From bbec683e42879134ddb5653762d0f4c0c9c83f5b Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 27 Sep 2016 12:40:17 +0200
Subject: [PATCH 1/7] ENH: provide list of enums for NamedEnum

- can be used to loop over all enumerations in the order of definition.
---
 applications/test/NamedEnum/Make/files        |  2 +-
 .../{Test-namedEnum.C => Test-NamedEnum.C}    | 58 +++++++++++++++----
 src/OpenFOAM/containers/NamedEnum/NamedEnum.C | 19 ++++++
 src/OpenFOAM/containers/NamedEnum/NamedEnum.H | 10 +++-
 4 files changed, 76 insertions(+), 13 deletions(-)
 rename applications/test/NamedEnum/{Test-namedEnum.C => Test-NamedEnum.C} (52%)

diff --git a/applications/test/NamedEnum/Make/files b/applications/test/NamedEnum/Make/files
index 755b72ba5e..a1a7086041 100644
--- a/applications/test/NamedEnum/Make/files
+++ b/applications/test/NamedEnum/Make/files
@@ -1,3 +1,3 @@
-Test-namedEnum.C
+Test-NamedEnum.C
 
 EXE = $(FOAM_USER_APPBIN)/Test-NamedEnum
diff --git a/applications/test/NamedEnum/Test-namedEnum.C b/applications/test/NamedEnum/Test-NamedEnum.C
similarity index 52%
rename from applications/test/NamedEnum/Test-namedEnum.C
rename to applications/test/NamedEnum/Test-NamedEnum.C
index 22f3596932..63386ed79e 100644
--- a/applications/test/NamedEnum/Test-namedEnum.C
+++ b/applications/test/NamedEnum/Test-NamedEnum.C
@@ -34,26 +34,28 @@ class namedEnumTest
 {
 public:
 
-    enum options
+    enum option
     {
         a,
         b,
-        c
+        c,
+        d
     };
 
-    static const Foam::NamedEnum<options, 3> namedEnum;
+    static const Foam::NamedEnum<option, 4> namedEnum;
 };
 
 
 template<>
-const char* Foam::NamedEnum<namedEnumTest::options, 3>::names[] =
+const char* Foam::NamedEnum<namedEnumTest::option, 4>::names[] =
 {
     "a",
     "b",
-    "c"
+    "c",
+    "d"
 };
 
-const Foam::NamedEnum<namedEnumTest::options, 3> namedEnumTest::namedEnum;
+const Foam::NamedEnum<namedEnumTest::option, 4> namedEnumTest::namedEnum;
 
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -61,11 +63,47 @@ const Foam::NamedEnum<namedEnumTest::options, 3> namedEnumTest::namedEnum;
 
 int main(int argc, char *argv[])
 {
-    Info<< namedEnumTest::namedEnum["a"] << endl;
-    Info<< namedEnumTest::namedEnum[namedEnumTest::a] << endl;
+    const List<namedEnumTest::option> options
+        = namedEnumTest::namedEnum.enums();
 
-    namedEnumTest::options hmm(namedEnumTest::namedEnum.read(Sin));
-    Info<< namedEnumTest::namedEnum[hmm] << endl;
+    Info<< "enums: " << options << nl;
+
+    Info<< "loop over enums (as list):" << nl;
+    forAll(options, i)
+    {
+        const namedEnumTest::option& opt = options[i];
+
+        Info<< "option[" << opt
+            << "] = '" << namedEnumTest::namedEnum[opt] << "'" << nl;
+    }
+
+#if __cplusplus > 201100L
+    // C++11
+    Info<< "loop over enums (C++11 for range):" << nl;
+    for (auto const& opt : options)
+    {
+        Info<< "option[" << opt
+            << "] = '" << namedEnumTest::namedEnum[opt] << "'" << nl;
+    }
+#else
+    Info<< "loop over enums (via iterator):" << nl;
+    forAllConstIter(List<namedEnumTest::option>, options, iter)
+    {
+        const namedEnumTest::option& opt = *iter;
+
+        Info<< "option[" << opt
+            << "] = '" << namedEnumTest::namedEnum[opt] << "'" << nl;
+    }
+#endif
+
+    Info<< nl
+        << namedEnumTest::namedEnum["a"] << nl
+        << namedEnumTest::namedEnum[namedEnumTest::a] << nl;
+
+    Info<< "--- test read construction ---" << endl;
+
+    namedEnumTest::option dummy(namedEnumTest::namedEnum.read(Sin));
+    Info<< namedEnumTest::namedEnum[dummy] << endl;
 
     Info<< "End\n" << endl;
 
diff --git a/src/OpenFOAM/containers/NamedEnum/NamedEnum.C b/src/OpenFOAM/containers/NamedEnum/NamedEnum.C
index ba5bd4999d..99f723d987 100644
--- a/src/OpenFOAM/containers/NamedEnum/NamedEnum.C
+++ b/src/OpenFOAM/containers/NamedEnum/NamedEnum.C
@@ -120,4 +120,23 @@ Foam::wordList Foam::NamedEnum<Enum, nEnum>::words()
 }
 
 
+template<class Enum, int nEnum>
+Foam::List<Enum> Foam::NamedEnum<Enum, nEnum>::enums()
+{
+    List<Enum> lst(nEnum);
+
+    label nElem = 0;
+    for (int enumI = 0; enumI < nEnum; ++enumI)
+    {
+        if (names[enumI] && names[enumI][0])
+        {
+            lst[nElem++] = Enum(enumI);
+        }
+    }
+
+    lst.setSize(nElem);
+    return lst;
+}
+
+
 // ************************************************************************* //
diff --git a/src/OpenFOAM/containers/NamedEnum/NamedEnum.H b/src/OpenFOAM/containers/NamedEnum/NamedEnum.H
index f4af06792c..6005f86a60 100644
--- a/src/OpenFOAM/containers/NamedEnum/NamedEnum.H
+++ b/src/OpenFOAM/containers/NamedEnum/NamedEnum.H
@@ -45,6 +45,9 @@ SourceFiles
 namespace Foam
 {
 
+// Forward declaration
+template<class Enum, int> class NamedEnum;
+
 /*---------------------------------------------------------------------------*\
                           Class NamedEnum Declaration
 \*---------------------------------------------------------------------------*/
@@ -60,10 +63,10 @@ class NamedEnum
     // Private Member Functions
 
         //- Disallow default bitwise copy construct
-        NamedEnum(const NamedEnum&);
+        NamedEnum(const NamedEnum&) = delete;
 
         //- Disallow default bitwise assignment
-        void operator=(const NamedEnum&);
+        void operator=(const NamedEnum&) = delete;
 
 
 public:
@@ -95,6 +98,9 @@ public:
         //- The set of names as a list of words
         static wordList words();
 
+        //- List of enumerations
+        static List<Enum> enums();
+
 
     // Member Operators
 

From 6d7ff59fc87933c1be10b36c9732a16c02e22fd2 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Wed, 28 Sep 2016 11:26:42 +0200
Subject: [PATCH 2/7] ENH: provide refOrNull method for autoPtr.

- Normally use '()' to deference. This has extra safety and issues a
  fatal error if the underlying pointer is not valid.

  However, in some cases we are happy with getting a null reference.
  The refOrNull() method returns the reference without any checking.

  Usage example:

      autoPtr<OFstream> osPtr;
      if (Pstream::master())
      {
          osPtr.reset(new OFstream(...));
      }
      writeViaMaster(osPtr.refOrNull());

      - The writeViaMaster() call takes an OFstream reference,
        but this is only used directly on the master.
        The slaves will pass things through to the master.
---
 src/OpenFOAM/memory/autoPtr/autoPtr.H  | 11 ++++++++++-
 src/OpenFOAM/memory/autoPtr/autoPtrI.H | 16 +++++++++++++++-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/OpenFOAM/memory/autoPtr/autoPtr.H b/src/OpenFOAM/memory/autoPtr/autoPtr.H
index 748975b5cf..a8802f23a9 100644
--- a/src/OpenFOAM/memory/autoPtr/autoPtr.H
+++ b/src/OpenFOAM/memory/autoPtr/autoPtr.H
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -104,6 +104,15 @@ public:
             inline void clear();
 
 
+        // Access
+
+            //- Return reference, without checking pointer validity.
+            inline T& refOrNull();
+
+            //- Return const reference, without checking pointer validity.
+            inline const T& refOrNull() const;
+
+
         // Member operators
 
             //- Return reference to the object data
diff --git a/src/OpenFOAM/memory/autoPtr/autoPtrI.H b/src/OpenFOAM/memory/autoPtr/autoPtrI.H
index ef199ca20c..7440bdce69 100644
--- a/src/OpenFOAM/memory/autoPtr/autoPtrI.H
+++ b/src/OpenFOAM/memory/autoPtr/autoPtrI.H
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -129,6 +129,20 @@ inline void Foam::autoPtr<T>::clear()
 }
 
 
+template<class T>
+inline T& Foam::autoPtr<T>::refOrNull()
+{
+    return *ptr_;
+}
+
+
+template<class T>
+inline const T& Foam::autoPtr<T>::refOrNull() const
+{
+    return *ptr_;
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class T>

From 1c2aadb8d825c3e55cf35f66c6c3a91e46499f25 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 28 Sep 2016 12:26:23 +0100
Subject: [PATCH 3/7] ENH: distributedTriSurfaceMesh: bail out if getting stuck
 due to precision errors

---
 .../distributedTriSurfaceMesh.C               | 26 +++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/parallel/distributed/distributedTriSurfaceMesh/distributedTriSurfaceMesh.C b/src/parallel/distributed/distributedTriSurfaceMesh/distributedTriSurfaceMesh.C
index 9db0d72d4a..de5557bcb5 100644
--- a/src/parallel/distributed/distributedTriSurfaceMesh/distributedTriSurfaceMesh.C
+++ b/src/parallel/distributed/distributedTriSurfaceMesh/distributedTriSurfaceMesh.C
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -1766,6 +1766,8 @@ void Foam::distributedTriSurfaceMesh::findLineAll
     e1.setSize(compactI);
     pointMap.setSize(compactI);
 
+
+    label iter = 0;
     while (returnReduce(e0.size(), sumOp<label>()) > 0)
     {
         findLine
@@ -1791,7 +1793,12 @@ void Foam::distributedTriSurfaceMesh::findLineAll
 
                 point pt = hitInfo[i].hitPoint() + smallVec[pointI];
 
-                if (((pt-start[pointI])&dirVec[pointI]) <= magSqrDirVec[pointI])
+                // Check current coordinate along ray
+                scalar d = ((pt-start[pointI])&dirVec[pointI]);
+
+                // Note check for d>0. Very occasionally the octree will find
+                // an intersection to the left of the ray due to tolerances.
+                if (d > 0 && d <= magSqrDirVec[pointI])
                 {
                     e0[compactI] = pt;
                     e1[compactI] = end[pointI];
@@ -1805,6 +1812,21 @@ void Foam::distributedTriSurfaceMesh::findLineAll
         e0.setSize(compactI);
         e1.setSize(compactI);
         pointMap.setSize(compactI);
+
+        iter++;
+
+        if (iter == 1000)
+        {
+            Pout<< "distributedTriSurfaceMesh::findLineAll :"
+                << " Exiting loop due to excessive number of"
+                << " intersections along ray"
+                << " start:" << UIndirectList<point>(start, pointMap)
+                << " end:" << UIndirectList<point>(end, pointMap)
+                << " e0:" << UIndirectList<point>(e0, pointMap)
+                << " e1:" << UIndirectList<point>(e1, pointMap)
+                << endl;
+            break;
+        }
     }
 }
 

From 5c4bd557cb37f304ab0b15dd6d9c3b9d80717598 Mon Sep 17 00:00:00 2001
From: Andrew Heather <a.heather@opencfd.co.uk>
Date: Wed, 28 Sep 2016 16:59:57 +0100
Subject: [PATCH 4/7] ENH: wallDist - added option to evaluate every XXX steps

---
 .../fvMesh/wallDist/wallDist/wallDist.C       | 30 ++++++++++++++++---
 .../fvMesh/wallDist/wallDist/wallDist.H       | 12 +++++++-
 2 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
index ae5be722b1..7d53f566b2 100644
--- a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
+++ b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2015-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -98,7 +98,13 @@ Foam::wallDist::wallDist(const fvMesh& mesh, const word& patchTypeName)
         static_cast<const fvSchemes&>(mesh).subDict(patchTypeName_ & "Dist")
        .lookupOrDefault<Switch>("nRequired", false)
     ),
-    n_(volVectorField::null())
+    n_(volVectorField::null()),
+    updateInterval_
+    (
+        static_cast<const fvSchemes&>(mesh).subDict(patchTypeName_ & "Dist")
+       .lookupOrDefault<label>("updateInterval", 1)
+    ),
+    requireUpdate_(true)
 {
     if (nRequired_)
     {
@@ -146,7 +152,13 @@ Foam::wallDist::wallDist
         static_cast<const fvSchemes&>(mesh).subDict(patchTypeName_ & "Dist")
        .lookupOrDefault<Switch>("nRequired", false)
     ),
-    n_(volVectorField::null())
+    n_(volVectorField::null()),
+    updateInterval_
+    (
+        static_cast<const fvSchemes&>(mesh).subDict(patchTypeName_ & "Dist")
+       .lookupOrDefault<label>("updateInterval", 1)
+    ),
+    requireUpdate_(true)
 {
     if (nRequired_)
     {
@@ -185,8 +197,17 @@ const Foam::volVectorField& Foam::wallDist::n() const
 
 bool Foam::wallDist::movePoints()
 {
-    if (pdm_->movePoints())
+    if ((mesh_.time().timeIndex() % updateInterval_) == 0)
     {
+        requireUpdate_ = true;
+    }
+
+    if (requireUpdate_ && pdm_->movePoints())
+    {
+        DebugInfo<< "Updating wall distance" << endl;
+
+        requireUpdate_ = false;
+
         if (nRequired_)
         {
             return pdm_->correct(y_, n_.ref());
@@ -206,6 +227,7 @@ bool Foam::wallDist::movePoints()
 void Foam::wallDist::updateMesh(const mapPolyMesh& mpm)
 {
     pdm_->updateMesh(mpm);
+    requireUpdate_ = true;
     movePoints();
 }
 
diff --git a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.H b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.H
index 9d4f0263b4..4cddaaa476 100644
--- a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.H
+++ b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.H
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -37,6 +37,10 @@ Description
             // Optional entry enabling the calculation
             // of the normal-to-wall field
             nRequired false;
+
+            // Optional entry delaying wall distance update to every n steps
+            // Default is 1 (update every step)
+            updateInterval 5;
         }
     \endverbatim
 
@@ -90,6 +94,12 @@ class wallDist
         //- Normal-to-wall field
         mutable tmp<volVectorField> n_;
 
+        //- Update wall distance every updateInterval_ steps
+        const label updateInterval_;
+
+        //- Flag to indicate whether the wall distance requires updating
+        bool requireUpdate_;
+
 
     // Private Member Functions
 

From 64560defc577ee0bc89c3ab8807b6f0020f24132 Mon Sep 17 00:00:00 2001
From: Andrew Heather <a.heather@opencfd.co.uk>
Date: Fri, 30 Sep 2016 11:47:38 +0100
Subject: [PATCH 5/7] ENH: wallDist - suppress calc if updateInterval is zero

---
 src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
index 7d53f566b2..d13c2bed1a 100644
--- a/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
+++ b/src/finiteVolume/fvMesh/wallDist/wallDist/wallDist.C
@@ -197,7 +197,11 @@ const Foam::volVectorField& Foam::wallDist::n() const
 
 bool Foam::wallDist::movePoints()
 {
-    if ((mesh_.time().timeIndex() % updateInterval_) == 0)
+    if
+    (
+        (updateInterval_ != 0)
+     && ((mesh_.time().timeIndex() % updateInterval_) == 0)
+    )
     {
         requireUpdate_ = true;
     }
@@ -227,6 +231,11 @@ bool Foam::wallDist::movePoints()
 void Foam::wallDist::updateMesh(const mapPolyMesh& mpm)
 {
     pdm_->updateMesh(mpm);
+
+    // Force update if performing topology change
+    // Note: needed?
+    // - field would have been mapped, so if using updateInterval option (!= 1)
+    //   live with error associated of not updating and use mapped values?
     requireUpdate_ = true;
     movePoints();
 }

From 598da1ac25deadeb7eadc8bc01ddc4b224a27d3e Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 3 Oct 2016 13:55:30 +0100
Subject: [PATCH 6/7] ENH: surfaceCheck: added -outputThreshold option to
 manage file writing

---
 .../surface/surfaceCheck/surfaceCheck.C       | 124 +++++++++++-------
 1 file changed, 73 insertions(+), 51 deletions(-)

diff --git a/applications/utilities/surface/surfaceCheck/surfaceCheck.C b/applications/utilities/surface/surfaceCheck/surfaceCheck.C
index c45d088c0f..ca2320a434 100644
--- a/applications/utilities/surface/surfaceCheck/surfaceCheck.C
+++ b/applications/utilities/surface/surfaceCheck/surfaceCheck.C
@@ -30,6 +30,26 @@ Group
 Description
     Checks geometric and topological quality of a surface.
 
+Usage
+    - surfaceCheck surfaceFile [OPTION]
+
+    \param -checkSelfIntersection \n
+    Check for self-intersection.
+
+    \param -splitNonManifold \n
+    Split surface along non-manifold edges.
+
+    \param -verbose \n
+    Extra verbosity.
+
+    \param -blockMesh \n
+    Write vertices/blocks for tight-fitting 1 cell blockMeshDict.
+
+    \param -outputThreshold \<num files\> \n
+    Specifies upper limit for the number of files written. This is useful to
+    prevent surfaces with lots of disconnected parts to write lots of files.
+    Default is 10. A special case is 0 which prevents writing any files.
+
 \*---------------------------------------------------------------------------*/
 
 #include "triangle.H"
@@ -356,6 +376,8 @@ int main(int argc, char *argv[])
     const bool checkSelfIntersect = args.optionFound("checkSelfIntersection");
     const bool verbose = args.optionFound("verbose");
     const bool splitNonManifold = args.optionFound("splitNonManifold");
+    label outputThreshold = 10;
+    args.optionReadIfPresent("outputThreshold", outputThreshold);
 
     Info<< "Reading surface from " << surfFileName << " ..." << nl << endl;
 
@@ -465,10 +487,14 @@ int main(int argc, char *argv[])
             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;
+            if (outputThreshold > 0)
+            {
+                OFstream str("illegalFaces");
+                Info<< "Dumping conflicting face labels to " << str.name()
+                    << endl
+                    << "Paste this into the input for surfaceSubset" << endl;
+                str << illegalFaces;
+            }
         }
         else
         {
@@ -543,6 +569,7 @@ int main(int argc, char *argv[])
         }
 
         // Dump for subsetting
+        if (outputThreshold > 0)
         {
             DynamicList<label> problemFaces(surf.size()/100+1);
 
@@ -723,12 +750,15 @@ int main(int argc, char *argv[])
 
         Info<< "Conflicting face labels:" << problemFaces.size() << endl;
 
-        OFstream str("problemFaces");
+        if (outputThreshold > 0)
+        {
+            OFstream str("problemFaces");
 
-        Info<< "Dumping conflicting face labels to " << str.name() << endl
-            << "Paste this into the input for surfaceSubset" << endl;
+            Info<< "Dumping conflicting face labels to " << str.name() << endl
+                << "Paste this into the input for surfaceSubset" << endl;
 
-        str << problemFaces;
+            str << problemFaces;
+        }
     }
     else
     {
@@ -760,7 +790,7 @@ int main(int argc, char *argv[])
 
         Info<< "Number of unconnected parts : " << numZones << endl;
 
-        if (numZones > 1)
+        if (numZones > 1 && outputThreshold > 0)
         {
             Info<< "Splitting surface into parts ..." << endl << endl;
 
@@ -768,7 +798,7 @@ int main(int argc, char *argv[])
             writeParts
             (
                 surf,
-                numZones,
+                min(outputThreshold, numZones),
                 faceZone,
                 surfFilePath,
                 surfFileNameBase
@@ -808,15 +838,26 @@ int main(int argc, char *argv[])
     if (numNormalZones > 1)
     {
         Info<< "More than one normal orientation." << endl;
-        writeZoning(surf, normalZone, "normal", surfFilePath, surfFileNameBase);
-        writeParts
-        (
-            surf,
-            numNormalZones,
-            normalZone,
-            surfFilePath,
-            surfFileNameBase + "_normal"
-        );
+
+        if (outputThreshold > 0)
+        {
+            writeZoning
+            (
+                surf,
+                normalZone,
+                "normal",
+                surfFilePath,
+                surfFileNameBase
+            );
+            writeParts
+            (
+                surf,
+                min(outputThreshold, numNormalZones),
+                normalZone,
+                surfFilePath,
+                surfFileNameBase + "_normal"
+            );
+        }
     }
     Info<< endl;
 
@@ -833,7 +874,11 @@ int main(int argc, char *argv[])
 
         const indexedOctree<treeDataTriSurface>& tree = querySurf.tree();
 
-        OBJstream intStream("selfInterPoints.obj");
+        autoPtr<OBJstream> intStreamPtr;
+        if (outputThreshold > 0)
+        {
+            intStreamPtr.reset(new OBJstream("selfInterPoints.obj"));
+        }
 
         label nInt = 0;
 
@@ -855,9 +900,9 @@ int main(int argc, char *argv[])
                 )
             );
 
-            if (hitInfo.hit())
+            if (hitInfo.hit() && intStreamPtr.valid())
             {
-                intStream.write(hitInfo.hitPoint());
+                intStreamPtr().write(hitInfo.hitPoint());
                 nInt++;
             }
         }
@@ -870,36 +915,13 @@ int main(int argc, char *argv[])
         {
             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;
-        //    }
-        //}
+            if (intStreamPtr.valid())
+            {
+                Info<< "Writing intersection points to "
+                    << intStreamPtr().name() << endl;
+            }
+        }
         Info<< endl;
     }
 

From 96c3a090247c85b34665d3e175af4339498562fe Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Mon, 3 Oct 2016 16:38:19 +0200
Subject: [PATCH 7/7] ENH: provide direct access to raw pointer/reference from
 autoPtr (issue #252)

All of the access methods for autoPtr include validity checks and will
fail if the underlying point is NULL. In some cases, however, we'd
like to retain the automatic deletion mechanism, but still address a
nullptr. This is mostly for cases in which a file-stream should be
allocated, but only on the master process. For these cases we'd still
like to pass through and reference the underlying pointer (eg, to
obtain the correct method call) without tripping the pointer check
mechanism. If we attempt to use the ptr() method, the autoPtr memory
management is bypassed and we risk memory leaks.

Instead provide an alternative mechanism to obtain the raw underlying
pointers/references. Use rawPtr() and rawRef() for these potentially
useful, but also potentially dangerous, operations.
---
 src/OpenFOAM/memory/autoPtr/autoPtr.H  | 16 ++++++++++++----
 src/OpenFOAM/memory/autoPtr/autoPtrI.H | 18 ++++++++++++++++--
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/OpenFOAM/memory/autoPtr/autoPtr.H b/src/OpenFOAM/memory/autoPtr/autoPtr.H
index a8802f23a9..00b8ed7809 100644
--- a/src/OpenFOAM/memory/autoPtr/autoPtr.H
+++ b/src/OpenFOAM/memory/autoPtr/autoPtr.H
@@ -106,11 +106,19 @@ public:
 
         // Access
 
-            //- Return reference, without checking pointer validity.
-            inline T& refOrNull();
+            //- Return the pointer, without nullptr checking.
+            //  Pointer remains under autoPtr management.
+            inline T* rawPtr();
 
-            //- Return const reference, without checking pointer validity.
-            inline const T& refOrNull() const;
+            //- Const access to the pointer, without nullptr checking.
+            //  Pointer remains under autoPtr management.
+            inline const T* rawPtr() const;
+
+            //- Return the reference, without nullptr checking.
+            inline T& rawRef();
+
+            //- Return the const reference, without nullptr checking.
+            inline const T& rawRef() const;
 
 
         // Member operators
diff --git a/src/OpenFOAM/memory/autoPtr/autoPtrI.H b/src/OpenFOAM/memory/autoPtr/autoPtrI.H
index 7440bdce69..c1e6b14464 100644
--- a/src/OpenFOAM/memory/autoPtr/autoPtrI.H
+++ b/src/OpenFOAM/memory/autoPtr/autoPtrI.H
@@ -130,14 +130,28 @@ inline void Foam::autoPtr<T>::clear()
 
 
 template<class T>
-inline T& Foam::autoPtr<T>::refOrNull()
+inline T* Foam::autoPtr<T>::rawPtr()
+{
+    return ptr_;
+}
+
+
+template<class T>
+inline const T* Foam::autoPtr<T>::rawPtr() const
+{
+    return ptr_;
+}
+
+
+template<class T>
+inline T& Foam::autoPtr<T>::rawRef()
 {
     return *ptr_;
 }
 
 
 template<class T>
-inline const T& Foam::autoPtr<T>::refOrNull() const
+inline const T& Foam::autoPtr<T>::rawRef() const
 {
     return *ptr_;
 }