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ENH: Change List<> to DynamicList<> in point insertion.

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Was a massive bottleneck
Also changed surface conformation to use findAllNearestEdges
This commit is contained in:
laurence 2012-01-17 16:21:04 +00:00
parent 34e088b228
commit 36419e5eff
8 changed files with 91 additions and 188 deletions
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16
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/conformalVoronoiMesh/conformalVoronoiMesh.C
View File

@ -793,7 +793,7 @@ bool Foam::conformalVoronoiMesh::distributeBackground()
void Foam::conformalVoronoiMesh::storeSizesAndAlignments()
{
List<Point> storePts;
DynamicList<Point> storePts(number_of_vertices());
for
(
@ -808,6 +808,8 @@ void Foam::conformalVoronoiMesh::storeSizesAndAlignments()
}
}
storePts.shrink();
storeSizesAndAlignments(storePts);
}
@ -1359,7 +1361,7 @@ void Foam::conformalVoronoiMesh::move()
true
);
List<Point> pointsToInsert;
DynamicList<Point> pointsToInsert(number_of_vertices());
for
(
@ -1640,13 +1642,9 @@ void Foam::conformalVoronoiMesh::move()
}
}
// Save displacements to file. To view, convert to vtk so that the times can
// be viewed in paraview:
//
// for i in {0..N}
// do
// objToVTK displacements$i.obj displacement$i.vtk
// done
pointsToInsert.shrink();
// Save displacements to file.
if (cvMeshControls().objOutput() && runTime_.outputTime())
{
Pout<< "Writing point displacement vectors to file." << endl;

216
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/conformalVoronoiMesh/conformalVoronoiMeshConformToSurface.C
View File

@ -193,6 +193,11 @@ void Foam::conformalVoronoiMesh::buildSurfaceConformation
{
const Foam::point vert = topoint(vit->point());
if (!positionOnThisProc(vert))
{
continue;
}
DynamicList<pointIndexHit> surfHitList;
DynamicList<label> hitSurfaceList;
@ -266,6 +271,10 @@ void Foam::conformalVoronoiMesh::buildSurfaceConformation
"edgeConformationLocations_initial.obj"
);
timeCheck("After initial conformation");
initialTotalHits = nSurfHits + nFeatEdHits;
// Filter small edges at the boundary by inserting surface point pairs
// for
// (
@ -338,9 +347,6 @@ void Foam::conformalVoronoiMesh::buildSurfaceConformation
// }
// }
timeCheck("After initial conformation");
initialTotalHits = nSurfHits + nFeatEdHits;
}
// Remember which vertices were referred to each processor so only updates
@ -647,8 +653,9 @@ bool Foam::conformalVoronoiMesh::dualCellSurfaceAllIntersections
continue;
}
// Construct the dual edge and search for intersections of the edge
// with the surface
Foam::point dE0 = topoint(dual(fit->first));
Foam::point dE1 = topoint(dual(fit->first->neighbor(fit->second)));
pointIndexHit infoIntersection;
@ -1834,12 +1841,12 @@ bool Foam::conformalVoronoiMesh::nearFeatureEdgeLocation
// 0.01 and 1000 determined from speed tests, varying the indexedOctree
// rebuild frequency and balance of additions to queries.
// if
// (
// newEdgeLocations.size()
// >= max(0.01*existingEdgeLocations.size(), 1000)
// )
// {
if
(
newEdgeLocations.size()
>= max(0.01*existingEdgeLocations.size(), 1000)
)
{
const label originalSize = existingEdgeLocations.size();
existingEdgeLocations.append(newEdgeLocations);
@ -1847,19 +1854,19 @@ bool Foam::conformalVoronoiMesh::nearFeatureEdgeLocation
buildEdgeLocationTree(edgeLocationTree, existingEdgeLocations);
newEdgeLocations.clear();
// }
// else
// {
// // Search for the nearest point in newEdgeLocations.
// // Searching here first, because the intention is that the value of
// // newEdgeLocationsSizeLimit should make this faster by design.
//
// if (min(magSqr(newEdgeLocations - pt)) <= exclusionRangeSqr)
// {
// // Average the points...
// return true;
// }
// }
}
else
{
// Search for the nearest point in newEdgeLocations.
// Searching here first, because the intention is that the value of
// newEdgeLocationsSizeLimit should make this faster by design.
if (min(magSqr(newEdgeLocations - pt)) <= exclusionRangeSqr)
{
// Average the points...
return true;
}
}
// Searching for the nearest point in existingEdgeLocations using the
// indexedOctree
@ -1989,123 +1996,8 @@ void Foam::conformalVoronoiMesh::addSurfaceAndEdgeHits
{
bool keepSurfacePoint = true;
const scalar targetCellSizeSqr = sqr(targetCellSize(vert));
DynamicList<label> pointsUsed;
// Place edge points for external edges.
forAll(surfHit, hI)
{
if (surfHit.size() < 2)
{
break;
}
const pointIndexHit& hitInfo = surfHit[hI];
const label& hitSurf = hitSurface[hI];
if (!hitInfo.hit())
{
continue;
}
vectorField norm1(1);
allGeometry_[hitSurf].getNormal
(
List<pointIndexHit>(1, hitInfo),
norm1
);
const vector& n1 = norm1[0];
const plane surfPlane(hitInfo.hitPoint(), n1);
pointsUsed.append(hI);
// Find the new edge points by finding the distance of the other surface
// points from the the plane that the first point is on.
forAll(surfHit, hI2)
{
bool alreadyUsed = false;
forAll(pointsUsed, puI)
{
if (hI2 == pointsUsed[puI])
{
alreadyUsed = true;
}
}
if (alreadyUsed == true)
{
continue;
}
const pointIndexHit& hitInfo2 = surfHit[hI2];
const label& hitSurf2 = hitSurface[hI2];
if (!hitInfo2.hit())
{
continue;
}
const Foam::point& surfPoint = hitInfo2.hitPoint();
const scalar d = surfPlane.distance(surfPoint);
vectorField norm2(1);
allGeometry_[hitSurf2].getNormal
(
List<pointIndexHit>(1, hitInfo2),
norm2
);
const vector& n2 = norm2[0];
// If the normals are nearly parallel then ignore.
if (areParallel(n1, n2))
{
continue;
}
const Foam::point newEdgePoint = surfPoint + n1*d;
pointIndexHit edHit;
label featureHit = -1;
geometryToConformTo_.findEdgeNearest
(
newEdgePoint,
edgeSearchDistCoeffSqr*targetCellSizeSqr,
edHit,
featureHit
);
if (edHit.hit())
{
if (!nearFeaturePt(edHit.hitPoint()))
{
if
(
!nearFeatureEdgeLocation
(
edHit,
newEdgeLocations,
existingEdgeLocations,
edgeLocationTree
)
)
{
featureEdgeHits.append(edHit);
featureEdgeFeaturesHit.append(featureHit);
newEdgeLocations.append(edHit.hitPoint());
}
}
}
}
}
const scalar cellSize = targetCellSize(vert);
const scalar cellSizeSqr = sqr(cellSize);
forAll(surfHit, sI)
{
@ -2131,15 +2023,17 @@ void Foam::conformalVoronoiMesh::addSurfaceAndEdgeHits
}
}
List<pointIndexHit> edHits;
List<List<pointIndexHit> > edHitsByFeature;
labelList featuresHit;
geometryToConformTo_.findEdgeNearestByType
const scalar searchRadiusSqr = edgeSearchDistCoeffSqr*cellSizeSqr;
geometryToConformTo_.findAllNearestEdges
(
surfHitI.hitPoint(),
edgeSearchDistCoeffSqr*targetCellSizeSqr,
edHits,
searchRadiusSqr,
edHitsByFeature,
featuresHit
);
@ -2149,31 +2043,22 @@ void Foam::conformalVoronoiMesh::addSurfaceAndEdgeHits
DynamicList<Foam::point> currentEdgeLocations;
forAll(edHits, i)
forAll(edHitsByFeature, i)
{
// Ignore external edges, they have been dealt with.
if (i == 0 && surfHit.size() > 1)
const label featureHit = featuresHit[i];
List<pointIndexHit>& edHits = edHitsByFeature[i];
forAll(edHits, eHitI)
{
continue;
}
pointIndexHit& edHit = edHits[i];
label featureHit = featuresHit[i];
if (edHit.hit())
{
if (!positionOnThisProc(edHit.hitPoint()))
{
continue;
}
pointIndexHit& edHit = edHits[eHitI];
if (!nearFeaturePt(edHit.hitPoint()))
{
if
(
magSqr(edHit.hitPoint() - surfHitI.hitPoint())
< surfacePtReplaceDistCoeffSqr*targetCellSizeSqr
< surfacePtReplaceDistCoeffSqr*cellSizeSqr
)
{
// If the point is within a given distance of a feature
@ -2224,6 +2109,9 @@ void Foam::conformalVoronoiMesh::storeSurfaceConformation()
surfaceConformationVertices_.clear();
// Use a temporary dynamic list to speed up insertion.
DynamicList<Vb> tempSurfaceVertices(number_of_vertices()/10);
for
(
Delaunay::Finite_vertices_iterator vit = finite_vertices_begin();
@ -2240,7 +2128,7 @@ void Foam::conformalVoronoiMesh::storeSurfaceConformation()
&& vit->index() >= startOfInternalPoints_
)
{
surfaceConformationVertices_.append
tempSurfaceVertices.append
(
Vb
(
@ -2252,6 +2140,10 @@ void Foam::conformalVoronoiMesh::storeSurfaceConformation()
}
}
tempSurfaceVertices.shrink();
surfaceConformationVertices_.transfer(tempSurfaceVertices);
Info<< " Stored "
<< returnReduce
(

24
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/autoDensity/autoDensity.C
View File

@ -177,7 +177,7 @@ bool Foam::autoDensity::combinedWellInside
void Foam::autoDensity::recurseAndFill
(
List<Vb::Point>& initialPoints,
DynamicList<Vb::Point>& initialPoints,
const treeBoundBox& bb,
label levelLimit,
word recursionName
@ -272,7 +272,7 @@ void Foam::autoDensity::recurseAndFill
bool Foam::autoDensity::fillBox
(
List<Vb::Point>& initialPoints,
DynamicList<Vb::Point>& initialPoints,
const treeBoundBox& bb,
bool overlapping
) const
@ -849,10 +849,7 @@ autoDensity::autoDensity
:
initialPointsMethod(typeName, initialPointsDict, cvMesh),
globalTrialPoints_(0),
minCellSizeLimit_
(
detailsDict().lookupOrDefault<scalar>("minCellSizeLimit", 0.0)
),
minCellSizeLimit_(readScalar(detailsDict().lookup("minCellSizeLimit"))),
minLevels_(readLabel(detailsDict().lookup("minLevels"))),
maxSizeRatio_(readScalar(detailsDict().lookup("maxSizeRatio"))),
volRes_(readLabel(detailsDict().lookup("sampleResolution"))),
@ -902,7 +899,18 @@ List<Vb::Point> autoDensity::initialPoints() const
);
}
List<Vb::Point> initialPoints;
// Initialise size of points list.
const scalar volumeBoundBox = Foam::pow3(hierBB.typDim());
const scalar volumeSmallestCell = Foam::pow3(minCellSizeLimit_);
const int initialPointEstimate
= min
(
static_cast<int>(volumeBoundBox/(volumeSmallestCell + SMALL)/10),
1e6
);
DynamicList<Vb::Point> initialPoints(initialPointEstimate);
Info<< nl << " " << typeName << endl;
@ -919,6 +927,8 @@ List<Vb::Point> autoDensity::initialPoints() const
"recursionBox"
);
initialPoints.shrink();
label nInitialPoints = initialPoints.size();
if (Pstream::parRun())

4
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/autoDensity/autoDensity.H
View File

@ -116,7 +116,7 @@ private:
//- Descend into octants of the supplied bound box
void recurseAndFill
(
List<Vb::Point>& initialPoints,
DynamicList<Vb::Point>& initialPoints,
const treeBoundBox& bb,
label levelLimit,
word recursionName
@ -127,7 +127,7 @@ private:
// in favour of further recursion.
bool fillBox
(
List<Vb::Point>& initialPoints,
DynamicList<Vb::Point>& initialPoints,
const treeBoundBox& bb,
bool overlapping
) const;

4
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/bodyCentredCubic/bodyCentredCubic.C
View File

@ -91,7 +91,7 @@ List<Vb::Point> bodyCentredCubic::initialPoints() const
scalar pert = randomPerturbationCoeff_*cmptMin(delta);
List<Vb::Point> initialPoints;
DynamicList<Vb::Point> initialPoints(ni*nj*nk/10);
for (label i = 0; i < ni; i++)
{
@ -183,7 +183,7 @@ List<Vb::Point> bodyCentredCubic::initialPoints() const
}
}
return initialPoints;
return initialPoints.shrink();
}

4
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/faceCentredCubic/faceCentredCubic.C
View File

@ -91,7 +91,7 @@ List<Vb::Point> faceCentredCubic::initialPoints() const
scalar pert = randomPerturbationCoeff_*cmptMin(delta);
List<Vb::Point> initialPoints;
DynamicList<Vb::Point> initialPoints(ni*nj*nk/10);
for (label i = 0; i < ni; i++)
{
@ -244,7 +244,7 @@ List<Vb::Point> faceCentredCubic::initialPoints() const
}
}
return initialPoints;
return initialPoints.shrink();
}

6
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/pointFile/pointFile.C
View File

@ -126,8 +126,6 @@ List<Vb::Point> pointFile::initialPoints() const
}
}
List<Vb::Point> initialPoints;
Field<bool> insidePoints = cvMesh_.geometryToConformTo().wellInside
(
points,
@ -138,6 +136,8 @@ List<Vb::Point> pointFile::initialPoints() const
)
);
DynamicList<Vb::Point> initialPoints(insidePoints.size()/10);
forAll(insidePoints, i)
{
if (insidePoints[i])
@ -148,6 +148,8 @@ List<Vb::Point> pointFile::initialPoints() const
}
}
initialPoints.shrink();
label nPointsRejected = points.size() - initialPoints.size();
if (Pstream::parRun())

5
applications/utilities/mesh/generation/cvMesh/conformalVoronoiMesh/initialPointsMethod/uniformGrid/uniformGrid.C
View File

@ -91,7 +91,8 @@ List<Vb::Point> uniformGrid::initialPoints() const
scalar pert = randomPerturbationCoeff_*cmptMin(delta);
List<Vb::Point> initialPoints;
// Initialise points list
DynamicList<Vb::Point> initialPoints(ni*nj*nk/10);
for (label i = 0; i < ni; i++)
{
@ -159,7 +160,7 @@ List<Vb::Point> uniformGrid::initialPoints() const
}
}
return initialPoints;
return initialPoints.shrink();
}