From 08c23685c340e87e04730d47f4f1410d7e8eca59 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 6 Feb 2024 09:26:55 +0100
Subject: [PATCH 1/5] BUG: incorrect cumulative area in triangulatedPatch
 (fixes #3097)

BUG: bad processor selection. Failed to select anything on non-master
---
 .../triangulatedPatch/triangulatedPatch.C     | 156 +++++++++++-------
 .../triangulatedPatch/triangulatedPatch.H     |  19 ++-
 2 files changed, 107 insertions(+), 68 deletions(-)

diff --git a/src/meshTools/triangulatedPatch/triangulatedPatch.C b/src/meshTools/triangulatedPatch/triangulatedPatch.C
index 513514cfbf..f80ec25595 100644
--- a/src/meshTools/triangulatedPatch/triangulatedPatch.C
+++ b/src/meshTools/triangulatedPatch/triangulatedPatch.C
@@ -5,7 +5,7 @@
     \\  /    A nd           | www.openfoam.com
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
-    Copyright (C) 2023 OpenCFD Ltd.
+    Copyright (C) 2023-2024 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -26,7 +26,6 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "triangulatedPatch.H"
-#include "triPointRef.H"
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
@@ -50,6 +49,8 @@ bool Foam::triangulatedPatch::randomPoint
 
     // Find corresponding decomposed face triangle
     // Note: triWght_ is sized nTri+1 (zero added at start)
+    //
+    // TBD: binary search with findLower(triWght_, c) ??
     label trii = 0;
     for (label i = 0; i < triWght_.size() - 1; ++i)
     {
@@ -62,11 +63,9 @@ bool Foam::triangulatedPatch::randomPoint
 
     // Find random point in triangle
     const pointField& points = patch_.points();
-    const face& tf = triFace_[trii];
-    const triPointRef tri(points[tf[0]], points[tf[1]], points[tf[2]]);
 
-    result = tri.randomPoint(rnd);
-    facei = triToFace_[trii];
+    result = triFace_[trii].tri(points).randomPoint(rnd);
+    facei = triFace_[trii].index();
     celli = patch_.faceCells()[facei];
 
     if (perturbTol_ > 0)
@@ -97,7 +96,6 @@ Foam::triangulatedPatch::triangulatedPatch
     patch_(patch),
     perturbTol_(perturbTol),
     triFace_(),
-    triToFace_(),
     triWght_()
 {
     update();
@@ -115,70 +113,95 @@ Foam::triangulatedPatch::triangulatedPatch
 {}
 
 
+// * * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * //
+
+void Foam::triangulatedPatch::triangulate
+(
+    const polyPatch& pp,
+    List<labelledTri>& tris
+)
+{
+    const pointField& points = pp.points();
+
+    // Triangulate the patch faces and create addressing
+    label nTris = 0;
+    for (const face& f : pp)
+    {
+        nTris += f.nTriangles();
+    }
+
+    DynamicList<labelledTri> dynTris(nTris);
+    DynamicList<face> tfaces(8);  // work array
+
+    label facei = 0;
+    for (const face& f : pp)
+    {
+        tfaces.clear();
+        f.triangles(points, tfaces);
+
+        for (const auto& t : tfaces)
+        {
+            dynTris.emplace_back(t[0], t[1], t[2], facei);
+        }
+        ++facei;
+    }
+
+    tris.transfer(dynTris);
+}
+
+
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 void Foam::triangulatedPatch::update()
 {
+    triFace_.clear();
+    triWght_.clear();
+
+    triangulate(patch_, triFace_);
+
     const pointField& points = patch_.points();
 
-    // Triangulate the patch faces and create addressing
-    DynamicList<label> triToFace(2*patch_.size());
-    DynamicList<face> triFace(2*patch_.size());
-    DynamicList<scalar> triWght(2*patch_.size());
-    DynamicList<face> tris(8);
+    const label myProci = UPstream::myProcNo();
+    const label numProc = UPstream::nProcs();
+
+    // Calculate the cumulative triangle weights
+    triWght_.resize_nocopy(triFace_.size()+1);
+
+    auto iter = triWght_.begin();
 
     // Set zero value at the start of the tri area/weight list
-    triWght.push_back(0);
+    scalar patchArea = 0;
+    *iter = patchArea;
+    ++iter;
 
-    forAll(patch_, facei)
+    // Calculate cumulative and total area (processor-local at this point)
+    for (const auto& t : triFace_)
     {
-        const face& f = patch_[facei];
+        patchArea += t.mag(points);
 
-        tris.clear();
-        f.triangles(points, tris);
-
-        for (const auto& t : tris)
-        {
-            triToFace.push_back(facei);
-            triFace.push_back(t);
-            triWght.push_back(t.mag(points));
-        }
+        *iter = patchArea;
+        ++iter;
     }
 
-    scalarList procSumWght(Pstream::nProcs()+1, Zero);
-    procSumWght[Pstream::myProcNo()+1] = sum(triWght);
+    // FIXME: use allGatherList of subslice
+    scalarList procSumWght(numProc+1, Foam::zero{});
+    procSumWght[myProci+1] = patchArea;
     Pstream::listCombineReduce(procSumWght, maxEqOp<scalar>());
 
+    // Convert to cumulative
     for (label i = 1; i < procSumWght.size(); ++i)
     {
-        // Convert to cumulative
         procSumWght[i] += procSumWght[i-1];
     }
 
-    const scalar offset = procSumWght[Pstream::myProcNo()];
-    forAll(triWght, i)
+    const scalar offset = procSumWght[myProci];
+    const scalar totalArea = procSumWght.back();
+
+    // Apply processor offset and normalise - for a global 0-1 interval
+    for (scalar& w : triWght_)
     {
-        if (i)
-        {
-            // Convert to cumulative
-            triWght[i] += triWght[i-1];
-        }
-
-        // Apply processor offset
-        triWght[i] += offset;
+        w = (w + offset) / totalArea;
     }
-
-    // Normalise
-    const scalar sumWght = procSumWght.back();
-    for (scalar& w : triWght)
-    {
-        w /= sumWght;
-    }
-
-    // Transfer to persistent storage
-    triFace_.transfer(triFace);
-    triToFace_.transfer(triToFace);
-    triWght_.transfer(triWght);
 }
 
 
@@ -190,6 +213,14 @@ bool Foam::triangulatedPatch::randomLocalPoint
     label& celli
 ) const
 {
+    if (triWght_.empty())
+    {
+        result = point::min;
+        facei = -1;
+        celli = -1;
+        return false;
+    }
+
     const scalar c = rnd.position<scalar>(triWght_.front(), triWght_.back());
 
     return randomPoint(rnd, c, result, facei, celli);
@@ -204,20 +235,23 @@ bool Foam::triangulatedPatch::randomGlobalPoint
     label& celli
 ) const
 {
-    boolList valid(UPstream::nProcs(), false);
-    valid[UPstream::myProcNo()] = randomLocalPoint(rnd, result, facei, celli);
-    UPstream::listGatherValues(valid);
-
-    forAll(valid, proci)
+    if (UPstream::parRun())
     {
-        // Choose first valid processor
-        if (valid[proci])
-        {
-            return (proci == UPstream::myProcNo());
-        }
-    }
+        const scalar c = rnd.sample01<scalar>();
+        const bool ok = randomPoint(rnd, c, result, facei, celli);
 
-    return false;
+        boolList valid(UPstream::listGatherValues(ok));
+
+        // Select the first valid processor
+        label proci = valid.find(true);
+        Pstream::broadcast(proci);
+
+        return (proci == UPstream::myProcNo());
+    }
+    else
+    {
+        return randomLocalPoint(rnd, result, facei, celli);
+    }
 }
 
 
diff --git a/src/meshTools/triangulatedPatch/triangulatedPatch.H b/src/meshTools/triangulatedPatch/triangulatedPatch.H
index caf3c8a4b8..af72ed4dc9 100644
--- a/src/meshTools/triangulatedPatch/triangulatedPatch.H
+++ b/src/meshTools/triangulatedPatch/triangulatedPatch.H
@@ -5,7 +5,7 @@
     \\  /    A nd           | www.openfoam.com
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
-    Copyright (C) 2023 OpenCFD Ltd.
+    Copyright (C) 2023-2024 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -35,6 +35,7 @@ Description
 #define Foam_triangulatedPatch_H
 
 #include "polyMesh.H"
+#include "labelledTri.H"
 #include "Random.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -55,13 +56,12 @@ class triangulatedPatch
         //- Perturbation tolerance to move the point towards the cell centre
         bool perturbTol_;
 
-        //- Face triangles
-        faceList triFace_;
+        //- The polyPatch faces as triangles, the index of each corresponds
+        //- to the undecomposed patch face index.
+        List<labelledTri> triFace_;
 
-        //- Triangle to patch face addressing
-        labelList triToFace_;
-
-        //- Triangle weights
+        //- The cumulative triangle area per triangle face,
+        //- globally normalised as a 0-1 interval.
         scalarList triWght_;
 
 
@@ -81,6 +81,11 @@ class triangulatedPatch
         ) const;
 
 
+    // Static Member Functions
+
+        //- Triangulate the patch faces and create addressing
+        static void triangulate(const polyPatch& pp, List<labelledTri>& tris);
+
 public:
 
     //- Constructors

From 852f66fc118922d64d8dda3cee29e003f4c13ae6 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 6 Feb 2024 22:12:12 +0100
Subject: [PATCH 2/5] CONFIG: add user/group libraries into path separately
 (#2948)

- on Darwin _foamAddLib() also checks the library path existence
  so passing in "path1:path2" together fails.
---
 etc/config.csh/setup | 4 ++--
 etc/config.sh/setup  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/etc/config.csh/setup b/etc/config.csh/setup
index 33b39c927f..c2b4d4c2ac 100644
--- a/etc/config.csh/setup
+++ b/etc/config.csh/setup
@@ -197,8 +197,8 @@ if ( "$FOAM_MPI" != dummy ) then
     _foamAddLib "${FOAM_LIBBIN}/${FOAM_MPI}"
 endif
 
-# OpenFOAM user, group libraries
-_foamAddLib  "${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}"
+_foamAddLib  "$FOAM_SITE_LIBBIN"  # OpenFOAM group libraries
+_foamAddLib  "$FOAM_USER_LIBBIN"  # OpenFOAM user  libraries
 
 if ( -d "$WM_PROJECT_DIR/doc/man1" ) then
     _foamAddMan "$WM_PROJECT_DIR/doc"
diff --git a/etc/config.sh/setup b/etc/config.sh/setup
index 837eb90de4..7e35c3dcb8 100644
--- a/etc/config.sh/setup
+++ b/etc/config.sh/setup
@@ -229,8 +229,8 @@ then
     _foamAddLib "$FOAM_LIBBIN/$FOAM_MPI"
 fi
 
-# OpenFOAM user, group libraries
-_foamAddLib  "$FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN"
+_foamAddLib  "$FOAM_SITE_LIBBIN"  # OpenFOAM group libraries
+_foamAddLib  "$FOAM_USER_LIBBIN"  # OpenFOAM user  libraries
 
 if [ -d "$WM_PROJECT_DIR/doc/man1" ]
 then

From a9b451b3e4f98933b8b3f7df13066f5537de5086 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 13 Feb 2024 09:30:45 +0100
Subject: [PATCH 3/5] SUBMODULE: re-enable turbulence-community build

- compilation issues caused by hidden python dependency now alleviated
---
 modules/turbulence-community | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/turbulence-community b/modules/turbulence-community
index a7af00a48d..06b391bb47 160000
--- a/modules/turbulence-community
+++ b/modules/turbulence-community
@@ -1 +1 @@
-Subproject commit a7af00a48d3a4962a08aeea445c6f8db797bc823
+Subproject commit 06b391bb475f0386342b6f9b7fe5496ae87e464f

From 08df02380899c595a889a5e752a8afebd136e7f1 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 20 Feb 2024 11:19:11 +0100
Subject: [PATCH 4/5] BUG: fvSchemes/fvSolution not properly updated on copy
 from fallback

---
 src/OpenFOAM/matrices/schemes/schemesLookup.C | 17 +++++++++++------
 src/OpenFOAM/matrices/solution/solution.C     | 17 +++++++++++------
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/OpenFOAM/matrices/schemes/schemesLookup.C b/src/OpenFOAM/matrices/schemes/schemesLookup.C
index c9a1b02865..2045a96dd4 100644
--- a/src/OpenFOAM/matrices/schemes/schemesLookup.C
+++ b/src/OpenFOAM/matrices/schemes/schemesLookup.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2015 OpenFOAM Foundation
-    Copyright (C) 2019-2023 OpenCFD Ltd.
+    Copyright (C) 2019-2024 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -133,7 +133,7 @@ Foam::schemesLookup::schemesLookup
             obr.time().system(),
             obr,
             rOpt,
-            IOobject::NO_WRITE
+            IOobjectOption::NO_WRITE
         ),
         fallback
     ),
@@ -153,18 +153,23 @@ Foam::schemesLookup::schemesLookup
     fluxRequiredDefault_(false),
     steady_(false)
 {
-    // Treat as MUST_READ_IF_MODIFIED whenever possible
+    // Treat as READ_MODIFIED whenever possible
     if
     (
-        readOpt() == IOobject::MUST_READ
+        readOpt() == IOobjectOption::MUST_READ
      || (isReadOptional() && headerOk())
     )
     {
-        readOpt(IOobject::MUST_READ_IF_MODIFIED);
+        readOpt(IOobjectOption::READ_MODIFIED);
         addWatch();
     }
 
-    if (readOpt() == IOobject::MUST_READ_IF_MODIFIED)
+    // Update: from values read or copied in
+    if
+    (
+        readOpt() == IOobjectOption::READ_MODIFIED
+     || !dictionary::empty()
+    )
     {
         read(selectedDict());
     }
diff --git a/src/OpenFOAM/matrices/solution/solution.C b/src/OpenFOAM/matrices/solution/solution.C
index e8c837a056..27b0eac1df 100644
--- a/src/OpenFOAM/matrices/solution/solution.C
+++ b/src/OpenFOAM/matrices/solution/solution.C
@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2016 OpenFOAM Foundation
-    Copyright (C) 2019-2023 OpenCFD Ltd.
+    Copyright (C) 2019-2024 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -174,7 +174,7 @@ Foam::solution::solution
             obr.time().system(),
             obr,
             rOpt,
-            IOobject::NO_WRITE
+            IOobjectOption::NO_WRITE
         ),
         fallback
     ),
@@ -184,18 +184,23 @@ Foam::solution::solution
     eqnRelaxDict_(),
     solvers_()
 {
-    // Treat as MUST_READ_IF_MODIFIED whenever possible
+    // Treat as READ_MODIFIED whenever possible
     if
     (
-        readOpt() == IOobject::MUST_READ
+        readOpt() == IOobjectOption::MUST_READ
      || (isReadOptional() && headerOk())
     )
     {
-        readOpt(IOobject::MUST_READ_IF_MODIFIED);
+        readOpt(IOobjectOption::READ_MODIFIED);
         addWatch();
     }
 
-    if (readOpt() == IOobject::MUST_READ_IF_MODIFIED)
+    // Update: from values read or copied in
+    if
+    (
+        readOpt() == IOobjectOption::READ_MODIFIED
+     || !dictionary::empty()
+    )
     {
         read(selectedDict());
     }

From 119dd843279259918433d8cc8120b8250e85fb81 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Tue, 20 Feb 2024 14:29:04 +0100
Subject: [PATCH 5/5] CONFIG: bump patch level

---
 META-INFO/api-info | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/META-INFO/api-info b/META-INFO/api-info
index 8e35a8bceb..1952c86b39 100644
--- a/META-INFO/api-info
+++ b/META-INFO/api-info
@@ -1,2 +1,2 @@
 api=2312
-patch=0
+patch=240220