From ffa75238a625aa38e477fbac1fcb328b611dc7e9 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Thu, 11 Dec 2008 15:49:29 +0000
Subject: [PATCH 1/5] comment

---
 .../utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
index 5777ae8a8a..43d550f406 100644
--- a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
+++ b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
@@ -292,6 +292,7 @@ meshQualityControls
     minFlatness 0.5;
 
     //- Minimum pyramid volume. Is absolute volume of cell pyramid.
+    //  Set to a sensible fraction of the smallest cell volume expected.
     //  Set to very negative number (e.g. -1E30) to disable.
     minVol 1e-13;
 

From 987b894e681103388d0705a6d4c717397249f1da Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Thu, 11 Dec 2008 15:50:29 +0000
Subject: [PATCH 2/5] hpmpi

---
 src/Pstream/Allwmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Pstream/Allwmake b/src/Pstream/Allwmake
index 3083370ad7..25886fbfac 100755
--- a/src/Pstream/Allwmake
+++ b/src/Pstream/Allwmake
@@ -5,7 +5,7 @@ set -x
 wmake libso dummy
 
 case "$WM_MPLIB" in
-LAM | OPENMPI | MPI | MPICH | MPICH-GM | HPMPI | MPIGAMMA )
+LAM | OPENMPI | MPI | MPICH | MPICH-GM | HPMPI )
    export WM_OPTIONS=${WM_OPTIONS}$WM_MPLIB
    set +x
    echo

From e9d5f929bc880373a938b2e890e519d8a8703086 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Thu, 11 Dec 2008 15:50:50 +0000
Subject: [PATCH 3/5] synchronisation of zones

---
 .../meshRefinement/meshRefinementBaffles.C    | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
index fdcd15f0e9..950cc7251b 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
@@ -205,7 +205,7 @@ Foam::label Foam::meshRefinement::getBafflePatch
 
     WarningIn
     (
-        "meshRefinement::getBafflePatch(const labelList& const label)"
+        "meshRefinement::getBafflePatch(const labelList&, const label)"
     )   << "Could not find boundary face neighbouring internal face "
         << faceI << " with face centre " << mesh_.faceCentres()[faceI]
         << nl
@@ -1854,18 +1854,17 @@ void Foam::meshRefinement::findCellZoneTopo
         {
             break;
         }
+
+	// Synchronise regionToCellZone.
+	// Note:
+	// - region numbers are identical on all processors
+	// - keepRegion is identical ,,
+	// - cellZones are identical ,,
+	Pstream::listCombineGather(regionToCellZone, maxEqOp<label>());
+	Pstream::listCombineScatter(regionToCellZone);
     }
 
 
-    // Synchronise regionToCellZone.
-    // Note:
-    // - region numbers are identical on all processors
-    // - keepRegion is identical ,,
-    // - cellZones are identical ,,
-    Pstream::listCombineGather(regionToCellZone, maxEqOp<label>());
-    Pstream::listCombineScatter(regionToCellZone);
-
-
     forAll(regionToCellZone, regionI)
     {
         label zoneI = regionToCellZone[regionI];

From 7fda35da9ce701d5b84604ae5212b4a355b83d55 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Thu, 11 Dec 2008 18:53:49 +0000
Subject: [PATCH 4/5] dynamicList setSize change

---
 .../meshCut/cellLooper/topoCellLooper.C       |  4 +-
 .../polyTopoChange/polyTopoChange.C           | 60 ++++++++-----------
 2 files changed, 26 insertions(+), 38 deletions(-)

diff --git a/src/dynamicMesh/meshCut/cellLooper/topoCellLooper.C b/src/dynamicMesh/meshCut/cellLooper/topoCellLooper.C
index e74a5691e3..39be5d1d2f 100644
--- a/src/dynamicMesh/meshCut/cellLooper/topoCellLooper.C
+++ b/src/dynamicMesh/meshCut/cellLooper/topoCellLooper.C
@@ -70,7 +70,7 @@ void Foam::topoCellLooper::subsetList
                 << "startI:" << startI << "  freeI:" << freeI
                 << "  lst:" << lst << abort(FatalError);
         }
-        lst.setSize(freeI);
+        lst.setCapacity(freeI);
     }
     else
     {
@@ -88,7 +88,7 @@ void Foam::topoCellLooper::subsetList
                 << "  lst:" << lst << abort(FatalError);
         }
 
-        lst.setSize(freeI - startI);
+        lst.setCapacity(freeI - startI);
     }
 }
 
diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
index d743891f94..1ec3f9d0f0 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
@@ -734,25 +734,21 @@ void Foam::polyTopoChange::reorderCompactFaces
 )
 {
     reorder(oldToNew, faces_);
-    faces_.setSize(newSize);
-    faces_.shrink();
+    faces_.setCapacity(newSize);
 
     reorder(oldToNew, region_);
-    region_.setSize(newSize);
-    region_.shrink();
+    region_.setCapacity(newSize);
 
     reorder(oldToNew, faceOwner_);
-    faceOwner_.setSize(newSize);
-    faceOwner_.shrink();
+    faceOwner_.setCapacity(newSize);
 
     reorder(oldToNew, faceNeighbour_);
-    faceNeighbour_.setSize(newSize);
-    faceNeighbour_.shrink();
+    faceNeighbour_.setCapacity(newSize);
 
     // Update faceMaps.
     reorder(oldToNew, faceMap_);
-    faceMap_.setSize(newSize);
-    faceMap_.shrink();
+    faceMap_.setCapacity(newSize);
+
     renumberReverseMap(oldToNew, reverseFaceMap_);
 
     renumberKey(oldToNew, faceFromPoint_);
@@ -932,13 +928,11 @@ void Foam::polyTopoChange::compact
         }
 
         reorder(localPointMap, points_);
-        points_.setSize(newPointI);
-        points_.shrink();
+        points_.setCapacity(newPointI);
 
         // Update pointMaps
         reorder(localPointMap, pointMap_);
-        pointMap_.setSize(newPointI);
-        pointMap_.shrink();
+        pointMap_.setCapacity(newPointI);
         renumberReverseMap(localPointMap, reversePointMap_);
 
         renumberKey(localPointMap, pointZone_);
@@ -1038,13 +1032,11 @@ void Foam::polyTopoChange::compact
         if (orderCells || (newCellI != cellMap_.size()))
         {
             reorder(localCellMap, cellMap_);
-            cellMap_.setSize(newCellI);
-            cellMap_.shrink();
+            cellMap_.setCapacity(newCellI);
             renumberReverseMap(localCellMap, reverseCellMap_);
 
             reorder(localCellMap, cellZone_);
-            cellZone_.setSize(newCellI);
-            cellZone_.shrink();
+            cellZone_.setCapacity(newCellI);
 
             renumberKey(localCellMap, cellFromPoint_);
             renumberKey(localCellMap, cellFromEdge_);
@@ -2157,9 +2149,9 @@ void Foam::polyTopoChange::addMesh
         const pointField& points = mesh.points();
         const pointZoneMesh& pointZones = mesh.pointZones();
 
-        // Resize
-        points_.setSize(points_.size() + points.size());
-        pointMap_.setSize(pointMap_.size() + points.size());
+        // Extend
+        points_.setCapacity(points_.size() + points.size());
+        pointMap_.setCapacity(pointMap_.size() + points.size());
         pointZone_.resize(pointZone_.size() + points.size()/100);
 
         // Precalc offset zones
@@ -2198,11 +2190,11 @@ void Foam::polyTopoChange::addMesh
         // always equals nCells
         label nAllCells = mesh.nCells();
 
-        cellMap_.setSize(cellMap_.size() + nAllCells);
+        cellMap_.setCapacity(cellMap_.size() + nAllCells);
         cellFromPoint_.resize(cellFromPoint_.size() + nAllCells/100);
         cellFromEdge_.resize(cellFromEdge_.size() + nAllCells/100);
         cellFromFace_.resize(cellFromFace_.size() + nAllCells/100);
-        cellZone_.setSize(cellZone_.size() + nAllCells);
+        cellZone_.setCapacity(cellZone_.size() + nAllCells);
 
 
         // Precalc offset zones
@@ -2258,11 +2250,11 @@ void Foam::polyTopoChange::addMesh
         // Resize
         label nAllFaces = mesh.faces().size();
 
-        faces_.setSize(faces_.size() + nAllFaces);
-        region_.setSize(region_.size() + nAllFaces);
-        faceOwner_.setSize(faceOwner_.size() + nAllFaces);
-        faceNeighbour_.setSize(faceNeighbour_.size() + nAllFaces);
-        faceMap_.setSize(faceMap_.size() + nAllFaces);
+        faces_.setCapacity(faces_.size() + nAllFaces);
+        region_.setCapacity(region_.size() + nAllFaces);
+        faceOwner_.setCapacity(faceOwner_.size() + nAllFaces);
+        faceNeighbour_.setCapacity(faceNeighbour_.size() + nAllFaces);
+        faceMap_.setCapacity(faceMap_.size() + nAllFaces);
         faceFromPoint_.resize(faceFromPoint_.size() + nAllFaces/100);
         faceFromEdge_.resize(faceFromEdge_.size() + nAllFaces/100);
         flipFaceFlux_.resize(flipFaceFlux_.size() + nAllFaces/100);
@@ -3006,9 +2998,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::changeMesh
     {
         retiredPoints_.clear();
         retiredPoints_.resize(0);
-
-        region_.clear();
-        region_.setSize(0);
+        region_.clearStorage();
     }
 
 
@@ -3072,8 +3062,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::changeMesh
         faceZoneFlip_.clear();
         faceZoneFlip_.resize(0);
 
-        cellZone_.clear();
-        cellZone_.setSize(0);
+        cellZone_.clearStorage();
     }
 
 
@@ -3240,8 +3229,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::makeMesh
     {
         retiredPoints_.clear();
         retiredPoints_.resize(0);
-        region_.clear();
-        region_.setSize(0);
+        region_.clearStorage();
     }
 
 
@@ -3368,7 +3356,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::makeMesh
         faceZoneFlip_.resize(0);
 
         cellZone_.clear();
-        cellZone_.setSize(0);
+        cellZone_.clearStorage();
     }
 
     // Patch point renumbering

From c7a0f553ef7ec1fc733167046a00c337ef07db7d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Thu, 11 Dec 2008 18:54:43 +0000
Subject: [PATCH 5/5] include file position

---
 applications/solvers/combustion/PDRFoam/Make/options | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/applications/solvers/combustion/PDRFoam/Make/options b/applications/solvers/combustion/PDRFoam/Make/options
index 9f019439a7..e765e61574 100644
--- a/applications/solvers/combustion/PDRFoam/Make/options
+++ b/applications/solvers/combustion/PDRFoam/Make/options
@@ -9,7 +9,8 @@ EXE_INC = \
     -I$(LIB_SRC)/thermophysicalModels/specie/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/combustion/lnInclude \
-    -I$(LIB_SRC)/turbulenceModels/RAS/compressible/lnInclude \
+    -I$(LIB_SRC)/turbulenceModels \
+    -I$(LIB_SRC)/turbulenceModels/compressible/RAS/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/laminarFlameSpeed/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/dynamicFvMesh/lnInclude \