From a9695503fc8fd625a047726b8e61362e704fe43f Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Tue, 25 Aug 2015 11:12:02 +0100
Subject: [PATCH 01/15] Report patch name instead of index in debug

---
 .../polyPatches/constraint/ggi/ggiPolyPatch.C        | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C b/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
index 23deecb82..9f5039e00 100644
--- a/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
+++ b/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
@@ -195,7 +195,8 @@ void Foam::ggiPolyPatch::calcPatchToPatch() const
         if (debug)
         {
             InfoIn("void ggiPolyPatch::calcPatchToPatch() const")
-                << "Calculating patch to patch interpolation" << endl;
+                << "Calculating patch to patch interpolation for patch" 
+                << name() << endl;
         }
 
         // Create interpolation for zones
@@ -258,6 +259,13 @@ void Foam::ggiPolyPatch::calcReconFaceCellCentres() const
             << abort(FatalError);
     }
 
+    if (debug)
+    {
+        InfoIn("void ggiPolyPatch::calcReconFaceCellCentres() const")
+            << "Calculating recon centres for patch" 
+            << name() << endl;
+    }
+
     // Create neighbouring face centres using interpolation
     if (master())
     {
@@ -366,7 +374,7 @@ void Foam::ggiPolyPatch::calcSendReceive() const
     if (debug)
     {
         Pout<< "ggiPolyPatch::calcSendReceive() const for patch "
-            << index() << endl;
+            << name() << endl;
     }
 
     if (!Pstream::parRun())

From 7d533e60ab4ecd8233c7ee9aeb142ad055f80c1f Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Tue, 25 Aug 2015 11:12:02 +0100
Subject: [PATCH 02/15] Report patch name instead of index in debug

---
 .../polyPatches/constraint/ggi/ggiPolyPatch.C        | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C b/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
index 9f5039e00..23deecb82 100644
--- a/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
+++ b/src/foam/meshes/polyMesh/polyPatches/constraint/ggi/ggiPolyPatch.C
@@ -195,8 +195,7 @@ void Foam::ggiPolyPatch::calcPatchToPatch() const
         if (debug)
         {
             InfoIn("void ggiPolyPatch::calcPatchToPatch() const")
-                << "Calculating patch to patch interpolation for patch" 
-                << name() << endl;
+                << "Calculating patch to patch interpolation" << endl;
         }
 
         // Create interpolation for zones
@@ -259,13 +258,6 @@ void Foam::ggiPolyPatch::calcReconFaceCellCentres() const
             << abort(FatalError);
     }
 
-    if (debug)
-    {
-        InfoIn("void ggiPolyPatch::calcReconFaceCellCentres() const")
-            << "Calculating recon centres for patch" 
-            << name() << endl;
-    }
-
     // Create neighbouring face centres using interpolation
     if (master())
     {
@@ -374,7 +366,7 @@ void Foam::ggiPolyPatch::calcSendReceive() const
     if (debug)
     {
         Pout<< "ggiPolyPatch::calcSendReceive() const for patch "
-            << name() << endl;
+            << index() << endl;
     }
 
     if (!Pstream::parRun())

From 1721f8ffc0a9a79a8d82e298ed90af06f2bef16a Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Thu, 3 Sep 2015 17:05:38 +0100
Subject: [PATCH 03/15] Bugfix: missing rho on dev(P). Jens Truemner

---
 .../compressible/RAS/LaunderGibsonRSTM/LaunderGibsonRSTM.C      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/turbulenceModels/compressible/RAS/LaunderGibsonRSTM/LaunderGibsonRSTM.C b/src/turbulenceModels/compressible/RAS/LaunderGibsonRSTM/LaunderGibsonRSTM.C
index 7ce693261..d1af0a898 100644
--- a/src/turbulenceModels/compressible/RAS/LaunderGibsonRSTM/LaunderGibsonRSTM.C
+++ b/src/turbulenceModels/compressible/RAS/LaunderGibsonRSTM/LaunderGibsonRSTM.C
@@ -446,7 +446,7 @@ void LaunderGibsonRSTM::correct()
         // Change for consistency with Fluent implementation.
         // Emil Baric, NUMAP-FOAM 2011
         // HJ, 13/Dec/2011
-      - Clg2_*(dev(P) - dev(C))
+      - Clg2_*(rho_*dev(P) - dev(C))
 
         // wall reflection terms
       + symm

From 161ad618de2dbe62f4e5a48716fb189518b841c0 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:07:36 +0100
Subject: [PATCH 04/15] Formatting

---
 .../basicSymmetry/basicSymmetryFvPatchScalarField.C      | 9 ++++++---
 .../derived/advective/advectiveFvPatchField.C            | 5 ++++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/basic/basicSymmetry/basicSymmetryFvPatchScalarField.C b/src/finiteVolume/fields/fvPatchFields/basic/basicSymmetry/basicSymmetryFvPatchScalarField.C
index 3fb6d398a..b40e7e713 100644
--- a/src/finiteVolume/fields/fvPatchFields/basic/basicSymmetry/basicSymmetryFvPatchScalarField.C
+++ b/src/finiteVolume/fields/fvPatchFields/basic/basicSymmetry/basicSymmetryFvPatchScalarField.C
@@ -51,7 +51,8 @@ void basicSymmetryFvPatchField<scalar>::evaluate(const Pstream::commsTypes)
     // Local typedefs
     typedef scalar Type;
     typedef outerProduct<vector, Type>::type gradType;
-    typedef GeometricField<gradType, Foam::fvPatchField, volMesh> gradFieldType;
+    typedef GeometricField<gradType, Foam::fvPatchField, volMesh>
+        gradFieldType;
 
     if (!updated())
     {
@@ -141,7 +142,8 @@ tmp<vectorField> basicSymmetryFvPatchField<vector>::snGrad() const
     // Local typedefs
     typedef vector Type;
     typedef outerProduct<vector, Type>::type gradType;
-    typedef GeometricField<gradType, Foam::fvPatchField, volMesh> gradFieldType;
+    typedef GeometricField<gradType, Foam::fvPatchField, volMesh>
+        gradFieldType;
 
     vectorField nHat = this->patch().nf();
 
@@ -214,7 +216,8 @@ void basicSymmetryFvPatchField<vector>::evaluate(const Pstream::commsTypes)
     // Local typedefs
     typedef vector Type;
     typedef outerProduct<vector, Type>::type gradType;
-    typedef GeometricField<gradType, Foam::fvPatchField, volMesh> gradFieldType;
+    typedef GeometricField<gradType, Foam::fvPatchField, volMesh>
+        gradFieldType;
 
     if (!updated())
     {
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/advective/advectiveFvPatchField.C b/src/finiteVolume/fields/fvPatchFields/derived/advective/advectiveFvPatchField.C
index 91578d12c..f212163db 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/advective/advectiveFvPatchField.C
+++ b/src/finiteVolume/fields/fvPatchFields/derived/advective/advectiveFvPatchField.C
@@ -172,7 +172,10 @@ template<class Type>
 tmp<scalarField> advectiveFvPatchField<Type>::advectionSpeed() const
 {
     const surfaceScalarField& phi =
-        this->db().objectRegistry::template lookupObject<surfaceScalarField>(phiName_);
+        this->db().objectRegistry::template lookupObject<surfaceScalarField>
+        (
+            phiName_
+        );
 
     fvsPatchField<scalar> phip = this->lookupPatchField
     (

From 4d4c7d0eed576f9d22ac5ce8391ca2ec4e043daf Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:08:41 +0100
Subject: [PATCH 05/15] Intel 2016 compiler porting

---
 .../octreeData/octreeDataTriSurfaceTreeLeaf.H |  2 +-
 src/surfMesh/MeshedSurface/MeshedSurface.C    | 30 ++++++++++---------
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.H b/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.H
index 4887ece59..58c86adb6 100644
--- a/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.H
+++ b/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.H
@@ -45,7 +45,7 @@ namespace Foam
 // Forward declaration of classes
 class octreeDataTriSurface;
 
-template<> inline
+template<>
 bool treeLeaf<octreeDataTriSurface>::findNearest
 (
     const octreeDataTriSurface& shapes,
diff --git a/src/surfMesh/MeshedSurface/MeshedSurface.C b/src/surfMesh/MeshedSurface/MeshedSurface.C
index a7205d8b6..5bb0cda5d 100644
--- a/src/surfMesh/MeshedSurface/MeshedSurface.C
+++ b/src/surfMesh/MeshedSurface/MeshedSurface.C
@@ -32,6 +32,8 @@ License
 #include "polyBoundaryMesh.H"
 #include "polyMesh.H"
 #include "surfMesh.H"
+#include "Xfer.H"
+#include "surfZone.H"
 #include "primitivePatch.H"
 #include "addToRunTimeSelectionTable.H"
 
@@ -170,9 +172,9 @@ Foam::MeshedSurface<Face>::MeshedSurface()
 template<class Face>
 Foam::MeshedSurface<Face>::MeshedSurface
 (
-    const Xfer< pointField >& pointLst,
-    const Xfer< List<Face> >& faceLst,
-    const Xfer< surfZoneList >& zoneLst
+    const Xfer<pointField >& pointLst,
+    const Xfer<List<Face> >& faceLst,
+    const Xfer<surfZoneList>& zoneLst
 )
 :
     ParentType(List<Face>(), pointField()),
@@ -185,8 +187,8 @@ Foam::MeshedSurface<Face>::MeshedSurface
 template<class Face>
 Foam::MeshedSurface<Face>::MeshedSurface
 (
-    const Xfer< pointField >& pointLst,
-    const Xfer< List<Face> >& faceLst,
+    const Xfer<pointField>& pointLst,
+    const Xfer<List<Face> >& faceLst,
     const UList<label>& zoneSizes,
     const UList<word>& zoneNames
 )
@@ -534,17 +536,17 @@ void Foam::MeshedSurface<Face>::reset
 
     // Take over new primitive data.
     // Optimized to avoid overwriting data at all
-    if (!pointLst().empty())
+    if (!pointLst->empty())
     {
         storedPoints().transfer(pointLst());
     }
 
-    if (!faceLst().empty())
+    if (!faceLst->empty())
     {
         storedFaces().transfer(faceLst());
     }
 
-    if (!zoneLst().empty())
+    if (!zoneLst->empty())
     {
         storedZones().transfer(zoneLst());
     }
@@ -554,26 +556,26 @@ void Foam::MeshedSurface<Face>::reset
 template<class Face>
 void Foam::MeshedSurface<Face>::reset
 (
-    const Xfer< List<point> >& pointLst,
-    const Xfer< List<Face> >& faceLst,
-    const Xfer< surfZoneList >& zoneLst
+    const Xfer<List<point> >& pointLst,
+    const Xfer<List<Face> >& faceLst,
+    const Xfer<surfZoneList>& zoneLst
 )
 {
     ParentType::clearOut();
 
     // Take over new primitive data.
     // Optimized to avoid overwriting data at all
-    if (!pointLst().empty())
+    if (!pointLst->empty())
     {
         storedPoints().transfer(pointLst());
     }
 
-    if (!faceLst().empty())
+    if (!faceLst->empty())
     {
         storedFaces().transfer(faceLst());
     }
 
-    if (!zoneLst().empty())
+    if (!zoneLst->empty())
     {
         storedZones().transfer(zoneLst());
     }

From 5039ed9a30b1d8d834a5bdf6718364e73eed3cea Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:09:27 +0100
Subject: [PATCH 06/15] Euler angle access

---
 .../sixDOF/finiteRotation/finiteRotation.C    | 33 +++++++++++++++++++
 .../sixDOF/finiteRotation/finiteRotation.H    |  8 +++++
 src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.H        |  5 ++-
 src/ODE/sixDOF/sixDOFqODE/sixDOFqODEI.H       |  6 ++++
 4 files changed, 51 insertions(+), 1 deletion(-)

diff --git a/src/ODE/sixDOF/finiteRotation/finiteRotation.C b/src/ODE/sixDOF/finiteRotation/finiteRotation.C
index 534799de6..501687de9 100644
--- a/src/ODE/sixDOF/finiteRotation/finiteRotation.C
+++ b/src/ODE/sixDOF/finiteRotation/finiteRotation.C
@@ -70,6 +70,33 @@ Foam::scalar Foam::finiteRotation::rotAngle(const tensor& rotT)
 }
 
 
+Foam::vector Foam::finiteRotation::eulerAngles(const tensor& rotT)
+{
+    // Define a vector containing euler angles (x = roll, y = pitch, z = yaw)
+    vector eulerAngles;
+
+    scalar& rollAngle = eulerAngles.x();
+    scalar& pitchAngle = eulerAngles.y();
+    scalar& yawAngle = eulerAngles.z();
+
+    // Calculate roll angle
+    rollAngle = atan2(rotT.yz(), rotT.zz());
+
+    const scalar c2 = sqrt(rotT.xx() + rotT.xy());
+
+    // Calculate pitch angle
+    pitchAngle = atan2(-rotT.xz(), c2);
+
+    const scalar s1 = sin(rollAngle);
+    const scalar c1 = cos(rollAngle);
+
+    // Calculate yaw angle
+    yawAngle = atan2(s1*rotT.zx() - c1*rotT.yx(), c1*rotT.yy() - s1*rotT.zy());
+
+    return eulerAngles;
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::finiteRotation::finiteRotation(const HamiltonRodriguezRot& rot)
@@ -139,6 +166,12 @@ Foam::scalar Foam::finiteRotation::rotAngle() const
 }
 
 
+Foam::vector Foam::finiteRotation::eulerAngles() const
+{
+    return eulerAngles(rotTensor_);
+}
+
+
 const Foam::tensor& Foam::finiteRotation::rotIncrementTensor() const
 {
     return rotIncrementTensor_;
diff --git a/src/ODE/sixDOF/finiteRotation/finiteRotation.H b/src/ODE/sixDOF/finiteRotation/finiteRotation.H
index 28f76849b..9b46b0191 100644
--- a/src/ODE/sixDOF/finiteRotation/finiteRotation.H
+++ b/src/ODE/sixDOF/finiteRotation/finiteRotation.H
@@ -69,6 +69,11 @@ class finiteRotation
         //- Calculate rotation angle from given rotation tensor
         static scalar rotAngle(const tensor& rotT);
 
+        //- Calculate Euler angles (x-y-z (roll-pitch-yaw) convenction) from
+        //  given rotation tensor. Reference: Mike Day, Insomniac Games,
+        //  Extracting Euler Angles from a Rotation Matrix.
+        static vector eulerAngles(const tensor& rotT);
+
 
 public:
 
@@ -110,6 +115,9 @@ public:
         //- Return rotation angle
         scalar rotAngle() const;
 
+        //- Return Euler angles (see static function eulerAngles for convention)
+        vector eulerAngles() const;
+
         // Transformations between new and previous rotation
         const tensor& rotIncrementTensor() const;
 
diff --git a/src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.H b/src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.H
index 38a0ab108..89023e608 100644
--- a/src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.H
+++ b/src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.H
@@ -236,6 +236,9 @@ public:
             //- Return average velocity of origin for the previous time-step
             inline const dimensionedVector& Uaverage() const;
 
+            //- Return finite rotation
+            inline const finiteRotation& rotation() const;
+
             //- Return acceleration of origin
             inline dimensionedVector A() const;
 
@@ -246,7 +249,7 @@ public:
             inline dimensionedScalar rotAngle() const;
 
 
-        // Non-constant access to
+        // Non-constant access
 
             //- Set position of origin
             inline void setXrel(const vector& x);
diff --git a/src/ODE/sixDOF/sixDOFqODE/sixDOFqODEI.H b/src/ODE/sixDOF/sixDOFqODE/sixDOFqODEI.H
index 4247263ab..75e878040 100644
--- a/src/ODE/sixDOF/sixDOFqODE/sixDOFqODEI.H
+++ b/src/ODE/sixDOF/sixDOFqODE/sixDOFqODEI.H
@@ -172,6 +172,12 @@ const Foam::dimensionedVector& Foam::sixDOFqODE::Uaverage() const
 }
 
 
+const Foam::finiteRotation& Foam::sixDOFqODE::rotation() const
+{
+    return rotation_;
+}
+
+
 Foam::vector Foam::sixDOFqODE::rotVectorAverage() const
 {
     return rotation_.rotVectorAverage();

From 927f5d01be2b07cd098cd557d9b3d96971fae2f5 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:36:46 +0100
Subject: [PATCH 07/15] Optimisation

---
 src/foam/algorithms/polygon/clipping/SutherlandHodgman.C | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/foam/algorithms/polygon/clipping/SutherlandHodgman.C b/src/foam/algorithms/polygon/clipping/SutherlandHodgman.C
index 18934eb97..caa37636f 100644
--- a/src/foam/algorithms/polygon/clipping/SutherlandHodgman.C
+++ b/src/foam/algorithms/polygon/clipping/SutherlandHodgman.C
@@ -24,7 +24,7 @@ License
 Author
     Martin Beaudoin, Hydro-Quebec, (2008)
 
-\*----------------------------------------------------------------------------*/
+\*---------------------------------------------------------------------------*/
 
 #include "SutherlandHodgman.H"
 
@@ -157,8 +157,8 @@ Foam::SutherlandHodgman::SutherlandHodgman
 
 Foam::List<Foam::point2D> Foam::SutherlandHodgman::evaluate()
 {
-    DynamicList<point2D> clippedPolygon(0);
-    DynamicList<bool> clippedVertexInside(0);
+    DynamicList<point2D, 8> clippedPolygon(0);
+    DynamicList<bool, 8> clippedVertexInside(0);
     point2D interSectPt;
 
     label S = subjectPolygon_.size() - 1;
@@ -249,7 +249,7 @@ Foam::List<Foam::point2D> Foam::SutherlandHodgman::evaluate()
     // Are we done?
     if (currentClipEdgeP2_ < clippingPolygon_.size())
     {
-        //clip against next edge, re-entrant.
+        // Clip against next edge, re-entrant.
         evaluate();
     }
 

From 7f8a25fb0f9b5793aa0e3f859397d8be89deceae Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:39:19 +0100
Subject: [PATCH 08/15] Compilation clean-up

---
 .../fvMatrices/fvBlockMatrix/fvBlockMatrix.C  | 39 ++++++++++++-------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/src/finiteVolume/fvMatrices/fvBlockMatrix/fvBlockMatrix.C b/src/finiteVolume/fvMatrices/fvBlockMatrix/fvBlockMatrix.C
index b7cc5bf30..294935d87 100644
--- a/src/finiteVolume/fvMatrices/fvBlockMatrix/fvBlockMatrix.C
+++ b/src/finiteVolume/fvMatrices/fvBlockMatrix/fvBlockMatrix.C
@@ -26,11 +26,16 @@ License
 #include "fvBlockMatrix.H"
 #include "IOstreams.H"
 
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
 template<class Type>
 template<class fieldType>
-void Foam::fvBlockMatrix<Type>::insertSolutionVector
+void fvBlockMatrix<Type>::insertSolutionVector
 (
     const direction dir,
     const Field<fieldType>& xSingle
@@ -59,7 +64,7 @@ void Foam::fvBlockMatrix<Type>::insertSolutionVector
 
 template<class Type>
 template<class matrixType>
-void Foam::fvBlockMatrix<Type>::insertDiagSource
+void fvBlockMatrix<Type>::insertDiagSource
 (
     const direction dir,
     fvMatrix<matrixType>& matrix
@@ -162,7 +167,7 @@ void Foam::fvBlockMatrix<Type>::insertDiagSource
 
 template<class Type>
 template<class matrixType>
-void Foam::fvBlockMatrix<Type>::insertUpperLower
+void fvBlockMatrix<Type>::insertUpperLower
 (
     const direction dir,
     const fvMatrix<matrixType>& matrix
@@ -290,7 +295,7 @@ void Foam::fvBlockMatrix<Type>::insertUpperLower
 
 template<class Type>
 template<class matrixType>
-void Foam::fvBlockMatrix<Type>::updateCouplingCoeffs
+void fvBlockMatrix<Type>::updateCouplingCoeffs
 (
     const direction dir,
     const fvMatrix<matrixType>& matrix
@@ -563,7 +568,7 @@ void Foam::fvBlockMatrix<Type>::insertBoundaryContributions
 
 
 template<class Type>
-void Foam::fvBlockMatrix<Type>::insertCouplingDiag
+void fvBlockMatrix<Type>::insertCouplingDiag
 (
     const direction dirI,
     const direction dirJ,
@@ -586,7 +591,7 @@ void Foam::fvBlockMatrix<Type>::insertCouplingDiag
 
 
 template<class Type>
-void Foam::fvBlockMatrix<Type>::insertCouplingUpperLower
+void fvBlockMatrix<Type>::insertCouplingUpperLower
 (
     const direction dirI,
     const direction dirJ,
@@ -673,7 +678,7 @@ void Foam::fvBlockMatrix<Type>::insertCouplingUpperLower
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class Type>
-Foam::fvBlockMatrix<Type>::fvBlockMatrix
+fvBlockMatrix<Type>::fvBlockMatrix
 (
     GeometricField<Type, fvPatchField, volMesh>& psi
 )
@@ -686,7 +691,7 @@ Foam::fvBlockMatrix<Type>::fvBlockMatrix
 
 
 template<class Type>
-Foam::fvBlockMatrix<Type>::fvBlockMatrix
+fvBlockMatrix<Type>::fvBlockMatrix
 (
     const fvBlockMatrix<Type>& bxs
 )
@@ -700,7 +705,7 @@ Foam::fvBlockMatrix<Type>::fvBlockMatrix
 
 template<class Type>
 template<class fieldType>
-void Foam::fvBlockMatrix<Type>::retrieveSolution
+void fvBlockMatrix<Type>::retrieveSolution
 (
     const direction dir,
     Field<fieldType>& xSingle
@@ -729,7 +734,7 @@ void Foam::fvBlockMatrix<Type>::retrieveSolution
 
 template<class Type>
 template<class matrixType>
-void Foam::fvBlockMatrix<Type>::insertEquation
+void fvBlockMatrix<Type>::insertEquation
 (
     const direction dir,
     fvMatrix<matrixType>& matrix
@@ -744,7 +749,7 @@ void Foam::fvBlockMatrix<Type>::insertEquation
 
 template<class Type>
 template<class blockType, class fieldType>
-void Foam::fvBlockMatrix<Type>::insertBlockCoupling
+void fvBlockMatrix<Type>::insertBlockCoupling
 (
     const direction dirI,
     const direction dirJ,
@@ -773,7 +778,7 @@ void Foam::fvBlockMatrix<Type>::insertEquationCoupling
 
 
 template<class Type>
-void Foam::fvBlockMatrix<Type>::blockAdd
+void fvBlockMatrix<Type>::blockAdd
 (
     const direction dir,
     const scalarField& xSingle,
@@ -822,7 +827,7 @@ void Foam::fvBlockMatrix<Type>::updateSourceCoupling()
 
 
 template<class Type>
-Foam::BlockSolverPerformance<Type> Foam::fvBlockMatrix<Type>::solve
+BlockSolverPerformance<Type> fvBlockMatrix<Type>::solve
 (
     const dictionary& solverControls
 )
@@ -844,7 +849,7 @@ Foam::BlockSolverPerformance<Type> Foam::fvBlockMatrix<Type>::solve
 
 
 template<class Type>
-Foam::BlockSolverPerformance<Type> Foam::fvBlockMatrix<Type>::solve()
+BlockSolverPerformance<Type> fvBlockMatrix<Type>::solve()
 {
     return solve(psi_.mesh().solutionDict().solverDict(psi_.name()));
 }
@@ -853,7 +858,7 @@ Foam::BlockSolverPerformance<Type> Foam::fvBlockMatrix<Type>::solve()
 // * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
 
 template<class Type>
-Foam::Ostream& Foam::operator<<
+Ostream& operator<<
 (
     Ostream& os,
     const fvBlockMatrix<Type>& bxs
@@ -866,4 +871,8 @@ Foam::Ostream& Foam::operator<<
 }
 
 
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
 // ************************************************************************* //

From c5bad50594ff81a43b7e3ca7665e75a15c828e08 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 11:40:00 +0100
Subject: [PATCH 09/15] Bugfix: Work-around for a cyclic interface bug for
 tensors

---
 .../constraint/cyclic/cyclicFvPatchField.H    | 35 +++++++++++++++++--
 .../cyclicLduInterfaceField.C                 | 20 ++++++++++-
 2 files changed, 52 insertions(+), 3 deletions(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/constraint/cyclic/cyclicFvPatchField.H b/src/finiteVolume/fields/fvPatchFields/constraint/cyclic/cyclicFvPatchField.H
index d6b164635..1c66c4bba 100644
--- a/src/finiteVolume/fields/fvPatchFields/constraint/cyclic/cyclicFvPatchField.H
+++ b/src/finiteVolume/fields/fvPatchFields/constraint/cyclic/cyclicFvPatchField.H
@@ -38,6 +38,7 @@ SourceFiles
 #include "coupledFvPatchField.H"
 #include "cyclicLduInterfaceField.H"
 #include "cyclicFvPatch.H"
+#include "transformField.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -159,11 +160,41 @@ public:
             //- Transform neighbour field
             virtual void transformCoupleField
             (
-                scalarField& f,
+                scalarField& pnf,
                 const direction cmpt
             ) const
             {
-                cyclicLduInterfaceField::transformCoupleField(f, cmpt);
+                // See comments in cyclicLduInterfaceField
+                // HJ, 3/Sep/2015
+//                 cyclicLduInterfaceField::transformCoupleField(pnf, cmpt);
+                if (doTransform())
+                {
+                    label sizeby2 = pnf.size()/2;
+
+                    Type powFwdTransform = transform
+                    (
+                        this->forwardT()[0],
+                        pTraits<Type>::one
+                    );
+
+                    scalar forwardScale =
+                        pow(component(powFwdTransform, cmpt), rank());
+
+                    Type powRevTransform = transform
+                    (
+                        this->reverseT()[0],
+                        pTraits<Type>::one
+                    );
+
+                    scalar reverseScale =
+                        pow(component(powRevTransform, cmpt), rank());
+
+                    for (label facei = 0; facei < sizeby2; facei++)
+                    {
+                        pnf[facei] *= forwardScale;
+                        pnf[facei + sizeby2] *= reverseScale;
+                    }
+                }
             }
 
             //- Update result field based on interface functionality
diff --git a/src/foam/matrices/lduMatrix/lduAddressing/lduInterfaceFields/cyclicLduInterfaceField/cyclicLduInterfaceField.C b/src/foam/matrices/lduMatrix/lduAddressing/lduInterfaceFields/cyclicLduInterfaceField/cyclicLduInterfaceField.C
index 338ae6b95..440e87d9e 100644
--- a/src/foam/matrices/lduMatrix/lduAddressing/lduInterfaceFields/cyclicLduInterfaceField/cyclicLduInterfaceField.C
+++ b/src/foam/matrices/lduMatrix/lduAddressing/lduInterfaceFields/cyclicLduInterfaceField/cyclicLduInterfaceField.C
@@ -52,13 +52,31 @@ void Foam::cyclicLduInterfaceField::transformCoupleField
     {
         label sizeby2 = pnf.size()/2;
 
+        //HJ This is wrong
+        // For a vector, the implicit contribution is correct:
+        // power of diagonal of the transformation tensor for the vector
+        // For a tensor this is wrong: the diag of transformation tensor
+        // is a vector and I am asking for a component cmpt which corresponds
+        // to the component of the variable I am offering.  If the variable
+        // is a tensor, it has got 6 or 9 components, so the component
+        // access is out of range and rubbish anyway
+        // The forwardScale/reverseScale should be the power of the complete
+        // transformation matrix for a tensor.  Something like:
+
+//         Type powTransform = transform(pTraits<Type>::one);
+//         forwardScale = pow(powTransform.component(cmpt), rank());
+
+        // This needs to be moved under templating into cyclicFvPatchField
+        // because it requires access to Type
+        // HJ, 3/Sep/2015
+
         scalar forwardScale =
             pow(diag(forwardT()[0]).component(cmpt), rank());
 
         scalar reverseScale =
             pow(diag(reverseT()[0]).component(cmpt), rank());
 
-        for (label facei=0; facei<sizeby2; facei++)
+        for (label facei = 0; facei < sizeby2; facei++)
         {
             pnf[facei] *= forwardScale;
             pnf[facei + sizeby2] *= reverseScale;

From 32b6159d367040ddfedcf2a50d88ed3fbba3c5e6 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 13:29:35 +0200
Subject: [PATCH 10/15] Optimising use of Dynamic lists in GGI

---
 .../GGIInterpolation/GGIInterpolationWeights.C             | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/foam/interpolations/GGIInterpolation/GGIInterpolationWeights.C b/src/foam/interpolations/GGIInterpolation/GGIInterpolationWeights.C
index 796cb304b..3a39d0223 100644
--- a/src/foam/interpolations/GGIInterpolation/GGIInterpolationWeights.C
+++ b/src/foam/interpolations/GGIInterpolation/GGIInterpolationWeights.C
@@ -270,11 +270,6 @@ void GGIInterpolation<MasterPatch, SlavePatch>::calcAddressing() const
                 << "This is strange..."  << endl;
         }
 
-        // The master face neighbours polygons projected in the plane UV
-        // We will only keep the ones with some area overlap
-        DynamicList<List<point2D> > masterNeighFace2DPolygonInUV;
-        DynamicList<scalarField> masterNeighFace2DPolygonInUVErrorProjection;
-
         // Next, project the candidate master neighbours faces points
         // onto the same plane using the new orthonormal basis
         const labelList& curCMN = candidateMasterNeighbors[faceMi];
@@ -614,7 +609,7 @@ GGIInterpolation<MasterPatch, SlavePatch>::findNonOverlappingFaces
     tmp<labelField> tpatchFaceNonOverlapAddr(new labelField());
     labelField& patchFaceNonOverlapAddr = tpatchFaceNonOverlapAddr();
 
-    DynamicList<label> patchFaceNonOverlap(patchWeights.size());
+    DynamicList<label, 64> patchFaceNonOverlap(patchWeights.size());
 
     // Scan the list of patch weights, looking for empty lists
     forAll (patchWeights, paWi)

From fb54ad74f5d37af99d093f113f54661e20e0eaf6 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Mon, 7 Sep 2015 15:49:49 +0100
Subject: [PATCH 11/15] Updated instructions.  Miguel Nobrega

---
 doc/buildInstructions/Windows/README.txt | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/doc/buildInstructions/Windows/README.txt b/doc/buildInstructions/Windows/README.txt
index d76ad1332..0f65bbd37 100644
--- a/doc/buildInstructions/Windows/README.txt
+++ b/doc/buildInstructions/Windows/README.txt
@@ -46,7 +46,7 @@ already have some of these system tools.
 1) Download and install 7-Zip (see reference list below). This is necessary to
    be able to unzip the rest of the required packages mentioned in later steps.
 
-2) Download and install wget, CMake, Git, MinGW-w64, ParaView and PExports (see
+2) Download and install wget, CMake, Git, MinGW-w64, ParaView, PExports, Java, Subversion, Python (see
    reference list below). Note that some components (example PExports and GMake)
    may already be available in other packages (such as Strawberry Perl), although
    you need to be careful of the version numbers.
@@ -115,6 +115,11 @@ Version: 1.9.5
 URL    : https://git-scm.com/download/win
 For    : Version control system. Choose "Use Git from the Windows command prompt" and "Check out as-is. Commit as-is" in installer.
 
+Name   : Java
+Version: Version 8 Update 60
+URL    : http://www.java.com
+For    : Not essential
+
 Name   : Microsoft Visual C++ 2010 Redistributable Package (x64)
 Version: 2010
 URL    : http://www.microsoft.com/en-us/download/details.aspx?id=14632
@@ -147,11 +152,21 @@ Version: 0.44 (or above)
 URL    : http://sourceforge.net/projects/mingw/files/MinGW/Extension/pexports/pexports-0.46/pexports-0.46-mingw32-bin.tar.xz/download
 For    : Extracting symbols from OpenMPI DLLs to pass to dlltool.exe (supplied in MinGW-w64 package). Move directory "bin" to "pexports-0.46" after unpacking.
 
+Name   : Pyhton
+Version: 2.7
+URL    : https://www.python.org/download/releases/2.7/
+For    : Not essential
+
 Name   : Strawberry Perl
 Version: 5.20.2.1 (or above)
 URL    : http://strawberryperl.com/download/5.20.2.1/strawberry-perl-5.20.2.1-64bit.msi
 For    : Running Perl scripts, "pexports.exe" and "gmake.exe" utilities
 
+Name   : Subversion
+Version: 1.8.13
+URL    : http://sourceforge.net/projects/win32svn/files/1.8.13/
+For    : ??????????
+
 Name   : wget
 Version: 1.11.4-1 (or above)
 URL    : http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-bin.zip, http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-dep.zip, http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-doc.zip

From c67d6b98d2fc693d7b8f112d793a094f8c241f83 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Tue, 8 Sep 2015 15:06:18 +0100
Subject: [PATCH 12/15] Octree search Windows port updates

---
 .../octreeData/octreeDataTriSurface.H         | 475 +++++++++---------
 .../octreeData/octreeDataTriSurfaceTreeLeaf.C | 166 +++---
 2 files changed, 323 insertions(+), 318 deletions(-)

diff --git a/src/meshTools/triSurface/octreeData/octreeDataTriSurface.H b/src/meshTools/triSurface/octreeData/octreeDataTriSurface.H
index 315883413..896ec77db 100644
--- a/src/meshTools/triSurface/octreeData/octreeDataTriSurface.H
+++ b/src/meshTools/triSurface/octreeData/octreeDataTriSurface.H
@@ -1,235 +1,240 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | foam-extend: Open Source CFD
-   \\    /   O peration     | Version:     3.2
-    \\  /    A nd           | Web:         http://www.foam-extend.org
-     \\/     M anipulation  | For copyright notice see file Copyright
--------------------------------------------------------------------------------
-License
-    This file is part of foam-extend.
-
-    foam-extend 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.
-
-    foam-extend 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 foam-extend.  If not, see <http://www.gnu.org/licenses/>.
-
-Class
-    Foam::octreeDataTriSurface
-
-Description
-    Encapsulates data for octree searches on triSurface.
-
-SourceFiles
-    octreeDataTriSurface.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef octreeDataTriSurface_H
-#define octreeDataTriSurface_H
-
-#include "treeBoundBoxList.H"
-#include "labelList.H"
-#include "point.H"
-#include "triSurface.H"
-#include "linePointRef.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// Forward declaration of classes
-template<class Type> class octree;
-
-/*---------------------------------------------------------------------------*\
-                           Class octreeDataTriSurface Declaration
-\*---------------------------------------------------------------------------*/
-
-class octreeDataTriSurface
-{
-    // Static data
-
-        //- tolerance on linear dimensions
-        static scalar tol;
-
-    // Private data
-
-        const triSurface& surface_;
-
-        const treeBoundBoxList allBb_;
-
-        // Extra data to speed up distance searches.
-        // Triangles expressed as base + spanning vectors
-        pointField base_;
-        pointField E0_;
-        pointField E1_;
-        scalarList a_;
-        scalarList b_;
-        scalarList c_;
-
-
-    // Private Static Functions
-
-        //- fast triangle nearest point calculation. Returns point in E0, E1
-        //  coordinate system:  base + s*E0 + t*E1
-        static void nearestCoords
-        (
-            const point& base,
-            const point& E0,
-            const point& E1,
-            const scalar a,
-            const scalar b,
-            const scalar c,
-            const point& P,
-            scalar& s,
-            scalar& t
-        );
-
-        //- Calculate bounding boxes for triangles
-        static treeBoundBoxList calcBb(const triSurface&);
-
-    // Private Member Functions
-
-        //- nearest point in xyz coord system
-        point nearestPoint(const label index, const point& P) const;
-
-public:
-
-    // Declare name of the class and its debug switch
-    ClassName("octreeDataTriSurface");
-
-
-    // Constructors
-
-        //- Construct from triSurface. Holds reference. Bounding box
-        //  calculated from triangle points.
-        octreeDataTriSurface(const triSurface&);
-
-        //- Construct from triSurface and bounding box.
-        //  Holds references.
-        octreeDataTriSurface(const triSurface&, const treeBoundBoxList&);
-
-
-    // Member Functions
-
-        // Access
-
-            const triSurface& surface() const
-            {
-                return surface_;
-            }
-
-            const treeBoundBoxList& allBb() const
-            {
-                return allBb_;
-            }
-
-            label size() const
-            {
-                return allBb_.size();
-            }
-
-        // Search
-
-            //- Get type of sample
-            label getSampleType
-            (
-                const octree<octreeDataTriSurface>&,
-                const point&
-            ) const;
-
-            //- Does (bb of) shape at index overlap bb
-            bool overlaps
-            (
-                const label index,
-                const treeBoundBox& sampleBb
-            ) const;
-
-            //- Does shape at index contain sample
-            bool contains
-            (
-                const label index,
-                const point& sample
-            ) const;
-
-            //- Segment (from start to end) intersection with shape
-            //  at index. If intersects returns true and sets intersectionPoint
-            bool intersects
-            (
-                const label index,
-                const point& start,
-                const point& end,
-                point& intersectionPoint
-            ) const;
-
-            //- Sets newTightest to bounding box (and returns true) if
-            //  nearer to sample than tightest bounding box. Otherwise
-            //  returns false.
-            bool findTightest
-            (
-                const label index,
-                const point& sample,
-                treeBoundBox& tightest
-            ) const;
-
-            //- Given index get unit normal and calculate (numerical) sign
-            //  of sample.
-            //  Used to determine accuracy of calcNearest or inside/outside.
-            scalar calcSign
-            (
-                const label index,
-                const point& sample,
-                vector& n
-            ) const;
-
-            //- Calculates nearest (to sample) point in shape.
-            //  Returns point and mag(nearest - sample)
-            scalar calcNearest
-            (
-                const label index,
-                const point& sample,
-                point& nearest
-            ) const;
-
-            //- Calculates nearest (to line segment) point in shape.
-            //  Returns distance and both point.
-            scalar calcNearest
-            (
-                const label index,
-                const linePointRef& ln,
-                point& linePt,          // nearest point on line
-                point& shapePt          // nearest point on shape
-            ) const;
-
-
-        // Write
-
-            // Write shape at index
-            void write(Ostream& os, const label index) const;
-
-
-    // IOstream Operators
-
-        friend Istream& operator>>(Istream&, octreeDataTriSurface&);
-        friend Ostream& operator<<(Ostream&, const octreeDataTriSurface&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
-#endif
-
-// ************************************************************************* //
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     3.2
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend 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.
+
+    foam-extend 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 foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::octreeDataTriSurface
+
+Description
+    Encapsulates data for octree searches on triSurface.
+
+SourceFiles
+    octreeDataTriSurface.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef octreeDataTriSurface_H
+#define octreeDataTriSurface_H
+
+#include "treeBoundBoxList.H"
+#include "labelList.H"
+#include "point.H"
+#include "triSurface.H"
+#include "linePointRef.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// Forward declaration of classes
+template<class Type> class octree;
+
+/*---------------------------------------------------------------------------*\
+                  Class octreeDataTriSurface Declaration
+\*---------------------------------------------------------------------------*/
+
+class octreeDataTriSurface
+{
+    // Static data
+
+        //- tolerance on linear dimensions
+        static scalar tol;
+
+    // Private data
+
+        const triSurface& surface_;
+
+        const treeBoundBoxList allBb_;
+
+        // Extra data to speed up distance searches.
+        // Triangles expressed as base + spanning vectors
+        pointField base_;
+        pointField E0_;
+        pointField E1_;
+        scalarList a_;
+        scalarList b_;
+        scalarList c_;
+
+
+    // Private Static Functions
+
+        //- fast triangle nearest point calculation. Returns point in E0, E1
+        //  coordinate system:  base + s*E0 + t*E1
+        static void nearestCoords
+        (
+            const point& base,
+            const point& E0,
+            const point& E1,
+            const scalar a,
+            const scalar b,
+            const scalar c,
+            const point& P,
+            scalar& s,
+            scalar& t
+        );
+
+        //- Calculate bounding boxes for triangles
+        static treeBoundBoxList calcBb(const triSurface&);
+
+
+    // Private Member Functions
+
+        //- nearest point in xyz coord system
+        point nearestPoint(const label index, const point& P) const;
+
+
+public:
+
+    // Declare name of the class and its debug switch
+    ClassName("octreeDataTriSurface");
+
+
+    // Constructors
+
+        //- Construct from triSurface. Holds reference. Bounding box
+        //  calculated from triangle points.
+        octreeDataTriSurface(const triSurface&);
+
+        //- Construct from triSurface and bounding box.
+        //  Holds references.
+        octreeDataTriSurface(const triSurface&, const treeBoundBoxList&);
+
+
+    // Member Functions
+
+        // Access
+
+            const triSurface& surface() const
+            {
+                return surface_;
+            }
+
+            const treeBoundBoxList& allBb() const
+            {
+                return allBb_;
+            }
+
+            label size() const
+            {
+                return allBb_.size();
+            }
+
+
+        // Search
+
+            //- Get type of sample
+            label getSampleType
+            (
+                const octree<octreeDataTriSurface>&,
+                const point&
+            ) const;
+
+            //- Does (bb of) shape at index overlap bb
+            bool overlaps
+            (
+                const label index,
+                const treeBoundBox& sampleBb
+            ) const;
+
+            //- Does shape at index contain sample
+            bool contains
+            (
+                const label index,
+                const point& sample
+            ) const;
+
+            //- Segment (from start to end) intersection with shape
+            //  at index. If intersects returns true and sets intersectionPoint
+            bool intersects
+            (
+                const label index,
+                const point& start,
+                const point& end,
+                point& intersectionPoint
+            ) const;
+
+            //- Sets newTightest to bounding box (and returns true) if
+            //  nearer to sample than tightest bounding box. Otherwise
+            //  returns false.
+            bool findTightest
+            (
+                const label index,
+                const point& sample,
+                treeBoundBox& tightest
+            ) const;
+
+            //- Given index get unit normal and calculate (numerical) sign
+            //  of sample.
+            //  Used to determine accuracy of calcNearest or inside/outside.
+            scalar calcSign
+            (
+                const label index,
+                const point& sample,
+                vector& n
+            ) const;
+
+            //- Calculates nearest (to sample) point in shape.
+            //  Returns point and mag(nearest - sample)
+            scalar calcNearest
+            (
+                const label index,
+                const point& sample,
+                point& nearest
+            ) const;
+
+            //- Calculates nearest (to line segment) point in shape.
+            //  Returns distance and both point.
+            scalar calcNearest
+            (
+                const label index,
+                const linePointRef& ln,
+                point& linePt,          // nearest point on line
+                point& shapePt          // nearest point on shape
+            ) const;
+
+
+        // Write
+
+            // Write shape at index
+            void write(Ostream& os, const label index) const;
+
+
+    // IOstream Operators
+
+        friend Istream& operator>>(Istream&, octreeDataTriSurface&);
+        friend Ostream& operator<<(Ostream&, const octreeDataTriSurface&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+#include "octreeDataTriSurfaceTreeLeaf.H"
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.C b/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.C
index d59ca7955..96e7722f8 100644
--- a/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.C
+++ b/src/meshTools/triSurface/octreeData/octreeDataTriSurfaceTreeLeaf.C
@@ -1,83 +1,83 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | foam-extend: Open Source CFD
-   \\    /   O peration     | Version:     3.2
-    \\  /    A nd           | Web:         http://www.foam-extend.org
-     \\/     M anipulation  | For copyright notice see file Copyright
--------------------------------------------------------------------------------
-License
-    This file is part of foam-extend.
-
-    foam-extend 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.
-
-    foam-extend 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 foam-extend.  If not, see <http://www.gnu.org/licenses/>.
-
-Description
-
-\*---------------------------------------------------------------------------*/
-
-#include "octreeDataTriSurfaceTreeLeaf.H"
-#include "octreeDataTriSurface.H"
-
-// * * * * * * * * * * * * * Template Specialisations  * * * * * * * * * * * //
-
-template<>
-bool Foam::treeLeaf<Foam::octreeDataTriSurface>::findNearest
-(
-    const octreeDataTriSurface& shapes,
-    const point& sample,
-    treeBoundBox& tightest,
-    label& tightestI,
-    scalar& tightestDist
-) const
-{
-    // Some aliases
-    const treeBoundBoxList& allBb = shapes.allBb();
-    point& min = tightest.min();
-    point& max = tightest.max();
-
-    point nearest;
-
-    bool changed = false;
-    forAll(indices_, i)
-    {
-        label faceI = indices_[i];
-
-        // Quick rejection test.
-        if (tightest.overlaps(allBb[faceI]))
-        {
-            // Full calculation
-            scalar dist = shapes.calcNearest(faceI, sample, nearest);
-
-            if (dist < tightestDist)
-            {
-                // Update bb (centered around sample, span is dist)
-                min.x() = sample.x() - dist;
-                min.y() = sample.y() - dist;
-                min.z() = sample.z() - dist;
-
-                max.x() = sample.x() + dist;
-                max.y() = sample.y() + dist;
-                max.z() = sample.z() + dist;
-
-                tightestI = faceI;
-                tightestDist = dist;
-
-                changed = true;
-            }
-        }
-    }
-    return changed;
-}
-
-
-// ************************************************************************* //
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     3.2
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend 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.
+
+    foam-extend 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 foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Description
+
+\*---------------------------------------------------------------------------*/
+
+#include "octreeDataTriSurface.H"
+#include "octreeDataTriSurfaceTreeLeaf.H"
+
+// * * * * * * * * * * * * * Template Specialisations  * * * * * * * * * * * //
+
+template<>
+bool Foam::treeLeaf<Foam::octreeDataTriSurface>::findNearest
+(
+    const octreeDataTriSurface& shapes,
+    const point& sample,
+    treeBoundBox& tightest,
+    label& tightestI,
+    scalar& tightestDist
+) const
+{
+    // Some aliases
+    const treeBoundBoxList& allBb = shapes.allBb();
+    point& min = tightest.min();
+    point& max = tightest.max();
+
+    point nearest;
+
+    bool changed = false;
+    forAll(indices_, i)
+    {
+        label faceI = indices_[i];
+
+        // Quick rejection test.
+        if (tightest.overlaps(allBb[faceI]))
+        {
+            // Full calculation
+            scalar dist = shapes.calcNearest(faceI, sample, nearest);
+
+            if (dist < tightestDist)
+            {
+                // Update bb (centered around sample, span is dist)
+                min.x() = sample.x() - dist;
+                min.y() = sample.y() - dist;
+                min.z() = sample.z() - dist;
+
+                max.x() = sample.x() + dist;
+                max.y() = sample.y() + dist;
+                max.z() = sample.z() + dist;
+
+                tightestI = faceI;
+                tightestDist = dist;
+
+                changed = true;
+            }
+        }
+    }
+    return changed;
+}
+
+
+// ************************************************************************* //

From 3a6cc671fa80f4c7b6aa3d8f87cc62abf3a91c32 Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Tue, 8 Sep 2015 15:06:53 +0100
Subject: [PATCH 13/15] Windows port: minor updates

---
 src/dbns/Make/options                             | 5 ++++-
 src/postProcessing/foamCalcFunctions/Make/options | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/dbns/Make/options b/src/dbns/Make/options
index c15372eed..7dda1a13e 100644
--- a/src/dbns/Make/options
+++ b/src/dbns/Make/options
@@ -9,6 +9,7 @@ EXE_INC = \
 
 LIB_LIBS = \
     -lfiniteVolume \
+    -lmeshTools \
     -L$(PARMGRIDGEN_LIB_DIR) -lIMlib -lmgrid
 
 #else
@@ -23,6 +24,8 @@ EXE_INC = \
 
 LIB_LIBS = \
     -lfiniteVolume \
+    -lmeshTools \
     -L$(PARMGRIDGEN_LIB_DIR) -lIMlib -lMGridGen
 
-#endif
\ No newline at end of file
+#endif
+
diff --git a/src/postProcessing/foamCalcFunctions/Make/options b/src/postProcessing/foamCalcFunctions/Make/options
index 71b787396..af3fbddd1 100644
--- a/src/postProcessing/foamCalcFunctions/Make/options
+++ b/src/postProcessing/foamCalcFunctions/Make/options
@@ -2,4 +2,5 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 LIB_LIBS = \
+    -lfoam \
     -lfiniteVolume

From 5f6a39a46e23c4f85e5fb101ba531cbe77e4a55c Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Tue, 8 Sep 2015 15:27:00 +0100
Subject: [PATCH 14/15] Build instructions update: Cesare Guardino

---
 ThirdParty/mingwBuild/clean.sh                |  5 +-
 bin/createWindowsBinaryPackage                | 71 +++++++++++--------
 doc/buildInstructions/Windows/README.txt      | 66 +++++++++--------
 .../Windows/READMEBinaryPackage.txt           |  2 +-
 etc/prefs.sh.mingw                            |  5 +-
 5 files changed, 87 insertions(+), 62 deletions(-)

diff --git a/ThirdParty/mingwBuild/clean.sh b/ThirdParty/mingwBuild/clean.sh
index c9f3f6bef..dade71657 100644
--- a/ThirdParty/mingwBuild/clean.sh
+++ b/ThirdParty/mingwBuild/clean.sh
@@ -23,10 +23,11 @@
 #     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Script
-#     build.sh
+#     clean.sh
 #
 # Description
-#     Removes previous thirdy-party dependencies build directories (does not remove installed packages directory)
+#     Removes previous thirdy-party dependencies build directories
+#     (does not remove installed packages directory)
 #
 # Author:
 #     Cesare Guardino, Alstom Power Ltd., (2015)
diff --git a/bin/createWindowsBinaryPackage b/bin/createWindowsBinaryPackage
index 0ea2fd269..43cb0b94d 100755
--- a/bin/createWindowsBinaryPackage
+++ b/bin/createWindowsBinaryPackage
@@ -23,7 +23,7 @@
 #     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Script
-#     createReleasePackage.mingw
+#     createWindowsBinaryPackage
 #
 # Description
 #     Creates stand-alone .zip packages for MinGW-based builds on Windows.
@@ -36,13 +36,19 @@
 cd ${0%/*} || exit 1    # run from this directory
 
 create_package() {
-    RELEASE_DIR=$1
+    PACKAGE_DIR=$1
     TYPE=$2
 
-    PACKAGE_FILE=$RELEASE_DIR.$TYPE
     echo ""
+
+    PACKAGE_FILE=$PACKAGE_DIR.$TYPE
+    if [ -f $PACKAGE_FILE ] ; then
+        echo "Removing previous $PACKAGE_FILE ..."
+        rm -f $PACKAGE_FILE
+    fi
+
     echo "Creating $PACKAGE_FILE ..."
-    7z -t$TYPE a $PACKAGE_FILE $RELEASE_DIR
+    7z -t$TYPE a $PACKAGE_FILE $PACKAGE_DIR
     
     if [ -f $PACKAGE_FILE ] ; then
         echo "Successfully created $PACKAGE_FILE"
@@ -52,7 +58,7 @@ create_package() {
 }
 
 echo
-echo "=========== FOAM-EXTEND WINDOWS STAND-ALONE PACKAGE CREATION SCRIPT ==========="
+echo "=========== FOAM-EXTEND STAND-ALONE PACKAGE CREATION SCRIPT FOR WINDOWS ==========="
 
 if [ "$PWD" != "$WM_PROJECT_DIR/bin" ]
 then
@@ -62,36 +68,43 @@ then
     exit 1
 fi
 
-RELEASE_DIR=$WM_PROJECT-$WM_FORK-$WM_PROJECT_VERSION-win-x64
-MPI_VERSION=`basename $FOAM_MPI_LIBBIN`
-if [ -d $RELEASE_DIR ] ; then
-    echo "Removing previous $RELEASE_DIR"
-    rm -rf $RELEASE_DIR
+RELEASE_DIR=$WM_PROJECT_DIR/releasePackages
+if [ ! -d $RELEASE_DIR ] ; then
+    echo "Creating $RELEASE_DIR ..."
+    mkdir $RELEASE_DIR
 fi
-mkdir $RELEASE_DIR
+
+PACKAGE_DIR=$RELEASE_DIR/$WM_PROJECT-$WM_FORK-$WM_PROJECT_VERSION-win-x64
+if [ -d $PACKAGE_DIR ] ; then
+    echo "Removing previous $PACKAGE_DIR ..."
+    rm -rf $PACKAGE_DIR
+fi
+echo "Creating $PACKAGE_DIR ..."
+mkdir $PACKAGE_DIR
 
 echo "Copying bin directory ..."
-cp -rp $FOAM_APPBIN $RELEASE_DIR/bin
+cp -rp $FOAM_APPBIN $PACKAGE_DIR/bin
 
 echo "Copying DLLs from lib directory ..."
-mkdir $RELEASE_DIR/lib
-cp -p $FOAM_LIBBIN/*.dll $RELEASE_DIR/lib
-mkdir $RELEASE_DIR/lib/$MPI_VERSION
-cp -p $FOAM_MPI_LIBBIN/*.dll $RELEASE_DIR/lib/$MPI_VERSION
+mkdir $PACKAGE_DIR/lib
+cp -p $FOAM_LIBBIN/*.dll $PACKAGE_DIR/lib
+
+echo "Copying extra files from bin directory ..."
+cp -p $WM_PROJECT_DIR/bin/setWindowsEnvironment.bat $PACKAGE_DIR/
+cp -p $WM_PROJECT_DIR/bin/foamWindowsShell.bat $PACKAGE_DIR/
+cp -p $WM_PROJECT_DIR/bin/paraFoam.bat $PACKAGE_DIR/bin
 
 echo "Copying extra files from etc directory ..."
-mkdir $RELEASE_DIR/etc
-cp -p $WM_PROJECT_DIR/bin/setWindowsEnvironment.bat $RELEASE_DIR/
-cp -p $WM_PROJECT_DIR/bin/foamWindowsShell.bat $RELEASE_DIR/
-cp -p $WM_PROJECT_DIR/etc/controlDict-EXAMPLE $RELEASE_DIR/etc
-cp -p $WM_PROJECT_DIR/etc/cellModels $RELEASE_DIR/etc
-cp -rp $WM_PROJECT_DIR/etc/thermoData $RELEASE_DIR/etc
-cp -p $WM_PROJECT_DIR/doc/buildInstructions/Windows/READMEBinaryPackage.txt $RELEASE_DIR/
-cp -p $WM_PROJECT_DIR/bin/paraFoam.bat $RELEASE_DIR/bin
-cp -p $WM_PROJECT_DIR/COPYING $RELEASE_DIR/LICENSE.txt
-unix2dos $RELEASE_DIR/LICENSE.txt
+mkdir $PACKAGE_DIR/etc
+cp -p $WM_PROJECT_DIR/etc/cellModels $PACKAGE_DIR/etc
+cp -rp $WM_PROJECT_DIR/etc/thermoData $PACKAGE_DIR/etc
 
-create_package $RELEASE_DIR zip
-#create_package $RELEASE_DIR 7z
+echo "Copying doc and license files ..."
+cp -p $WM_PROJECT_DIR/doc/buildInstructions/Windows/READMEBinaryPackage.txt $PACKAGE_DIR/
+cp -p $WM_PROJECT_DIR/COPYING $PACKAGE_DIR/LICENSE.txt
+unix2dos $PACKAGE_DIR/LICENSE.txt
 
-rm -rf $RELEASE_DIR
+create_package $PACKAGE_DIR zip
+create_package $PACKAGE_DIR 7z
+
+rm -rf $PACKAGE_DIR
diff --git a/doc/buildInstructions/Windows/README.txt b/doc/buildInstructions/Windows/README.txt
index 0f65bbd37..a620d5ac9 100644
--- a/doc/buildInstructions/Windows/README.txt
+++ b/doc/buildInstructions/Windows/README.txt
@@ -37,7 +37,7 @@
 
 It is strongly recommended to install all required systems tools and utilities
 in a directory with no embedded white spaces. You can skip some steps if you
-already have some of these system tools.
+already have the correct tools installed on your system.
 
 
 2. INSTRUCTIONS FOR BUILDING ON WINDOWS
@@ -46,22 +46,32 @@ already have some of these system tools.
 1) Download and install 7-Zip (see reference list below). This is necessary to
    be able to unzip the rest of the required packages mentioned in later steps.
 
-2) Download and install wget, CMake, Git, MinGW-w64, ParaView, PExports, Java, Subversion, Python (see
-   reference list below). Note that some components (example PExports and GMake)
-   may already be available in other packages (such as Strawberry Perl), although
-   you need to be careful of the version numbers.
+2) Download and install wget, CMake, Git, MinGW-w64, ParaView, PExports, Java,
+   Subversion, Python (see reference list below). Note that some components
+   (for example PExports and GMake) may already be available in other packages
+   (such as Strawberry Perl), although you need to be careful of the
+    version numbers.
 
 3) Download and install MSYS (see reference list below).  If this is your first
-   use of MSYS, create a file fstab in cMinGW/1.0/etc with single-line contents:
+   use of MSYS, create a file fstab in c/MinGW/msys/1.0/etc with single-line
+   contents:
 
-   c/mingw /mingw
+   c:/mingw /mingw
 
-   to mount your home directory.  From Windows, you will find your home directory
-   under c:/MinGW/msys/1.0/home/<user name>
+   to mount your home directory (this assumes you have installed MSYS to the default
+   c:/MinGW directory).
+   From Windows, you will find your home directory under
+   c:/MinGW/msys/1.0/home/<user name>
 
-4) Download the foam-extend source code from http://sourceforge.net/projects/openfoam-extend/
+4) Download the foam-extend source code from
 
-5) Open a new MSYS shell and chdir to your foam-extend-3.1 source directory.
+   http://sourceforge.net/projects/openfoam-extend/
+
+   using the command:
+
+   git clone --branch nextRelease git://git.code.sf.net/p/openfoam-extend/foam-extend-3.1 foam-extend-3.2
+
+5) Open a new MSYS shell and chdir to your foam-extend-3.2 source directory.
 
 6) Edit the user-modifiable entries in etc/bashrc.mingw to point to the
    locations where you have installed the required system tools in the first two
@@ -92,9 +102,9 @@ already have some of these system tools.
         approach for developers.
 
    (b). From a standard Windows CMD.exe command prompt using the created
-        foam-extend-3.1-win-x64.zip stand-alone package. This can be used on any
-        Windows machine without access to MSYS shells or compilers. See the README.txt
-        contained within the package for further details.
+        foam-extend-3.2-win-x64.zip stand-alone package. This can be used on any
+        Windows machine without access to MSYS shells or compilers. See the
+        READMEBinaryPackage.txt contained within the package for further details.
 
 
 3. EXTERNAL PACKAGE REFERENCE
@@ -175,22 +185,22 @@ For    : Automatically downloading files from internet (eg. for use in automated
 git clone --branch nextRelease git://git.code.sf.net/p/openfoam-extend/foam-extend-3.1
 
 
-4. EXAMPLE OUTPUT FROM SOUCING etc/bashrc.mingw
-===============================================
+4. EXAMPLE OUTPUT FROM SOURCING etc/bashrc.mingw
+================================================
 
 $ . etc/bashrc.mingw
 Setting environment variables for user-defined installed system tools and utilities ...
 
-Sourcing: /c/Users/UserName/Git/foam-extend-3.1/etc/bashrc
-Sourcing: /c/Users/UserName/Git/foam-extend-3.1/etc/prefs.sh.mingw
-Sourcing: /c/Users/UserName/Git/foam-extend-3.1/etc/settings.sh
-    MESQUITE_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/mesquite-2.1.2
-    METIS_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/metis-5.1.0
-    PARMETIS_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/parmetis-4.0.3
-    PARMGRIDGEN_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/ParMGridGen-1.0
+Sourcing: /c/Users/UserName/Git/foam-extend-3.2/etc/bashrc
+Sourcing: /c/Users/UserName/Git/foam-extend-3.2/etc/prefs.sh.mingw
+Sourcing: /c/Users/UserName/Git/foam-extend-3.2/etc/settings.sh
+    MESQUITE_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/mesquite-2.1.2
+    METIS_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/metis-5.1.0
+    PARMETIS_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/parmetis-4.0.3
+    PARMGRIDGEN_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/ParMGridGen-1.0
     LIBCCMIO_DIR is initialized to:
-    SCOTCH_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/scotch_6.0.0
-    SCOTCH_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/packages/scotch_6.0.0
+    SCOTCH_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/scotch_6.0.0
+    SCOTCH_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/packages/scotch_6.0.0
     CMAKE_DIR is initialized to:
     M4_DIR is initialized to:
     BISON_DIR is initialized to:
@@ -198,13 +208,13 @@ Sourcing: /c/Users/UserName/Git/foam-extend-3.1/etc/settings.sh
     ZOLTAN_DIR is initialized to:
     PYTHON_DIR is initialized to:
     PYFOAM_DIR is initialized to:
-    PYFOAM_SITE_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.1/ThirdParty/PyFoamSiteScripts
+    PYFOAM_SITE_DIR is initialized to: /c/Users/UserName/Git/foam-extend-3.2/ThirdParty/PyFoamSiteScripts
     HWLOC_DIR is initialized to:
     QT_DIR is initialized to:
     PARAVIEW_DIR is initialized to:
     LLVM_DIR is initialized to:
     MESA_DIR is initialized to:
-Sourcing: /c/Users/UserName/Git/foam-extend-3.1/etc/aliases.sh
+Sourcing: /c/Users/UserName/Git/foam-extend-3.2/etc/aliases.sh
 
 Adding user-defined installed system tools to PATH ...
 Setting OpenMPI environment settings ...
@@ -233,6 +243,6 @@ Wget:        /c/Programs/wget-1.11.4-1/bin/wget.exe [GNU Wget 1.11.4 Copyright (
 
 
 FOAM_INST_DIR=/c/Users/UserName/Git
-WM_PROJECT_DIR=/c/Users/UserName/Git/foam-extend-3.1
+WM_PROJECT_DIR=/c/Users/UserName/Git/foam-extend-3.2
 WM_OSTYPE=MSWindows
 ENVIRONMENT SETUP COMPLETE.
diff --git a/doc/buildInstructions/Windows/READMEBinaryPackage.txt b/doc/buildInstructions/Windows/READMEBinaryPackage.txt
index 33bfa3160..ecf9af4ab 100644
--- a/doc/buildInstructions/Windows/READMEBinaryPackage.txt
+++ b/doc/buildInstructions/Windows/READMEBinaryPackage.txt
@@ -22,7 +22,7 @@
 #     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 #
 # File
-#     README_Windows.txt
+#     READMEBinaryPackage.txt
 #
 # Description
 #     Installation and usage instructions for stand-alone Windows builds.
diff --git a/etc/prefs.sh.mingw b/etc/prefs.sh.mingw
index 67f196672..acafa9304 100644
--- a/etc/prefs.sh.mingw
+++ b/etc/prefs.sh.mingw
@@ -22,10 +22,11 @@
 #     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 #
 # File
-#     etc/prefs.sh
+#     etc/prefs.sh.mingw
 #
 # Description
-#     Preset variables for the FOAM configuration - POSIX shell syntax.
+#     Preset variables for the FOAM configuration - POSIX shell syntax
+#     for MS Windows
 #
 #     The prefs.sh file will be sourced by the FOAM etc/bashrc when it is
 #     found

From e411de9576229e1762b59c6884ad1be14163a9dd Mon Sep 17 00:00:00 2001
From: Hrvoje Jasak <h.jasak@wikki.co.uk>
Date: Fri, 11 Sep 2015 16:08:23 +0100
Subject: [PATCH 15/15] Better bounding on topo change

---
 .../solvers/compressible/sonicDyMFoam/sonicDyMFoam.C        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/applications/solvers/compressible/sonicDyMFoam/sonicDyMFoam.C b/applications/solvers/compressible/sonicDyMFoam/sonicDyMFoam.C
index 4fb6e2572..cf821dbc4 100644
--- a/applications/solvers/compressible/sonicDyMFoam/sonicDyMFoam.C
+++ b/applications/solvers/compressible/sonicDyMFoam/sonicDyMFoam.C
@@ -85,9 +85,9 @@ int main(int argc, char *argv[])
         // Mesh motion update
         if (meshChanged)
         {
-            T = max(T, TMin);
-            p = max(p, pMin);
-            e = max(e, thermo.Cv()*TMin);
+            T.max(TMin);
+            p.max(pMin);
+            e == max(e, thermo.Cv()*TMin);
 
             thermo.correct();
             rho = thermo.rho();