From a11a6867c727d346e15243b5d2de99643f78a301 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 10 Jul 2013 12:28:18 +0100
Subject: [PATCH 1/6] BUG: wallPoint: I/O operators missing space

---
 src/meshTools/cellDist/wallPoint/wallPoint.C     |  4 ++--
 src/meshTools/cellDist/wallPoint/wallPointData.C | 11 +++++------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/meshTools/cellDist/wallPoint/wallPoint.C b/src/meshTools/cellDist/wallPoint/wallPoint.C
index 16f67df42a..3f4aa14399 100644
--- a/src/meshTools/cellDist/wallPoint/wallPoint.C
+++ b/src/meshTools/cellDist/wallPoint/wallPoint.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
@@ -29,7 +29,7 @@ License
 
 Foam::Ostream& Foam::operator<<(Foam::Ostream& os, const Foam::wallPoint& wDist)
 {
-    return os << wDist.origin() << wDist.distSqr();
+    return os << wDist.origin() << token::SPACE << wDist.distSqr();
 }
 
 Foam::Istream& Foam::operator>>(Foam::Istream& is, Foam::wallPoint& wDist)
diff --git a/src/meshTools/cellDist/wallPoint/wallPointData.C b/src/meshTools/cellDist/wallPoint/wallPointData.C
index 7379e2c113..1fbbf05f8a 100644
--- a/src/meshTools/cellDist/wallPoint/wallPointData.C
+++ b/src/meshTools/cellDist/wallPoint/wallPointData.C
@@ -39,9 +39,10 @@ Ostream& operator<<
     const wallPointData<Type>& wDist
 )
 {
-    operator<<(os, static_cast<const wallPoint&>(wDist));
-
-    return os << wDist.data();
+    return os
+        << static_cast<const wallPoint&>(wDist)
+        << token::SPACE
+        << wDist.data();
 }
 
 
@@ -52,9 +53,7 @@ Istream& operator>>
     wallPointData<Type>& wDist
 )
 {
-    operator>>(is, static_cast<wallPoint&>(wDist));
-
-    return is >> wDist.data_;
+    return is >> static_cast<wallPoint&>(wDist) >> wDist.data_;
 }
 
 

From f9664eb3e464a04c5412e8261949e87693a4f597 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 10 Jul 2013 12:29:07 +0100
Subject: [PATCH 2/6] STYLE: indexedOctree: removed commented out code

---
 .../algorithms/indexedOctree/indexedOctree.C  | 97 -------------------
 .../algorithms/indexedOctree/indexedOctree.H  | 20 ----
 2 files changed, 117 deletions(-)

diff --git a/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.C b/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.C
index a19b16a672..b83b7ba1a1 100644
--- a/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.C
+++ b/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.C
@@ -508,66 +508,6 @@ Foam::volumeType Foam::indexedOctree<Type>::getSide
 //
 
 
-//template<class Type>
-//bool Foam::indexedOctree<Type>::findAnyOverlap
-//(
-//    const label nodeI,
-//    const point& sample,
-//    const scalar nearestDistSqr
-//) const
-//{
-//    const node& nod = nodes_[nodeI];
-//
-//    // Determine order to walk through octants
-//    FixedList<direction, 8> octantOrder;
-//    nod.bb_.searchOrder(sample, octantOrder);
-//
-//    // Go into all suboctants (one containing sample first) and update
-//    // nearest.
-//    for (direction i = 0; i < 8; i++)
-//    {
-//        direction octant = octantOrder[i];
-//
-//        labelBits index = nod.subNodes_[octant];
-//
-//        if (isNode(index))
-//        {
-//            label subNodeI = getNode(index);
-//
-//            const treeBoundBox& subBb = nodes_[subNodeI].bb_;
-//
-//            if (overlaps(subBb.min(), subBb.max(), nearestDistSqr, sample))
-//            {
-//                return findAnyOverlap
-//                (
-//                    subNodeI,
-//                    sample,
-//                    nearestDistSqr
-//                );
-//            }
-//        }
-//        else if (isContent(index))
-//        {
-//            if
-//            (
-//                overlaps
-//                (
-//                    nod.bb_,
-//                    octant,
-//                    nearestDistSqr,
-//                    sample
-//                )
-//            )
-//            {
-//                return true;
-//            }
-//        }
-//    }
-//
-//    return false;
-//}
-
-
 // Find nearest point starting from nodeI
 template<class Type>
 template<class FindNearestOp>
@@ -1819,11 +1759,6 @@ Foam::pointIndexHit Foam::indexedOctree<Type>::findLine
     label i = 0;
     for (; i < 100000; i++)
     {
-//        if (isLineInsideOrOutside(nodeI, treeStart, treeEnd))
-//        {
-//            return hitInfo;
-//        }
-
         // Ray-trace to end of current node. Updates point (either on triangle
         // in case of hit or on node bounding box in case of miss)
 
@@ -1981,38 +1916,6 @@ Foam::pointIndexHit Foam::indexedOctree<Type>::findLine
 }
 
 
-//template<class Type>
-//bool Foam::indexedOctree<Type>::isLineInsideOrOutside
-//(
-//    const label nodeI,
-//    const point& start,
-//    const point& end
-//) const
-//{
-//    const node& nod = nodes_[nodeI];
-//
-//    direction startOctant = nod.bb_.subOctant(start);
-//    direction endOctant = nod.bb_.subOctant(end);
-//
-//    if (startOctant == endOctant)
-//    {
-//        volumeType startOctantType
-//            = volumeType(nodeTypes_.get((nodeI<<3) + startOctant));
-//
-//        if
-//        (
-//            startOctantType == INSIDE || startOctantType == OUTSIDE
-//        )
-//        {
-//            //Info<< nodeI << " | " << start << " " << end << endl;
-//            return true;
-//        }
-//    }
-//
-//    return false;
-//}
-
-
 // Find first intersection
 template<class Type>
 template<class FindIntersectOp>
diff --git a/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.H b/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.H
index eaa51c175d..83b773289b 100644
--- a/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.H
+++ b/src/OpenFOAM/algorithms/indexedOctree/indexedOctree.H
@@ -319,13 +319,6 @@ private:
                 const bool verbose = false
             ) const;
 
-//            bool isLineInsideOrOutside
-//            (
-//                const label nodeI,
-//                const point& start,
-//                const point& end
-//            ) const;
-
             //- Find any or nearest intersection of line between start and end.
             template<class FindIntersectOp>
             pointIndexHit findLine
@@ -549,19 +542,6 @@ public:
                 const FindNearestOp& fnOp
             ) const;
 
-//            bool findAnyOverlap
-//            (
-//                const point& sample,
-//                const scalar nearestDistSqr
-//            ) const;
-//
-//            bool findAnyOverlap
-//            (
-//                const label nodeI,
-//                const point& sample,
-//                const scalar nearestDistSqr
-//            ) const;
-
             //- Low level: calculate nearest starting from subnode.
             template<class FindNearestOp>
             void findNearest

From c2ff0a8779cfd25574b59d4700926b951efe8458 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 10 Jul 2013 12:29:40 +0100
Subject: [PATCH 3/6] ENH: addPatchCellLayer: additional checking

---
 .../polyTopoChange/addPatchCellLayer.C        | 26 ++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C b/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
index bc9b292aab..58d39bc3cf 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -848,6 +848,30 @@ void Foam::addPatchCellLayer::setRefinement
         }
     }
 
+    forAll(globalEdgeFaces, edgeI)
+    {
+        if (globalEdgeFaces[edgeI].size() > 2)
+        {
+            const edge& e = pp.edges()[edgeI];
+
+            if (nPointLayers[e[0]] > 0 || nPointLayers[e[1]] > 0)
+            {
+                FatalErrorIn
+                (
+                    "addPatchCellLayer::setRefinement"
+                    "(const scalar, const indirectPrimitivePatch&"
+                    ", const labelList&, const vectorField&, polyTopoChange&)"
+                )   << "Trying to extrude edge "
+                    << e.line(pp.localPoints())
+                    << " which is non-manifold (has "
+                    << globalEdgeFaces[edgeI].size()
+                    << " faces using it)"
+                    << abort(FatalError);
+            }
+        }
+    }
+
+
     const labelList& meshPoints = pp.meshPoints();
 
     // Some storage for edge-face-addressing.

From c2e3902e7a3f3dbb1640dad2571d7d79b9f17acc Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 10 Jul 2013 12:36:23 +0100
Subject: [PATCH 4/6] ENH: printStack: offsets are size_t

---
 src/OSspecific/POSIX/printStack.C             | 10 +--
 src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.C  | 76 +++++++++++++++++++
 src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.H  | 63 +++++++++++++++
 .../db/IOstreams/Sstreams/readHexLabel.C      | 41 +---------
 4 files changed, 147 insertions(+), 43 deletions(-)
 create mode 100644 src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.C
 create mode 100644 src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.H

diff --git a/src/OSspecific/POSIX/printStack.C b/src/OSspecific/POSIX/printStack.C
index 4a3859dcae..d94451e5aa 100644
--- a/src/OSspecific/POSIX/printStack.C
+++ b/src/OSspecific/POSIX/printStack.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -28,7 +28,7 @@ License
 #include "OStringStream.H"
 #include "OSspecific.H"
 #include "IFstream.H"
-#include "readHexLabel.H"
+#include "ReadHex.H"
 
 #include <cxxabi.h>
 #include <execinfo.h>
@@ -100,8 +100,8 @@ void printSourceFileAndLine
         unsigned long offset = ulong(info.dli_fbase);
 
         IStringStream addressStr(address.substr(2));
-        label addressValue = readHexLabel(addressStr);
-        label relativeAddress = addressValue-offset;
+        long addressValue = ReadHex<long>(addressStr);
+        long relativeAddress = addressValue-offset;
 
         // Reconstruct hex word from address
         OStringStream nStream;
@@ -211,7 +211,7 @@ void error::printStack(Ostream& os)
             {
                 string offsetString(line.substr(0, line.find('-')));
                 IStringStream offsetStr(offsetString);
-                addressMap.insert(libPath, readHexLabel(offsetStr));
+                addressMap.insert(libPath, ReadHex<label>(offsetStr));
             }
         }
     }
diff --git a/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.C b/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.C
new file mode 100644
index 0000000000..e79d27420d
--- /dev/null
+++ b/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.C
@@ -0,0 +1,76 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2013 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/>.
+
+Description
+    Read a non-delimited hex label
+
+\*---------------------------------------------------------------------------*/
+
+#include "ReadHex.H"
+#include <cctype>
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+template<class T>
+T Foam::ReadHex(ISstream& is)
+{
+    // Takes into account that 'a' (or 'A') is 10
+    static const int alphaOffset = toupper('A') - 10;
+    // Takes into account that '0' is 0
+    static const int zeroOffset = int('0');
+
+    char c = 0;
+
+    // Get next non-whitespace character
+    while (is.get(c) && isspace(c))
+    {}
+
+    register T result = 0;
+    do
+    {
+        if (isspace(c) || c == 0) break;
+
+        if (!isxdigit(c))
+        {
+            FatalIOErrorIn("ReadHex(ISstream&)", is)
+                << "Illegal hex digit: '" << c << "'"
+                << exit(FatalIOError);
+        }
+
+        result <<= 4;
+
+        if (isdigit(c))
+        {
+            result += int(c) - zeroOffset;
+        }
+        else
+        {
+            result += toupper(c) - alphaOffset;
+        }
+    } while (is.get(c));
+
+    return result;
+}
+
+
+// ************************************************************************* //
diff --git a/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.H b/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.H
new file mode 100644
index 0000000000..72b38e5ec3
--- /dev/null
+++ b/src/OpenFOAM/db/IOstreams/Sstreams/ReadHex.H
@@ -0,0 +1,63 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2013 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/>.
+
+InNamespace
+    Foam
+
+Description
+    Read a hex integer from an input stream
+
+SourceFiles
+    ReadHex.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef ReadHex_H
+#define ReadHex_H
+
+#include "ISstream.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+//- Read a hex label from an input stream
+template<class T>
+T ReadHex(ISstream&);
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#ifdef NoRepository
+#   include "ReadHex.C"
+#endif
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/OpenFOAM/db/IOstreams/Sstreams/readHexLabel.C b/src/OpenFOAM/db/IOstreams/Sstreams/readHexLabel.C
index 1243b1d318..d50601aa93 100644
--- a/src/OpenFOAM/db/IOstreams/Sstreams/readHexLabel.C
+++ b/src/OpenFOAM/db/IOstreams/Sstreams/readHexLabel.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
@@ -27,48 +27,13 @@ Description
 \*---------------------------------------------------------------------------*/
 
 #include "readHexLabel.H"
-#include <cctype>
+#include "ReadHex.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 Foam::label Foam::readHexLabel(ISstream& is)
 {
-    // Takes into account that 'a' (or 'A') is 10
-    static const label alphaOffset = toupper('A') - 10;
-    // Takes into account that '0' is 0
-    static const label zeroOffset = int('0');
-
-    char c = 0;
-
-    // Get next non-whitespace character
-    while (is.get(c) && isspace(c))
-    {}
-
-    register label result = 0;
-    do
-    {
-        if (isspace(c) || c == 0) break;
-
-        if (!isxdigit(c))
-        {
-            FatalIOErrorIn("readHexLabel(ISstream&)", is)
-                << "Illegal hex digit: '" << c << "'"
-                << exit(FatalIOError);
-        }
-
-        result <<= 4;
-
-        if (isdigit(c))
-        {
-            result += int(c) - zeroOffset;
-        }
-        else
-        {
-            result += toupper(c) - alphaOffset;
-        }
-    } while (is.get(c));
-
-    return result;
+    return ReadHex<label>(is);
 }
 
 

From 9dce138da417f03ff082ddc079d22c9061a75381 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 11 Jul 2013 11:48:55 +0100
Subject: [PATCH 5/6] ENH: foamyHexMesh: add patch type so we can run with
 snappyHexMesh

---
 tutorials/mesh/foamyHexMesh/flange/system/foamyHexMeshDict | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tutorials/mesh/foamyHexMesh/flange/system/foamyHexMeshDict b/tutorials/mesh/foamyHexMesh/flange/system/foamyHexMeshDict
index 00b03b6a69..12a0994df8 100644
--- a/tutorials/mesh/foamyHexMesh/flange/system/foamyHexMeshDict
+++ b/tutorials/mesh/foamyHexMesh/flange/system/foamyHexMeshDict
@@ -57,6 +57,7 @@ surfaceConformation
                 {
                     patchInfo
                     {
+                        type        wall;
                         inGroups    (groupFlange groupWalls);
                     }
                 }
@@ -65,6 +66,7 @@ surfaceConformation
                 {
                     patchInfo
                     {
+                        type        wall;
                         inGroups    (groupFlange groupWalls);
                     }
                 }
@@ -73,6 +75,7 @@ surfaceConformation
                 {
                     patchInfo
                     {
+                        type        wall;
                         inGroups    (groupFlange);
                     }
                 }

From 7c081ac3e79a4b70552be4c6e0313c69764b80b9 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 11 Jul 2013 12:03:01 +0100
Subject: [PATCH 6/6] ENH: snappyHexMeshDict: fix header

---
 .../snappyMultiRegionHeater/system/snappyHexMeshDict            | 2 +-
 tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict    | 2 +-
 .../multiphase/LTSInterFoam/wigleyHull/system/snappyHexMeshDict | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tutorials/heatTransfer/chtMultiRegionFoam/snappyMultiRegionHeater/system/snappyHexMeshDict b/tutorials/heatTransfer/chtMultiRegionFoam/snappyMultiRegionHeater/system/snappyHexMeshDict
index 8a0767ebaf..a0510435ba 100644
--- a/tutorials/heatTransfer/chtMultiRegionFoam/snappyMultiRegionHeater/system/snappyHexMeshDict
+++ b/tutorials/heatTransfer/chtMultiRegionFoam/snappyMultiRegionHeater/system/snappyHexMeshDict
@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       dictionary;
-    object      autoHexMeshDict;
+    object      snappyHexMeshDict;
 }
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict b/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
index e290f4ff9c..d100d0749b 100644
--- a/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
+++ b/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       dictionary;
-    object      autoHexMeshDict;
+    object      snappyHexMeshDict;
 }
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/tutorials/multiphase/LTSInterFoam/wigleyHull/system/snappyHexMeshDict b/tutorials/multiphase/LTSInterFoam/wigleyHull/system/snappyHexMeshDict
index dbb112f074..012ba92343 100644
--- a/tutorials/multiphase/LTSInterFoam/wigleyHull/system/snappyHexMeshDict
+++ b/tutorials/multiphase/LTSInterFoam/wigleyHull/system/snappyHexMeshDict
@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       dictionary;
-    object      autoHexMeshDict;
+    object      snappyHexMeshDict;
 }
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //