From 3186bd87dec2fd82f6ff9ed1f4c030b057553ef9 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 15 Oct 2020 09:41:21 +0100
Subject: [PATCH 1/8] BUG: regionToFace: does not stop walking. Fixes #1882

Problem was initial value of zone (transported label) was
still 0. Fixed by properly checking for 'valid' state.
---
 .../sets/faceSources/regionToFace/regionToFace.C     | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/meshTools/sets/faceSources/regionToFace/regionToFace.C b/src/meshTools/sets/faceSources/regionToFace/regionToFace.C
index f4e84e77b2..960e08a2ac 100644
--- a/src/meshTools/sets/faceSources/regionToFace/regionToFace.C
+++ b/src/meshTools/sets/faceSources/regionToFace/regionToFace.C
@@ -78,7 +78,7 @@ void Foam::regionToFace::markZone
     const indirectPrimitivePatch& patch,
     const label proci,
     const label facei,
-    const label zoneI,
+    const label zonei,
     labelList& faceZone
 ) const
 {
@@ -100,7 +100,7 @@ void Foam::regionToFace::markZone
                 edgeTopoDistanceData<label>
                 (
                     0,          // distance
-                    zoneI
+                    zonei
                 )
             );
         }
@@ -124,9 +124,13 @@ void Foam::regionToFace::markZone
 
     forAll(allFaceInfo, facei)
     {
-        if (allFaceInfo[facei].data() == zoneI)
+        if
+        (
+            allFaceInfo[facei].valid(calc.data())
+         && allFaceInfo[facei].data() == zonei
+        )
         {
-            faceZone[facei] = zoneI;
+            faceZone[facei] = zonei;
         }
     }
 }

From 3e4d9e15c077bbe4ceeb132dfa93c95c35bcde09 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Fri, 23 Oct 2020 09:28:07 +0200
Subject: [PATCH 2/8] BUG: using FatalIOErrorInLookup with incorrect exit type
 (fixes #1898)

- two occurrences where FatalIOErrorInLookup used exit(FatalError)
  instead of exit(FatalIOError), which caused the error messages
  to be lost.
---
 src/ODE/ODESolvers/ODESolver/ODESolverNew.C                   | 4 ++--
 .../surfaceInterpolationScheme/surfaceInterpolationScheme.C   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/ODE/ODESolvers/ODESolver/ODESolverNew.C b/src/ODE/ODESolvers/ODESolver/ODESolverNew.C
index ce70fb45af..1ed2d81c87 100644
--- a/src/ODE/ODESolvers/ODESolver/ODESolverNew.C
+++ b/src/ODE/ODESolvers/ODESolver/ODESolverNew.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2015 OpenFOAM Foundation
-    Copyright (C) 2019 OpenCFD Ltd.
+    Copyright (C) 2019-2020 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -49,7 +49,7 @@ Foam::autoPtr<Foam::ODESolver> Foam::ODESolver::New
             "ODESolver",
             solverType,
             *dictionaryConstructorTablePtr_
-        ) << exit(FatalError);
+        ) << exit(FatalIOError);
     }
 
     return autoPtr<ODESolver>(cstrIter()(odes, dict));
diff --git a/src/finiteVolume/interpolation/surfaceInterpolation/surfaceInterpolationScheme/surfaceInterpolationScheme.C b/src/finiteVolume/interpolation/surfaceInterpolation/surfaceInterpolationScheme/surfaceInterpolationScheme.C
index a1a5676181..ef00d57858 100644
--- a/src/finiteVolume/interpolation/surfaceInterpolation/surfaceInterpolationScheme/surfaceInterpolationScheme.C
+++ b/src/finiteVolume/interpolation/surfaceInterpolation/surfaceInterpolationScheme/surfaceInterpolationScheme.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2016 OpenFOAM Foundation
-    Copyright (C) 2019 OpenCFD Ltd.
+    Copyright (C) 2019-2020 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -68,7 +68,7 @@ Foam::surfaceInterpolationScheme<Type>::New
             "discretisation",
             schemeName,
             *MeshConstructorTablePtr_
-        ) << exit(FatalError);
+        ) << exit(FatalIOError);
     }
 
     return cstrIter()(mesh, schemeData);

From 9dc4f76b0360eba4933632fc209c4a59c51c9e69 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Fri, 23 Oct 2020 09:34:07 +0200
Subject: [PATCH 3/8] BUG: incorrect boundary type for expressions variables
 (fixes #1889)

- had calculated boundaries (default) for the evaluated variables,
  which meant they retained their initialized values (usually Zero).

  This normally goes unnoticed, since the boundary values are largely
  irrelevant in the volField expressions. However, when applying
  functions that balk at a zero value - eg, log() - this raises a
  floating point exception.

  These boundary should be zeroGradient, since the evaluated variables
  correspond to the internalField only. Could continue to use
  calculated, but then need to set the calculated boundary values from
  the patch internal field manually.
---
 .../expressions/base/fvExprDriverTemplates.C          | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/finiteVolume/expressions/base/fvExprDriverTemplates.C b/src/finiteVolume/expressions/base/fvExprDriverTemplates.C
index 70eda6a08d..c1c411c504 100644
--- a/src/finiteVolume/expressions/base/fvExprDriverTemplates.C
+++ b/src/finiteVolume/expressions/base/fvExprDriverTemplates.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2010-2018 Bernhard Gschaider <bgschaid@hfd-research.com>
-    Copyright (C) 2019 OpenCFD Ltd.
+    Copyright (C) 2019-2020 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -261,7 +261,14 @@ Foam::tmp<GeomField> Foam::expressions::fvExprDriver::getOrReadFieldImpl
 
         tfield.reset
         (
-            GeomField::New(name, meshRef, dimensioned<Type>(Zero))
+            GeomField::New
+            (
+                name,
+                meshRef,
+                dimensioned<Type>(Zero),
+                // Patch is zeroGradient (volFields) or calculated (other)
+                defaultBoundaryType(GeomField::null())
+            )
         );
 
         GeomField& fld = tfield.ref();

From bed1305d96c9a5ff73fe89419fd9c811ae46320b Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Thu, 29 Oct 2020 10:02:59 +0100
Subject: [PATCH 4/8] BUG: extraneous brackets after Fluent cell types (fixes
 #1872)

ENH: limit output to 25 cell types per line for readability

- makes it easier to trace potential format errors etc

STYLE: downgrade warning about polyhedrals to a simple info message

- can assume that polyhedral support is widespread enough to not
  warrant a warning.
---
 .../foamMeshToFluent/fluentFvMesh.C           | 66 ++++++++++++-------
 1 file changed, 41 insertions(+), 25 deletions(-)

diff --git a/applications/utilities/mesh/conversion/foamMeshToFluent/fluentFvMesh.C b/applications/utilities/mesh/conversion/foamMeshToFluent/fluentFvMesh.C
index 2d3521328d..180d18669a 100644
--- a/applications/utilities/mesh/conversion/foamMeshToFluent/fluentFvMesh.C
+++ b/applications/utilities/mesh/conversion/foamMeshToFluent/fluentFvMesh.C
@@ -6,6 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2016 OpenFOAM Foundation
+    Copyright (C) 2020 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -62,13 +63,13 @@ void Foam::fluentFvMesh::writeFluentMesh() const
       / time().caseName() + ".msh"
     );
 
-    Info<< "Writing Header" << endl;
+    Info<< "Writing Fluent Mesh" << endl;
 
     fluentMeshFile
-        << "(0 \"FOAM to Fluent Mesh File\")" << std::endl << std::endl
-        << "(0 \"Dimension:\")" << std::endl
-        << "(2 3)" << std::endl << std::endl
-        << "(0 \"Grid dimensions:\")" << std::endl;
+        << "(0 \"OpenFOAM to Fluent Mesh File\")" << nl << nl
+        << "(0 \"Dimension:\")" << nl
+        << "(2 3)" << nl << nl
+        << "(0 \"Grid dimensions:\")" << nl;
 
     // Writing number of points
     fluentMeshFile
@@ -217,8 +218,8 @@ void Foam::fluentFvMesh::writeFluentMesh() const
 
     // Writing cells
     fluentMeshFile
-        << "(12 (1 1 "
-        << nCells() << " 1 0)(" << std::endl;
+        << "(12 (1 1 " << nCells() << " 1 0)" << nl
+        << '(';
 
     const cellModel& hex = cellModel::ref(cellModel::HEX);
     const cellModel& prism = cellModel::ref(cellModel::PRISM);
@@ -227,44 +228,59 @@ void Foam::fluentFvMesh::writeFluentMesh() const
 
     const cellShapeList& cells = cellShapes();
 
-    bool hasWarned = false;
+    label nPolys = 0;
+
+    int nElemPerLine = 25;  // Start with linebreak and indent
 
     forAll(cells, celli)
     {
+        if (nElemPerLine == 25)
+        {
+            // 25 elements per line with initial indent (readability)
+            fluentMeshFile << "\n   ";
+            nElemPerLine = 0;
+        }
+        else if (!(nElemPerLine % 5))
+        {
+            // Format in blocks of 5 (readability)
+            fluentMeshFile << token::SPACE;
+        }
+        fluentMeshFile << token::SPACE;
+        ++nElemPerLine;
+
+
         if (cells[celli].model() == tet)
         {
-            fluentMeshFile << " " << 2;
+            fluentMeshFile << 2;
         }
         else if (cells[celli].model() == hex)
         {
-            fluentMeshFile << " " << 4;
+            fluentMeshFile << 4;
         }
         else if (cells[celli].model() == pyr)
         {
-            fluentMeshFile << " " << 5;
+            fluentMeshFile << 5;
         }
         else if (cells[celli].model() == prism)
         {
-            fluentMeshFile << " " << 6;
+            fluentMeshFile << 6;
         }
         else
         {
-            if (!hasWarned)
-            {
-                hasWarned = true;
-
-                WarningInFunction
-                    << "foamMeshToFluent: cell shape for cell "
-                    << celli << " only supported by Fluent polyhedral meshes."
-                    << nl
-                    << "    Suppressing any further messages for polyhedral"
-                    << " cells." << endl;
-            }
-            fluentMeshFile << " " << 7;
+            fluentMeshFile << 7;
+            ++nPolys;
         }
     }
 
-    fluentMeshFile << ")())" << std::endl;
+    fluentMeshFile
+        << nl << "))" << nl;
+
+
+    if (nPolys)
+    {
+        Info<< "Mesh had " << nPolys << " polyhedrals." << endl;
+    }
+
 
     // Return to dec
     fluentMeshFile.setf(ios::dec, ios::basefield);

From 5e660c36e9d863ceea6399b3eaffc228879fbda7 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 3 Nov 2020 20:20:40 +0100
Subject: [PATCH 5/8] CONFIG: ptscotch header not found on RedHat/Fedora (fixes
 #1904)

- no limit to the number of ways of filing ptscotch libraries.
  RedHat/Fedora/CentOS should look for these directories:

      ptscotch include=/usr/include/openmpi-x86_64
      ptscotch library=/usr/lib64/openmpi/lib

  when MPI_ARCH_PATH=/usr/lib64/openmpi
  and mpicc --showme:compile yields -I/usr/include/openmpi-x86_64
---
 wmake/scripts/have_scotch | 56 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/wmake/scripts/have_scotch b/wmake/scripts/have_scotch
index fb7182a0dd..fdae90a59b 100644
--- a/wmake/scripts/have_scotch
+++ b/wmake/scripts/have_scotch
@@ -37,6 +37,50 @@
 #     PTSCOTCH_INC_DIR
 #     PTSCOTCH_LIB_DIR
 #
+#
+# System files can be hiding in a large variety of locations.
+# For x86_64 system:
+#
+# ArchLinux
+# ---------
+#     scotch   include: /usr/include/scotch
+#     scotch   library: /usr/lib64
+#
+#     ptscotch include: /usr/include/ptscotch
+#     ptscotch library: /usr/lib64
+#
+#
+# Debian/Ubuntu
+# -------------
+#     scotch   include: /usr/include/scotch-int32
+#     scotch   library: /usr/lib/x86_64-linux-gnu
+#
+#     ptscotch include: /usr/include/scotch-int32
+#     ptscotch library: /usr/lib/x86_64-linux-gnu
+#
+#
+# RedHat
+# ------
+#     scotch   include: /usr/include
+#     scotch   library: /usr/lib64
+#
+#     ptscotch include: /usr/include/openmpi-x86_64
+#     ptscotch library: /usr/lib64/openmpi/lib
+#
+# when MPI_ARCH_PATH=/usr/lib64/openmpi
+# and mpicc --showme:compile -> -I/usr/include/openmpi-x86_64
+#
+#
+# openSUSE
+# --------
+#     scotch   include: /usr/include
+#     scotch   library: /usr/lib64
+#
+#     ptscotch include: /usr/lib64/mpi/gcc/openmpi2/include
+#     ptscotch library: /usr/lib64/mpi/gcc/openmpi2/lib64
+#
+# when MPI_ARCH_PATH=/usr/lib64/mpi/gcc/openmpi2
+#
 #------------------------------------------------------------------------------
 . ${WM_PROJECT_DIR:?}/wmake/scripts/sysFunctions    # General system functions
 
@@ -192,6 +236,9 @@ search_ptscotch()
     local prefix="${1:-system}"
     local header library
 
+    local mpiPrefix="$MPI_ARCH_PATH"
+    local mpiName="${MPI_ARCH_PATH##*/}"
+
     # ----------------------------------
     if isNone "$prefix"
     then
@@ -204,7 +251,10 @@ search_ptscotch()
             "$prefix/include/$localDir/$incName" \
             "$prefix/include/ptscotch/$incName" \
             "$prefix/include/scotch/$incName" \
-            "$prefix/include/$incName"
+            "$prefix/include/$incName" \
+            "$mpiPrefix/include/$incName" \
+            "$prefix/include/$mpiName/$incName" \
+            "$prefix/include/${mpiName}-$(uname -m)/$incName" \
         )
         library="$(findExtLib $FOAM_MPI/$libName $libName)"
     elif isSystem "$prefix"
@@ -218,6 +268,9 @@ search_ptscotch()
             "/usr/include/ptscotch/$incName" \
             "/usr/include/scotch/$incName" \
             "/usr/include/$incName" \
+            "$mpiPrefix/include/$incName" \
+            "/usr/include/$mpiName/$incName" \
+            "$prefix/include/${mpiName}-$(uname -m)/$incName" \
         )
         prefix=$(sysPrefix "$header")
     else
@@ -235,6 +288,7 @@ search_ptscotch()
     # Library
     [ -n "$library" ] \
     || library=$(findLibrary -prefix="$prefix" -name="$libName" -local="$localDir") \
+    || library=$(findLibrary -prefix="$mpiPrefix" -name="$libName" -local="$localDir") \
     || {
         [ -n "$warn" ] && echo "$warn (no library)"
         return 2

From fc541cee407ac87d708f6961259ddee696989c57 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Fri, 13 Nov 2020 10:53:12 +0100
Subject: [PATCH 6/8] BUG: crash during gap refinement (fixes #1919)

- fixed indexing error (crashes under windows).
  No crash but still incorrect on other systems
---
 .../meshRefinement/meshRefinementGapRefine.C             | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/mesh/snappyHexMesh/meshRefinement/meshRefinementGapRefine.C b/src/mesh/snappyHexMesh/meshRefinement/meshRefinementGapRefine.C
index 60621e2cd9..ceacaf9fcf 100644
--- a/src/mesh/snappyHexMesh/meshRefinement/meshRefinementGapRefine.C
+++ b/src/mesh/snappyHexMesh/meshRefinement/meshRefinementGapRefine.C
@@ -453,12 +453,13 @@ Foam::label Foam::meshRefinement::markSurfaceGapRefinement
 
         forAll(surf1, i)
         {
-            // Combine selfProx of shell and surfaces. Ignore regions for
-            // now
+            // Combine selfProx of shell and surfaces.
+            // Ignore regions for now
             const label cellI = cellMap[i];
+
             const label shelli =
             (
-                cellToCompact[cellI] != -1
+                (cellI != -1 && cellToCompact[cellI] != -1)
               ? gapShell[cellToCompact[cellI]]
               : -1
             );
@@ -482,8 +483,6 @@ Foam::label Foam::meshRefinement::markSurfaceGapRefinement
             )
             {
                 // Found intersection with surface. Check opposite normal.
-                label cellI = cellMap[i];
-
                 if
                 (
                     cellI != -1

From da7165077c1c611aaff5faf8d745354fc5b35f01 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Wed, 18 Nov 2020 16:05:54 +0100
Subject: [PATCH 7/8] BUG: typo in solidProperties prevents re-reading of "Hf"
 (fixes #1927)

---
 .../solidProperties/solidProperties/solidProperties.C         | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/thermophysicalModels/thermophysicalProperties/solidProperties/solidProperties/solidProperties.C b/src/thermophysicalModels/thermophysicalProperties/solidProperties/solidProperties/solidProperties.C
index 3c12e9733f..d2afd3e5ec 100644
--- a/src/thermophysicalModels/thermophysicalProperties/solidProperties/solidProperties/solidProperties.C
+++ b/src/thermophysicalModels/thermophysicalProperties/solidProperties/solidProperties/solidProperties.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2017 OpenFOAM Foundation
-    Copyright (C) 2018-2019 OpenCFD Ltd.
+    Copyright (C) 2018-2020 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -77,7 +77,7 @@ void Foam::solidProperties::readIfPresent(const dictionary& dict)
     dict.readIfPresent("rho", rho_);
     dict.readIfPresent("Cp", Cp_);
     dict.readIfPresentCompat("kappa", {{"K", 1612}}, kappa_);
-    dict.readIfPresent("Hf_", Hf_);
+    dict.readIfPresent("Hf", Hf_);
     dict.readIfPresent("emissivity", emissivity_);
     dict.readIfPresent("W", W_);
 }

From ac98e498fef67708f758e99217df95c7ca5d72f7 Mon Sep 17 00:00:00 2001
From: Andrew Heather <>
Date: Tue, 24 Nov 2020 12:01:15 +0000
Subject: [PATCH 8/8] BUG: meshToMesh - corrected mapping of internal field for
 tgt->src mapping. Fixes #1935

---
 src/sampling/meshToMesh/meshToMesh.C | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/sampling/meshToMesh/meshToMesh.C b/src/sampling/meshToMesh/meshToMesh.C
index 90d7b8b4d5..3bb266dc6d 100644
--- a/src/sampling/meshToMesh/meshToMesh.C
+++ b/src/sampling/meshToMesh/meshToMesh.C
@@ -157,7 +157,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }
 
 
@@ -170,7 +170,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }
 
 
@@ -183,7 +183,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }
 
 
@@ -196,7 +196,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }
 
 
@@ -209,7 +209,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }
 
 
@@ -222,7 +222,7 @@ void Foam::meshToMesh::mapInternalTgtToSrc
     const bool secondOrder
 ) const
 {
-    mapSrcToTgt(field, cop, result.primitiveFieldRef());
+    mapTgtToSrc(field, cop, result.primitiveFieldRef());
 }