Merge branch 'master' of /home/dm4/OpenFOAM/OpenFOAM-dev

applications/test/GAMGAgglomeration/Test-GAMGAgglomeration.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -35,6 +35,116 @@ Description
 #include "meshTools.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void checkConnectedAgglomeration
+(
+    const lduMesh& mesh,
+    const labelUList& restrict,
+    const label nCoarse
+)
+{
+    if (mesh.lduAddr().size() != restrict.size())
+    {
+        FatalErrorIn
+        (
+            "checkConnectedAgglomeration(const lduMesh&, const labelList&)"
+        )   << "nCells:" << mesh.lduAddr().size()
+            << " agglom:" << restrict.size()
+            << abort(FatalError);
+    }
+
+    // Seed (master) for every region
+    labelList regionToMaster(nCoarse, -1);
+    labelList master(mesh.lduAddr().size(), -1);
+    forAll(restrict, cellI)
+    {
+        label region = restrict[cellI];
+        if (regionToMaster[region] == -1)
+        {
+            // Set cell to be master for region
+            //Pout<< "For region " << region
+            //    << " allocating local master " << cellI
+            //    << endl;
+            regionToMaster[region] = cellI;
+            master[cellI] = cellI;
+        }
+    }
+
+    // Now loop and transport master through region
+    const labelUList& lower = mesh.lduAddr().lowerAddr();
+    const labelUList& upper = mesh.lduAddr().upperAddr();
+
+    while (true)
+    {
+        label nChanged = 0;
+
+        forAll(lower, faceI)
+        {
+            label own = lower[faceI];
+            label nei = upper[faceI];
+
+            if (restrict[own] == restrict[nei])
+            {
+                // Region-internal face
+
+                if (master[own] != -1)
+                {
+                    if (master[nei] == -1)
+                    {
+                        master[nei] = master[own];
+                        nChanged++;
+                    }
+                    else if (master[nei] != master[own])
+                    {
+                        FatalErrorIn("checkConnectedAgglomeration(..)")
+                            << "problem" << abort(FatalError);
+                    }
+                }
+                else if (master[nei] != -1)
+                {
+                    master[own] = master[nei];
+                    nChanged++;
+                }
+            }
+        }
+
+        reduce(nChanged, sumOp<label>());
+
+        if (nChanged == 0)
+        {
+            break;
+        }
+    }
+
+    // Check that master is set for all cells
+    boolList singleRegion(nCoarse, true);
+    label nSet = nCoarse;
+    forAll(master, cellI)
+    {
+        if (master[cellI] == -1)
+        {
+            label region = restrict[cellI];
+            if (singleRegion[region] == true)
+            {
+                singleRegion[region] = false;
+                nSet--;
+            }
+        }
+    }
+
+    label totalNCoarse = returnReduce(nCoarse, sumOp<label>());
+    label totalNVisited = returnReduce(nSet, sumOp<label>());
+
+    if (totalNVisited < totalNCoarse)
+    {
+        WarningIn("checkConnectedAgglomeration(..)")
+            << "out of " << totalNCoarse
+            << " agglomerated cells have " << totalNCoarse-totalNVisited
+            << " cells that are not a single connected region" << endl;
+    }
+}
+
+
 // Main program:
 
 int main(int argc, char *argv[])
@@ -117,6 +227,14 @@ int main(int argc, char *argv[])
             << "    agglomerated size : "
             << returnReduce(coarseSize, sumOp<label>()) << endl;
 
+        checkConnectedAgglomeration
+        (
+            agglom.meshLevel(level),
+            addr,
+            coarseSize
+        );
+
+
         forAll(addr, fineI)
         {
             const labelList& cellLabels = coarseToCell[fineI];

applications/utilities/surface/surfaceLambdaMuSmooth/surfaceLambdaMuSmooth.C

@@ -222,14 +222,6 @@ int main(int argc, char *argv[])
     }
 
     Info<< "Writing surface to " << outFileName << " ..." << endl;
-
-//    meshedSurface
-//    (
-//        xferMove(newPoints),
-//        xferCopy(surf1.localFaces()),
-//        xferCopy(surf1.surfZones())
-//    ).write(outFileName);
-
     surf1.write(outFileName);
 
     Info<< "End\n" << endl;

bin/foamInstallationTest

@@ -457,7 +457,7 @@ hline
 echo "$COL1 $COL2 $COL3"
 hline
 reportExecutable flex
-reportExecutable gcc
+reportExecutable "$WM_CC"
 reportExecutable gzip
 if [ "$OSTYPE" = Linux ]
 then

bin/tools/pre-commit-hook

@@ -147,7 +147,7 @@ checkIllegalCode()
     do
         case "$f" in
         # exclude potential makefiles
-        (*[Mm]akefile* | wmake/rules/* | *.f* | *.v[cf]proj | *.pdf | *.png | *.html | *.gif | *.css)
+        (*[Mm]akefile* | wmake/rules/* | *.f* | *.v[cf]proj | *.pdf | *.png | *.html | *.gif | *.css | *.gz)
         ;;
         (*)
             fileType=`file -b $f`

tutorials/incompressible/pimpleDyMFoam/oscillatingInletACMI2D/README

@@ -105,3 +105,30 @@ Boundary conditions must then be applied to all geometric patches in the usual,
 manner, and the cases can be executed in parallel (as shown when running the
 Allrun-parallel script) without any speacial treatment, i.e. the case set-up is
 the same as when operating in serial mode.
+
+
+checkMesh
+---------
+checkMesh will see the 'duplicate' boundary faces but does not know about
+the area factors so will complain:
+
+     ***Boundary openness (-0.0103092 2.3845e-17 3.80774e-17) possible hole in boundary description.
+     ***Open cells found, max cell openness: 0.333333, number of open cells 136
+      <<Writing 136 non closed cells to set nonClosedCells
+
+As long as these non-closed cells are on the ACMI they can be ignored.
+
+
+paraFoam
+--------
+- display: it will not display the outside of the ACMI, there will be a hole.
+- cuttingPlanes: they leave out the duplicate faces (i.e. the cells on
+  the ACMI patches)
+- interpolation: the interpolation does not take into account the
+area-weights on the ACMI.
+
+
+pointFields
+-----------
+Same as paraFoam: the interpolation does not take into account the
+area-weights on the ACMI.

tutorials/mesh/foamyHexMesh/blob/Allrun

@@ -4,8 +4,12 @@ cd ${0%/*} || exit 1    # run from this directory
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
+# copy flange surface from resources folder
+cp $FOAM_TUTORIALS/resources/geometry/blob.stl.gz constant/triSurface/
+
 runApplication foamyHexMesh
 runApplication collapseEdges -latestTime -collapseFaces
 runApplication checkMesh -latestTime -allGeometry -allTopology
 
+
 # ----------------------------------------------------------------- end-of-file

tutorials/mesh/foamyHexMesh/blob/Allrun-parallel

@@ -7,6 +7,9 @@ cd ${0%/*} || exit 1    # run from this directory
 # Get the number of processors to run on from system/decomposeParDict
 nProc=$(getNumberOfProcessors)
 
+# copy flange surface from resources folder
+cp $FOAM_TUTORIALS/resources/geometry/blob.stl.gz constant/triSurface/
+
 runApplication blockMesh
 runApplication decomposePar
 
@@ -16,4 +19,5 @@ runParallel checkMesh $nProc -latestTime -allTopology -allGeometry
 
 runApplication reconstructParMesh -latestTime
 
+
 # ----------------------------------------------------------------- end-of-file

tutorials/mesh/foamyHexMesh/blob/Alltest

@@ -1,18 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # run from this directory
-
-# Source tutorial run functions
-. $WM_PROJECT_DIR/bin/tools/RunFunctions
-
-runApplication foamyHexMesh
-
-# Change collapseEdges to only do one iteration
-cp system/collapseDict system/collapseDict.org
-
-sed -e s/"\(maximumIterations[ \t]*\)\([0-9]*\);"/"\1 1;"/g \
-system/collapseDict.org > system/collapseDict
-
-runApplication collapseEdges -latestTime -collapseFaces
-
-
-# ----------------------------------------------------------------- end-of-file

tutorials/mesh/foamyHexMesh/blob/constant/polyMesh/boundary

@@ -1,28 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  dev                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       polyBoundaryMesh;
-    location    "constant/polyMesh";
-    object      boundary;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-1
-(
-    walls
-    {
-        type            wall;
-        nFaces          638;
-        startFace       2948;
-    }
-)
-
-// ************************************************************************* //

tutorials/mesh/foamyHexMesh/blob/constant/triSurface/README

@@ -0,0 +1,4 @@
+Folder to house tri-surfaces
+
+The Allrun script copies the surface from the $FOAM_TUTORIALS/resources/geometry
+folder

tutorials/mesh/foamyHexMesh/simpleShapes/Allrun

@@ -4,24 +4,22 @@ cd ${0%/*} || exit 1    # run from this directory
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Remove any small triangles (edges < 1e-4, sliver with Q < 1e-6) from surface
-# (cvMesh will try to conform to every feature).
-runApplication surfaceClean \
-    constant/triSurface/coneAndSphere.obj \
-    1e-4 1e-6 \
-    constant/triSurface/coneAndSphere_clean.obj
-mv log.surfaceClean log.surfaceClean.coneAndSphere
-# Orient so point to be meshed is inside surface
 runApplication surfaceOrient \
-    constant/triSurface/coneAndSphere_clean.obj \
+    constant/triSurface/cone.stl \
     -inside '(0 -0.5 0)' \
-    constant/triSurface/coneAndSphere_clean_orient.obj
+    constant/triSurface/cone_orient.stl
-mv log.surfaceOrient log.surfaceOrient.coneAndSphere
+mv log.surfaceOrient log.surfaceOrient.cone
 
-unset FOAM_SIGFPE
+runApplication surfaceOrient \
+    constant/triSurface/sphere.stl \
+    -inside '(0 -0.5 0)' \
+    constant/triSurface/sphere_orient.stl
+mv log.surfaceOrient log.surfaceOrient.sphere
+
+runApplication surfaceBooleanFeatures intersection \
+                       constant/triSurface/cone_orient.stl \
+                       constant/triSurface/sphere_orient.stl
 
-# Generate aligned points (in constant/internalDelaunayVertices) and a
-# mesh from that.
 runApplication foamyHexMesh
 
 

tutorials/mesh/foamyHexMesh/simpleShapes/system/foamyHexMeshDict

@@ -19,10 +19,15 @@ FoamFile
 
 geometry
 {
-    // Internal shape
+    sphere_orient.stl
-    coneAndSphere_clean_orient.obj
     {
-        name coneAndSphere;
+        name sphere;
+        type triSurfaceMesh;
+    }
+
+    cone_orient.stl
+    {
+        name cone;
         type triSurfaceMesh;
     }
 
@@ -43,27 +48,53 @@ surfaceConformation
 
     featurePointControls
     {
-        specialiseFeaturePoints on;
+        specialiseFeaturePoints off;
-        edgeAiming              on;
+        edgeAiming              off;
         guardFeaturePoints      off;
-        snapFeaturePoints       on;
+        snapFeaturePoints       off;
         circulateEdges          off;
     }
 
     // Geometry to mesh to
     geometryToConformTo
     {
-        coneAndSphere
+        cone
         {
-            featureMethod           extractFeatures;
+            featureMethod   extractFeatures;
-            includedAngle           140;
+            includedAngle   140;
+
+            patchInfo
+            {
+                type        wall;
+                inGroups    (groupConeAndSphere);
+            }
+        }
+
+        sphere
+        {
+            featureMethod   none;
+
+            patchInfo
+            {
+                type        wall;
+                inGroups    (groupConeAndSphere);
+            }
         }
 
         domain
         {
-            featureMethod           extractFeatures;
+            featureMethod   extractFeatures;
-            includedAngle           100;
+            includedAngle   100;
-            mode                    outside;
+            mode            outside;
+        }
+    }
+
+    additionalFeatures
+    {
+        coneSphereIntersection
+        {
+            featureMethod           extendedFeatureEdgeMesh;
+            extendedFeatureEdgeMesh "cone_orient_sphere_orient_intersection.extendedFeatureEdgeMesh";
         }
     }
 }
@@ -71,7 +102,7 @@ surfaceConformation
 
 initialPoints
 {
-    initialPointsMethod             autoDensity;
+    initialPointsMethod         autoDensity;
 
     autoDensityCoeffs
     {
@@ -97,7 +128,24 @@ motionControl
 
     shapeControlFunctions
     {
-        coneAndSphere
+        sphere
+        {
+            type                searchableSurfaceControl;
+            priority            1;
+            mode                bothSides;
+
+            surfaceCellSizeFunction uniformValue;
+            uniformValueCoeffs
+            {
+                surfaceCellSizeCoeff 0.5;
+            }
+
+            cellSizeFunction        uniform;
+            uniformCoeffs
+            {}
+        }
+
+        cone
         {
             type                searchableSurfaceControl;
             priority            1;