[0] == f[2] || f[1] == f[2])
{
// WarningIn(args.executable())
// << "Illegal triangle " << facei << " vertices " << f
// << " coords " << f.points(surf.points()) << endl;
}
else
{
triQ[facei] = triPointRef
(
surf.points()[f[0]],
surf.points()[f[1]],
surf.points()[f[2]]
).quality();
}
}
labelList binCount = countBins(0, 1, 20, triQ);
Info<< "Triangle quality (equilateral=1, collapsed=0):"
<< endl;
OSstream& os = Info;
os.width(4);
scalar dist = (1.0 - 0.0)/20.0;
scalar min = 0;
forAll(binCount, binI)
{
Info<< " " << min << " .. " << min+dist << " : "
<< 1.0/surf.size() * binCount[binI]
<< endl;
min += dist;
}
Info<< endl;
label minIndex = findMin(triQ);
label maxIndex = findMax(triQ);
Info<< " min " << triQ[minIndex] << " for triangle " << minIndex
<< nl
<< " max " << triQ[maxIndex] << " for triangle " << maxIndex
<< nl
<< endl;
if (triQ[minIndex] < small)
{
WarningInFunction
<< triQ[minIndex] << ". This might give problems in"
<< " self-intersection testing later on." << endl;
}
// Dump for subsetting
{
DynamicList<label> problemFaces(surf.size()/100+1);
forAll(triQ, facei)
{
if (triQ[facei] < 1e-11)
{
problemFaces.append(facei);
}
}
if (!problemFaces.empty())
{
OFstream str("badFaces");
Info<< "Dumping bad quality faces to " << str.name() << endl
<< "Paste this into the input for surfaceSubset" << nl
<< nl << endl;
str << problemFaces;
}
}
}
// Edges
// ~~~~~
{
const edgeList& edges = surf.edges();
const pointField& localPoints = surf.localPoints();
scalarField edgeMag(edges.size());
forAll(edges, edgeI)
{
edgeMag[edgeI] = edges[edgeI].mag(localPoints);
}
label minEdgeI = findMin(edgeMag);
label maxEdgeI = findMax(edgeMag);
const edge& minE = edges[minEdgeI];
const edge& maxE = edges[maxEdgeI];
Info<< "Edges:" << nl
<< " min " << edgeMag[minEdgeI] << " for edge " << minEdgeI
<< " points " << localPoints[minE[0]] << localPoints[minE[1]]
<< nl
<< " max " << edgeMag[maxEdgeI] << " for edge " << maxEdgeI
<< " points " << localPoints[maxE[0]] << localPoints[maxE[1]]
<< nl
<< endl;
}
// Close points
// ~~~~~~~~~~~~
{
const edgeList& edges = surf.edges();
const pointField& localPoints = surf.localPoints();
const boundBox bb(localPoints);
scalar smallDim = 1e-6 * bb.mag();
Info<< "Checking for points less than 1e-6 of bounding box ("
<< bb.span() << " metre) apart."
<< endl;
// Sort points
SortableList<scalar> sortedMag(mag(localPoints));
label nClose = 0;
for (label i = 1; i < sortedMag.size(); i++)
{
label ptI = sortedMag.indices()[i];
label prevPtI = sortedMag.indices()[i-1];
if (mag(localPoints[ptI] - localPoints[prevPtI]) < smallDim)
{
// Check if neighbours.
const labelList& pEdges = surf.pointEdges()[ptI];
label edgeI = -1;
forAll(pEdges, i)
{
const edge& e = edges[pEdges[i]];
if (e[0] == prevPtI || e[1] == prevPtI)
{
// point1 and point0 are connected through edge.
edgeI = pEdges[i];
break;
}
}
nClose++;
if (edgeI == -1)
{
Info<< " close unconnected points "
<< ptI << ' ' << localPoints[ptI]
<< " and " << prevPtI << ' '
<< localPoints[prevPtI]
<< " distance:"
<< mag(localPoints[ptI] - localPoints[prevPtI])
<< endl;
}
else
{
Info<< " small edge between points "
<< ptI << ' ' << localPoints[ptI]
<< " and " << prevPtI << ' '
<< localPoints[prevPtI]
<< " distance:"
<< mag(localPoints[ptI] - localPoints[prevPtI])
<< endl;
}
}
}
Info<< "Found " << nClose << " nearby points." << nl
<< endl;
}
// Check manifold
// ~~~~~~~~~~~~~~
DynamicList<label> problemFaces(surf.size()/100 + 1);
const labelListList& eFaces = surf.edgeFaces();
label nSingleEdges = 0;
forAll(eFaces, edgeI)
{
const labelList& myFaces = eFaces[edgeI];
if (myFaces.size() == 1)
{
problemFaces.append(myFaces[0]);
nSingleEdges++;
}
}
label nMultEdges = 0;
forAll(eFaces, edgeI)
{
const labelList& myFaces = eFaces[edgeI];
if (myFaces.size() > 2)
{
forAll(myFaces, myFacei)
{
problemFaces.append(myFaces[myFacei]);
}
nMultEdges++;
}
}
problemFaces.shrink();
if ((nSingleEdges != 0) || (nMultEdges != 0))
{
Info<< "Surface is not closed since not all edges connected to "
<< "two faces:" << endl
<< " connected to one face : " << nSingleEdges << endl
<< " connected to >2 faces : " << nMultEdges << endl;
Info<< "Conflicting face labels:" << problemFaces.size() << endl;
OFstream str("problemFaces");
Info<< "Dumping conflicting face labels to " << str.name() << endl
<< "Paste this into the input for surfaceSubset" << endl;
str << problemFaces;
}
else
{
Info<< "Surface is closed. All edges connected to two faces." << endl;
}
Info<< endl;
// Check singly connected domain
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
boolList borderEdge(surf.nEdges(), false);
if (splitNonManifold)
{
const labelListList& eFaces = surf.edgeFaces();
forAll(eFaces, edgeI)
{
if (eFaces[edgeI].size() > 2)
{
borderEdge[edgeI] = true;
}
}
}
labelList faceZone;
label numZones = surf.markZones(borderEdge, faceZone);
Info<< "Number of unconnected parts : " << numZones << endl;
if (numZones > 1)
{
Info<< "Splitting surface into parts ..." << endl << endl;
fileName surfFileNameBase(surfFileName.name());
const word fileType = surfFileNameBase.ext();
// Strip extension
surfFileNameBase = surfFileNameBase.lessExt();
// If extension was .gz strip original extension
if (fileType == "gz")
{
surfFileNameBase = surfFileNameBase.lessExt();
}
{
Info<< "Writing zoning to "
<< fileName
(
"zone_"
+ surfFileNameBase
+ '.'
+ vtkSurfaceWriter::typeName
)
<< "..." << endl << endl;
// Convert data
scalarField scalarFaceZone(faceZone.size());
forAll(faceZone, i)
{
scalarFaceZone[i] = faceZone[i];
}
faceList faces(surf.size());
forAll(surf, i)
{
faces[i] = surf[i].triFaceFace();
}
vtkSurfaceWriter(IOstream::ASCII, IOstream::UNCOMPRESSED).write
(
surfFileName.path(),
"zone_" + surfFileNameBase,
surf.points(),
faces,
false, // face based data
"zone",
scalarFaceZone
);
}
for (label zone = 0; zone < numZones; zone++)
{
boolList includeMap(surf.size(), false);
forAll(faceZone, facei)
{
if (faceZone[facei] == zone)
{
includeMap[facei] = true;
}
}
labelList pointMap;
labelList faceMap;
triSurface subSurf
(
surf.subsetMesh
(
includeMap,
pointMap,
faceMap
)
);
fileName subName(surfFileNameBase + "_" + name(zone) + ".obj");
Info<< "writing part " << zone << " size " << subSurf.size()
<< " to " << subName << endl;
subSurf.write(subName);
}
}
}
// Check orientation
// ~~~~~~~~~~~~~~~~~
labelHashSet borderEdge(surf.size()/1000);
PatchTools::checkOrientation(surf, false, &borderEdge);
//
// Colour all faces into zones using borderEdge
//
labelList normalZone;
label numNormalZones = PatchTools::markZones(surf, borderEdge, normalZone);
Info<< endl
<< "Number of zones (connected area with consistent normal) : "
<< numNormalZones << endl;
if (numNormalZones > 1)
{
Info<< "More than one normal orientation." << endl;
}
Info<< endl;
// Check self-intersection
// ~~~~~~~~~~~~~~~~~~~~~~~
if (checkSelfIntersect)
{
Info<< "Checking self-intersection." << endl;
triSurfaceSearch querySurf(surf);
const indexedOctree<treeDataTriSurface>& tree = querySurf.tree();
OBJstream intStream("selfInterPoints.obj");
label nInt = 0;
forAll(surf.edges(), edgeI)
{
const edge& e = surf.edges()[edgeI];
pointIndexHit hitInfo
(
tree.findLine
(
surf.points()[surf.meshPoints()[e[0]]],
surf.points()[surf.meshPoints()[e[1]]],
treeDataTriSurface::findSelfIntersectOp
(
tree,
edgeI
)
)
);
if (hitInfo.hit())
{
intStream.write(hitInfo.hitPoint());
nInt++;
}
}
if (nInt == 0)
{
Info<< "Surface is not self-intersecting" << endl;
}
else
{
Info<< "Surface is self-intersecting at " << nInt
<< " locations." << endl;
Info<< "Writing intersection points to " << intStream.name()
<< endl;
}
// surfaceIntersection inter(querySurf);
//
// if (inter.cutEdges().empty() && inter.cutPoints().empty())
//{
// Info<< "Surface is not self-intersecting" << endl;
//}
// else
//{
// Info<< "Surface is self-intersecting" << endl;
// Info<< "Writing edges of intersection to selfInter.obj" << endl;
//
// OFstream intStream("selfInter.obj");
// forAll(inter.cutPoints(), cutPointi)
// {
// const point& pt = inter.cutPoints()[cutPointi];
//
// intStream << "v " << pt.x() << ' ' << pt.y() << ' ' << pt.z()
// << endl;
// }
// forAll(inter.cutEdges(), cutEdgeI)
// {
// const edge& e = inter.cutEdges()[cutEdgeI];
//
// intStream << "l " << e.start()+1 << ' ' << e.end()+1 << endl;
// }
//}
Info<< endl;
}
Info<< "\nEnd\n" << endl;
return 0;
}
// ************************************************************************* //