From 1d949e5ffc81d2b6d6a3f5f301177abacb6c279b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Mon, 24 Jun 2024 16:10:07 +0200
Subject: [PATCH 01/18] It kind of runs

---
 channel-transport/transport-openfoam/0/T      |  69 +++++++++
 channel-transport/transport-openfoam/0/U      |  39 +++++
 channel-transport/transport-openfoam/clean.sh |   6 +
 .../constant/transportProperties              |   9 ++
 channel-transport/transport-openfoam/run.sh   |  12 ++
 .../transport-openfoam/system/blockMeshDict   | 146 ++++++++++++++++++
 .../transport-openfoam/system/controlDict     |  44 ++++++
 .../system/decomposeParDict                   |  16 ++
 .../transport-openfoam/system/fvSchemes       |  39 +++++
 .../transport-openfoam/system/fvSolution      |  25 +++
 .../transport-openfoam/system/preciceDict     |  37 +++++
 11 files changed, 442 insertions(+)
 create mode 100644 channel-transport/transport-openfoam/0/T
 create mode 100644 channel-transport/transport-openfoam/0/U
 create mode 100755 channel-transport/transport-openfoam/clean.sh
 create mode 100644 channel-transport/transport-openfoam/constant/transportProperties
 create mode 100755 channel-transport/transport-openfoam/run.sh
 create mode 100644 channel-transport/transport-openfoam/system/blockMeshDict
 create mode 100644 channel-transport/transport-openfoam/system/controlDict
 create mode 100644 channel-transport/transport-openfoam/system/decomposeParDict
 create mode 100644 channel-transport/transport-openfoam/system/fvSchemes
 create mode 100644 channel-transport/transport-openfoam/system/fvSolution
 create mode 100644 channel-transport/transport-openfoam/system/preciceDict

diff --git a/channel-transport/transport-openfoam/0/T b/channel-transport/transport-openfoam/0/T
new file mode 100644
index 000000000..a64055ab1
--- /dev/null
+++ b/channel-transport/transport-openfoam/0/T
@@ -0,0 +1,69 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      T;
+}
+
+dimensions      [0 2 -2 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    inlet
+    {
+        type            zeroGradient;
+    }
+
+    outlet
+    {
+        type            fixedValue;
+        value           uniform 0;
+    }
+
+    obstacle
+    {
+        type            zeroGradient;
+    }
+    
+    upperWall
+    {
+        type            zeroGradient;
+    }
+
+    lowerWall
+    {
+        type            zeroGradient;
+    }
+
+    frontAndBack
+    {
+        type            empty;
+    }
+
+    blob
+    {
+      type codedFixedValue;
+      value uniform 0;
+      redirectType    fixedValue;
+      code
+      #{
+          const fvPatch& boundaryPatch = patch();
+          scalarField& field = *this;
+
+          // Blob parameters
+          vector xblob(1, 1, 0);  // Center of the blob
+          scalar R = 0.5;         // Characteristic length (radius)
+          scalar width = 0.1;     // Smoothing factor
+
+          forAll(boundaryPatch, faceI)
+          {
+              const point& faceCenter = boundaryPatch.faceCentres()[faceI];
+              scalar distanceSquared = magSqr(faceCenter - xblob.xy());
+              field[faceI] = 0.5 - 0.5 * tanh((distanceSquared - R*R) / width);
+          }
+      #};
+    }
+}
diff --git a/channel-transport/transport-openfoam/0/U b/channel-transport/transport-openfoam/0/U
new file mode 100644
index 000000000..2cf022003
--- /dev/null
+++ b/channel-transport/transport-openfoam/0/U
@@ -0,0 +1,39 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    object      U;
+}
+
+dimensions      [0 1 -1 0 0 0 0];
+internalField   uniform (10 0 0);
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedValue;
+        value           $internalField;
+    }
+    outlet
+    {
+        type            zeroGradient;
+    }
+    obstacle
+    {
+        type            noSlip;
+    }
+    upperWall
+    {
+        type            noSlip;
+    }
+    lowerWall
+    {
+        type            noSlip;
+    }
+    frontAndBack
+    {
+        type            empty;
+    }
+}
diff --git a/channel-transport/transport-openfoam/clean.sh b/channel-transport/transport-openfoam/clean.sh
new file mode 100755
index 000000000..b64fc5101
--- /dev/null
+++ b/channel-transport/transport-openfoam/clean.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_openfoam .
diff --git a/channel-transport/transport-openfoam/constant/transportProperties b/channel-transport/transport-openfoam/constant/transportProperties
new file mode 100644
index 000000000..43d8644a6
--- /dev/null
+++ b/channel-transport/transport-openfoam/constant/transportProperties
@@ -0,0 +1,9 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      transportProperties;
+}
+
+DT 0.01;
diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
new file mode 100755
index 000000000..8f55fbfa5
--- /dev/null
+++ b/channel-transport/transport-openfoam/run.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+blockMesh
+
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+
+close_log
diff --git a/channel-transport/transport-openfoam/system/blockMeshDict b/channel-transport/transport-openfoam/system/blockMeshDict
new file mode 100644
index 000000000..bdb4fe67b
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/blockMeshDict
@@ -0,0 +1,146 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+
+x0 0.;
+x1 2.;
+x2 3.;
+x3 6.;
+
+y0 0.;
+y1 1.;
+y2 2.;
+
+z0 0;
+z1 1;
+
+vertices
+(
+    ($x0 $y0 $z0 )         // 0
+    ($x1 $y0 $z0 )         // 1
+    ($x2 $y0 $z0 )         // 2
+    ($x3 $y0 $z0 )         // 3
+    ($x0 $y1 $z0 )         // 4
+    ($x1 $y1 $z0 )         // 5
+    ($x2 $y1 $z0 )         // 6
+    ($x3 $y1 $z0 )         // 7
+    ($x0 $y2 $z0 )         // 8
+    ($x1 $y2 $z0 )         // 9
+    ($x2 $y2 $z0 )         // 10
+    ($x3 $y2 $z0 )         // 11
+
+    ($x0 $y0 $z1 )         // 12
+    ($x1 $y0 $z1 )         // 13
+    ($x2 $y0 $z1 )         // 14
+    ($x3 $y0 $z1 )         // 15
+    ($x0 $y1 $z1 )         // 16
+    ($x1 $y1 $z1 )         // 17
+    ($x2 $y1 $z1 )         // 18
+    ($x3 $y1 $z1 )         // 19
+    ($x0 $y2 $z1 )         // 20
+    ($x1 $y2 $z1 )         // 21
+    ($x2 $y2 $z1 )         // 22
+    ($x3 $y2 $z1 )         // 23
+);
+
+
+// Grading
+h1 16;
+h2 8;
+h3 24;
+v1 8;
+
+blocks
+(
+    hex (   0   1   5   4   12  13  17  16  )
+    ($h1 $v1 1 )
+    simpleGrading (1 1 1)
+
+    hex (   2   3   7   6   14  15  19  18  )
+    ($h3 $v1 1)
+    simpleGrading (1 1 1)
+
+    hex (   4   5   9   8   16  17  21  20  )
+    ($h1 $v1 1)
+    simpleGrading (1 1 1)
+
+    hex (   5   6   10  9   17  18  22  21  )
+    ($h2 $v1 1)
+    simpleGrading (1 1 1)
+
+    hex (   6   7   11  10  18  19  23  22  )
+    ($h3 $v1 1 )
+    simpleGrading (1 1 1)
+);
+
+boundary
+(
+    inlet
+    {
+        type patch;
+        faces
+        (
+            (  0   4   16  12  )
+            (  4   8   20  16  )
+        );
+    }
+    outlet
+    {
+        type patch;
+        faces
+        (
+            (   3   7   19  15  )
+            (   7   11  23  19  )
+        );
+    }
+    obstacle
+    {
+        type wall;
+        faces
+        (
+            (   1   5   17  13  )
+            (   5   6   18  17  )
+            (   6   2   14  18  )
+        );
+    }
+    upperWall
+    {
+        type wall;
+        faces
+        (
+            (   8   9   21  20  )
+            (   9   10  22  21  )
+            (   10  11  23  22  )
+        );
+    }
+    lowerWall
+    {
+        type wall;
+        faces
+        (
+            (   0   1   13  12  )
+            (   2   3   15  14  )
+        );
+    }
+    frontAndBack
+    {
+        type empty;
+        faces
+        (
+            (   0   1   5   4   )
+            (   2   3   7   6   )
+            (   4   5   9   8   )
+            (   5   6   10  9   )
+            (   6   7   11  10  )
+            (   12  13  17  16  )
+            (   14  15  19  18  )
+            (   16  17  21  20  )
+            (   17  18  22  21  )
+            (   18  19  23  22  )
+        );
+    }
+);
\ No newline at end of file
diff --git a/channel-transport/transport-openfoam/system/controlDict b/channel-transport/transport-openfoam/system/controlDict
new file mode 100644
index 000000000..6211271cc
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/controlDict
@@ -0,0 +1,44 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      controlDict;
+}
+
+application     scalarTransportFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         1.0;
+
+deltaT          0.005;
+
+writeControl    adjustableRunTime;
+
+writeInterval   0.005;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+functions
+{
+    preCICE_Adapter
+    {
+        type preciceAdapterFunctionObject;
+        libs ("libpreciceAdapterFunctionObject.so");
+    }
+}
diff --git a/channel-transport/transport-openfoam/system/decomposeParDict b/channel-transport/transport-openfoam/system/decomposeParDict
new file mode 100644
index 000000000..f9eae003a
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/decomposeParDict
@@ -0,0 +1,16 @@
+FoamFile {
+    version     2.0;
+    class       dictionary;
+    object      decomposeParDict;
+    format      ascii;
+}
+
+numberOfSubdomains 4;
+
+method          simple;
+
+simpleCoeffs
+{
+    n               (2 2 1);
+    delta           0.001;
+}
\ No newline at end of file
diff --git a/channel-transport/transport-openfoam/system/fvSchemes b/channel-transport/transport-openfoam/system/fvSchemes
new file mode 100644
index 000000000..7ffafdece
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/fvSchemes
@@ -0,0 +1,39 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      fvSchemes;
+}
+
+ddtSchemes
+{
+    default         Euler;
+}
+
+gradSchemes
+{
+    default         Gauss linear;
+}
+
+divSchemes
+{
+    default         none;
+    div(phi,T)      Gauss linearUpwind grad(T);
+}
+
+laplacianSchemes
+{
+    default         none;
+    laplacian(DT,T) Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+    default         linear;
+}
+
+snGradSchemes
+{
+    default         corrected;
+}
diff --git a/channel-transport/transport-openfoam/system/fvSolution b/channel-transport/transport-openfoam/system/fvSolution
new file mode 100644
index 000000000..df39d3595
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/fvSolution
@@ -0,0 +1,25 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+
+solvers
+{
+  T
+  {
+    solver PBiCGStab;
+    preconditioner   DILU;
+    tolerance        1e-6;
+    relTol 	         0;
+    norm default;
+  }
+}
+
+SIMPLE
+{
+    nNonOrthogonalCorrectors 0;
+}
diff --git a/channel-transport/transport-openfoam/system/preciceDict b/channel-transport/transport-openfoam/system/preciceDict
new file mode 100644
index 000000000..aca923918
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/preciceDict
@@ -0,0 +1,37 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      preciceDict;
+}
+
+preciceConfig "../precice-config.xml";
+
+participant Transport;
+
+modules (FF);
+
+interfaces
+{
+  Interface1
+  {
+    mesh              Transport-Mesh;
+    patches           ();
+    locations         volumeCenters;
+    
+    readData
+    (
+      Velocity
+    );
+
+    writeData
+    (
+    );
+  };
+};
+
+FF
+{
+  solverType incompressible;
+}

From ea64e381d460245850947b38207eb311411ceb72 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Mon, 24 Jun 2024 16:52:14 +0200
Subject: [PATCH 02/18] remove blob

---
 channel-transport/transport-openfoam/0/T | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/channel-transport/transport-openfoam/0/T b/channel-transport/transport-openfoam/0/T
index a64055ab1..d2d0bf23d 100644
--- a/channel-transport/transport-openfoam/0/T
+++ b/channel-transport/transport-openfoam/0/T
@@ -42,28 +42,4 @@ boundaryField
     {
         type            empty;
     }
-
-    blob
-    {
-      type codedFixedValue;
-      value uniform 0;
-      redirectType    fixedValue;
-      code
-      #{
-          const fvPatch& boundaryPatch = patch();
-          scalarField& field = *this;
-
-          // Blob parameters
-          vector xblob(1, 1, 0);  // Center of the blob
-          scalar R = 0.5;         // Characteristic length (radius)
-          scalar width = 0.1;     // Smoothing factor
-
-          forAll(boundaryPatch, faceI)
-          {
-              const point& faceCenter = boundaryPatch.faceCentres()[faceI];
-              scalar distanceSquared = magSqr(faceCenter - xblob.xy());
-              field[faceI] = 0.5 - 0.5 * tanh((distanceSquared - R*R) / width);
-          }
-      #};
-    }
 }

From a1c142cdb08f5a498c0bd7b69db7e5f60e509ed2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Mon, 24 Jun 2024 16:53:09 +0200
Subject: [PATCH 03/18] Maybe right?

---
 channel-transport/transport-openfoam/0/U | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/channel-transport/transport-openfoam/0/U b/channel-transport/transport-openfoam/0/U
index 2cf022003..1f4cb2292 100644
--- a/channel-transport/transport-openfoam/0/U
+++ b/channel-transport/transport-openfoam/0/U
@@ -7,7 +7,7 @@ FoamFile
 }
 
 dimensions      [0 1 -1 0 0 0 0];
-internalField   uniform (10 0 0);
+internalField   uniform (0 0 0);
 
 boundaryField
 {

From f2fb4f3fa23ec32566df4368d003025a22cb994a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Mon, 24 Jun 2024 17:00:46 +0200
Subject: [PATCH 04/18] setup setFields

---
 .../transport-openfoam/{0 => 0.orig}/T        |  0
 .../transport-openfoam/{0 => 0.orig}/U        |  0
 channel-transport/transport-openfoam/run.sh   |  2 ++
 .../transport-openfoam/system/setFieldsDict   | 24 +++++++++++++++++++
 4 files changed, 26 insertions(+)
 rename channel-transport/transport-openfoam/{0 => 0.orig}/T (100%)
 rename channel-transport/transport-openfoam/{0 => 0.orig}/U (100%)
 create mode 100644 channel-transport/transport-openfoam/system/setFieldsDict

diff --git a/channel-transport/transport-openfoam/0/T b/channel-transport/transport-openfoam/0.orig/T
similarity index 100%
rename from channel-transport/transport-openfoam/0/T
rename to channel-transport/transport-openfoam/0.orig/T
diff --git a/channel-transport/transport-openfoam/0/U b/channel-transport/transport-openfoam/0.orig/U
similarity index 100%
rename from channel-transport/transport-openfoam/0/U
rename to channel-transport/transport-openfoam/0.orig/U
diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
index 8f55fbfa5..3cbec2a56 100755
--- a/channel-transport/transport-openfoam/run.sh
+++ b/channel-transport/transport-openfoam/run.sh
@@ -5,6 +5,8 @@ set -e -u
 exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
+cp -r 0.orig 0
+setFields
 
 ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
diff --git a/channel-transport/transport-openfoam/system/setFieldsDict b/channel-transport/transport-openfoam/system/setFieldsDict
new file mode 100644
index 000000000..c0c2e35b3
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/setFieldsDict
@@ -0,0 +1,24 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      setFieldsDict;
+}
+
+defaultFieldValues
+(
+    volScalarFieldValue T 0
+);
+
+regions
+(
+    boxToCell
+    {
+       box (0.5 0.5 0) (1.5 1.5 1);
+        fieldValues
+        (
+            volScalarFieldValue T 1
+        );
+    }
+);

From 9a1e7b90d6e57d8043596ec44417e8249eb70a27 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Tue, 25 Jun 2024 15:57:16 +0200
Subject: [PATCH 05/18] Set a cylinder, increase mesh cells, add U_vol
 workaround

---
 channel-transport/transport-openfoam/clean.sh |  1 +
 .../transport-openfoam/constant/fvOptions     | 44 +++++++++++++++++++
 .../constant/transportProperties              |  2 +-
 channel-transport/transport-openfoam/run.sh   |  1 +
 .../transport-openfoam/system/blockMeshDict   | 20 ++++++---
 .../transport-openfoam/system/fvSchemes       |  4 +-
 .../transport-openfoam/system/fvSolution      |  4 +-
 .../transport-openfoam/system/preciceDict     |  1 +
 .../transport-openfoam/system/setFieldsDict   |  8 +++-
 .../transport-openfoam/system/topoSetDict     | 20 +++++++++
 10 files changed, 94 insertions(+), 11 deletions(-)
 create mode 100644 channel-transport/transport-openfoam/constant/fvOptions
 create mode 100644 channel-transport/transport-openfoam/system/topoSetDict

diff --git a/channel-transport/transport-openfoam/clean.sh b/channel-transport/transport-openfoam/clean.sh
index b64fc5101..5120c1355 100755
--- a/channel-transport/transport-openfoam/clean.sh
+++ b/channel-transport/transport-openfoam/clean.sh
@@ -4,3 +4,4 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
+rm -rf ./0/
diff --git a/channel-transport/transport-openfoam/constant/fvOptions b/channel-transport/transport-openfoam/constant/fvOptions
new file mode 100644
index 000000000..8cea42d49
--- /dev/null
+++ b/channel-transport/transport-openfoam/constant/fvOptions
@@ -0,0 +1,44 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      fvOptions;
+}
+
+codedSource
+{
+    type            vectorCodedSource;
+    // selectionMode   all;
+    selectionMode     cellSet;
+    cellSet           box1;
+
+    fields          (U);
+    name            sourceTime;
+
+    codeConstrain //constrain
+    #{
+        return;
+    #};
+
+    codeCorrect //correct
+    #{
+        const labelList& cells = this->cells();
+        const volVectorField& U_vol = mesh_.lookupObject<volVectorField>("U_vol");
+        for(auto cell : cells)
+        {
+            fld[cell].x() = U_vol[cell].x();
+        }
+    #};
+
+    codeAddSup // source term
+    #{
+        return;
+    #};
+
+    codeAddSupRho
+    #{
+        return;
+    #};
+}
+// vim:ft=foam
diff --git a/channel-transport/transport-openfoam/constant/transportProperties b/channel-transport/transport-openfoam/constant/transportProperties
index 43d8644a6..8d841ddc5 100644
--- a/channel-transport/transport-openfoam/constant/transportProperties
+++ b/channel-transport/transport-openfoam/constant/transportProperties
@@ -6,4 +6,4 @@ FoamFile
     object      transportProperties;
 }
 
-DT 0.01;
+DT 0.1;
diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
index 3cbec2a56..20b10d2a4 100755
--- a/channel-transport/transport-openfoam/run.sh
+++ b/channel-transport/transport-openfoam/run.sh
@@ -5,6 +5,7 @@ set -e -u
 exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
+topoSet
 cp -r 0.orig 0
 setFields
 
diff --git a/channel-transport/transport-openfoam/system/blockMeshDict b/channel-transport/transport-openfoam/system/blockMeshDict
index bdb4fe67b..19774348b 100644
--- a/channel-transport/transport-openfoam/system/blockMeshDict
+++ b/channel-transport/transport-openfoam/system/blockMeshDict
@@ -49,10 +49,20 @@ vertices
 
 
 // Grading
-h1 16;
-h2 8;
-h3 24;
-v1 8;
+//h1 16;
+//h2 8;
+//h3 24;
+//v1 8;
+
+//h1 40;
+//h2 20;
+//h3 60;
+//v1 32;
+
+h1 20;
+h2 10;
+h3 30;
+v1 16;
 
 blocks
 (
@@ -143,4 +153,4 @@ boundary
             (   18  19  23  22  )
         );
     }
-);
\ No newline at end of file
+);
diff --git a/channel-transport/transport-openfoam/system/fvSchemes b/channel-transport/transport-openfoam/system/fvSchemes
index 7ffafdece..6bb4d7d8c 100644
--- a/channel-transport/transport-openfoam/system/fvSchemes
+++ b/channel-transport/transport-openfoam/system/fvSchemes
@@ -19,12 +19,14 @@ gradSchemes
 divSchemes
 {
     default         none;
-    div(phi,T)      Gauss linearUpwind grad(T);
+    div(phi,U)      Gauss linear;
+    div(phi,T)      Gauss upwind; //linearUpwind grad(T);
 }
 
 laplacianSchemes
 {
     default         none;
+    laplacian(DT,U) Gauss linear corrected;
     laplacian(DT,T) Gauss linear corrected;
 }
 
diff --git a/channel-transport/transport-openfoam/system/fvSolution b/channel-transport/transport-openfoam/system/fvSolution
index df39d3595..74640654b 100644
--- a/channel-transport/transport-openfoam/system/fvSolution
+++ b/channel-transport/transport-openfoam/system/fvSolution
@@ -11,11 +11,11 @@ solvers
 {
   T
   {
-    solver PBiCGStab;
+    solver           PBiCGStab;
     preconditioner   DILU;
     tolerance        1e-6;
     relTol 	         0;
-    norm default;
+    norm             default;
   }
 }
 
diff --git a/channel-transport/transport-openfoam/system/preciceDict b/channel-transport/transport-openfoam/system/preciceDict
index aca923918..205148959 100644
--- a/channel-transport/transport-openfoam/system/preciceDict
+++ b/channel-transport/transport-openfoam/system/preciceDict
@@ -34,4 +34,5 @@ interfaces
 FF
 {
   solverType incompressible;
+  nameU U_vol;
 }
diff --git a/channel-transport/transport-openfoam/system/setFieldsDict b/channel-transport/transport-openfoam/system/setFieldsDict
index c0c2e35b3..245a5ca0e 100644
--- a/channel-transport/transport-openfoam/system/setFieldsDict
+++ b/channel-transport/transport-openfoam/system/setFieldsDict
@@ -13,12 +13,16 @@ defaultFieldValues
 
 regions
 (
-    boxToCell
+    cylinderToCell
     {
-       box (0.5 0.5 0) (1.5 1.5 1);
+        p1 (1 1 0);
+        p2 (1 1 1);
+        radius 0.5;
+
         fieldValues
         (
             volScalarFieldValue T 1
+            //TODO "0.5 - 0.5 * tanh(((x - 1)*(x - 1) + (y - 1)*(y - 1) - 0.5) / 0.1)"
         );
     }
 );
diff --git a/channel-transport/transport-openfoam/system/topoSetDict b/channel-transport/transport-openfoam/system/topoSetDict
new file mode 100644
index 000000000..0c557f640
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/topoSetDict
@@ -0,0 +1,20 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      topoSetDict;
+}
+
+actions
+(
+    {
+        name    box1;
+        type    cellSet;
+        action  new;
+        source  boxToCell;
+        box     (0 0 0) (2 2 1);
+    }
+);
+
+

From e3631451aa3caf842a0abc62a0d9db4dee59465c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 10:09:11 +0200
Subject: [PATCH 06/18] Add modified solver

---
 .../transport-openfoam/.gitignore             |   2 +
 channel-transport/transport-openfoam/0.orig/T |   3 +-
 .../transport-openfoam/Make/files             |   3 +
 .../transport-openfoam/Make/options           |  10 ++
 .../transport-openfoam/constant/fvOptions     |   6 +-
 .../transport-openfoam/createFields.H         |  43 +++++++
 .../dynamicScalarTransportFoam.C              | 113 ++++++++++++++++++
 channel-transport/transport-openfoam/run.sh   |   1 -
 .../transport-openfoam/system/controlDict     |   2 +-
 .../transport-openfoam/system/topoSetDict     |  20 ----
 10 files changed, 176 insertions(+), 27 deletions(-)
 create mode 100644 channel-transport/transport-openfoam/.gitignore
 create mode 100644 channel-transport/transport-openfoam/Make/files
 create mode 100644 channel-transport/transport-openfoam/Make/options
 create mode 100644 channel-transport/transport-openfoam/createFields.H
 create mode 100644 channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
 delete mode 100644 channel-transport/transport-openfoam/system/topoSetDict

diff --git a/channel-transport/transport-openfoam/.gitignore b/channel-transport/transport-openfoam/.gitignore
new file mode 100644
index 000000000..52b9cb41a
--- /dev/null
+++ b/channel-transport/transport-openfoam/.gitignore
@@ -0,0 +1,2 @@
+Make/
+0/
diff --git a/channel-transport/transport-openfoam/0.orig/T b/channel-transport/transport-openfoam/0.orig/T
index d2d0bf23d..3125d4d34 100644
--- a/channel-transport/transport-openfoam/0.orig/T
+++ b/channel-transport/transport-openfoam/0.orig/T
@@ -19,8 +19,7 @@ boundaryField
 
     outlet
     {
-        type            fixedValue;
-        value           uniform 0;
+        type            zeroGradient;
     }
 
     obstacle
diff --git a/channel-transport/transport-openfoam/Make/files b/channel-transport/transport-openfoam/Make/files
new file mode 100644
index 000000000..6a9053551
--- /dev/null
+++ b/channel-transport/transport-openfoam/Make/files
@@ -0,0 +1,3 @@
+dynamicScalarTransportFoam.C
+
+EXE = $(FOAM_USER_APPBIN)/dynamicScalarTransportFoam
diff --git a/channel-transport/transport-openfoam/Make/options b/channel-transport/transport-openfoam/Make/options
new file mode 100644
index 000000000..acbe7a647
--- /dev/null
+++ b/channel-transport/transport-openfoam/Make/options
@@ -0,0 +1,10 @@
+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/sampling/lnInclude
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -lfvOptions \
+    -lmeshTools \
+    -lsampling
diff --git a/channel-transport/transport-openfoam/constant/fvOptions b/channel-transport/transport-openfoam/constant/fvOptions
index 8cea42d49..efde08222 100644
--- a/channel-transport/transport-openfoam/constant/fvOptions
+++ b/channel-transport/transport-openfoam/constant/fvOptions
@@ -9,9 +9,7 @@ FoamFile
 codedSource
 {
     type            vectorCodedSource;
-    // selectionMode   all;
-    selectionMode     cellSet;
-    cellSet           box1;
+    selectionMode   all;
 
     fields          (U);
     name            sourceTime;
@@ -28,6 +26,8 @@ codedSource
         for(auto cell : cells)
         {
             fld[cell].x() = U_vol[cell].x();
+            fld[cell].y() = U_vol[cell].y();
+            fld[cell].z() = U_vol[cell].z();
         }
     #};
 
diff --git a/channel-transport/transport-openfoam/createFields.H b/channel-transport/transport-openfoam/createFields.H
new file mode 100644
index 000000000..82417fbb0
--- /dev/null
+++ b/channel-transport/transport-openfoam/createFields.H
@@ -0,0 +1,43 @@
+Info << "Reading field T\n"
+     << endl;
+
+volScalarField T(
+    IOobject(
+        "T",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE),
+    mesh);
+
+Info << "Reading field U\n"
+     << endl;
+
+volVectorField U(
+    IOobject(
+        "U",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE),
+    mesh);
+
+Info << "Reading transportProperties\n"
+     << endl;
+
+IOdictionary transportProperties(
+    IOobject(
+        "transportProperties",
+        runTime.constant(),
+        mesh,
+        IOobject::MUST_READ_IF_MODIFIED,
+        IOobject::NO_WRITE));
+
+Info << "Reading diffusivity DT\n"
+     << endl;
+
+dimensionedScalar DT("DT", dimViscosity, transportProperties);
+
+#include "createPhi.H"
+
+#include "createFvOptions.H"
diff --git a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
new file mode 100644
index 000000000..f26165ffd
--- /dev/null
+++ b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
@@ -0,0 +1,113 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | www.openfoam.com
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+    Copyright (C) 2011-2017 OpenFOAM Foundation
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Application
+    scalarTransportFoam
+
+Group
+    grpBasicSolvers
+
+Description
+    Passive scalar transport equation solver.
+
+    \heading Solver details
+    The equation is given by:
+
+    \f[
+        \ddt{T} + \div \left(\vec{U} T\right) - \div \left(D_T \grad T \right)
+        = S_{T}
+    \f]
+
+    Where:
+    \vartable
+        T       | Passive scalar
+        D_T     | Diffusion coefficient
+        S_T     | Source
+    \endvartable
+
+    \heading Required fields
+    \plaintable
+        T       | Passive scalar
+        U       | Velocity [m/s]
+    \endplaintable
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "fvOptions.H"
+#include "simpleControl.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+int main(int argc, char *argv[])
+{
+  argList::addNote(
+      "Passive scalar transport equation solver.");
+
+#include "addCheckCaseOptions.H"
+#include "createMesh.H"
+#include "createTime.H"
+#include "setRootCaseLists.H"
+
+  simpleControl simple(mesh);
+
+#include "createFields.H"
+
+  // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+  Info << "\nCalculating scalar transport\n"
+       << endl;
+
+#include "CourantNo.H"
+
+  while (simple.loop()) {
+    Info << "Time = " << runTime.timeName() << nl << endl;
+
+    while (simple.correctNonOrthogonal()) {
+      // TODO directly read from U
+      fvOptions.correct(U);
+      phi = fvc::flux(U);
+      // fvOptions.correct(phi);
+
+      fvScalarMatrix TEqn(
+          fvm::ddt(T) + fvm::div(phi, T) - fvm::laplacian(DT, T) ==
+          fvOptions(T));
+
+      TEqn.relax();
+      fvOptions.constrain(TEqn);
+      TEqn.solve();
+      fvOptions.correct(T);
+    }
+
+    runTime.write();
+  }
+
+  Info << "End\n"
+       << endl;
+
+  return 0;
+}
+
+// ************************************************************************* //
diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
index 20b10d2a4..3cbec2a56 100755
--- a/channel-transport/transport-openfoam/run.sh
+++ b/channel-transport/transport-openfoam/run.sh
@@ -5,7 +5,6 @@ set -e -u
 exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
-topoSet
 cp -r 0.orig 0
 setFields
 
diff --git a/channel-transport/transport-openfoam/system/controlDict b/channel-transport/transport-openfoam/system/controlDict
index 6211271cc..ef74b7f99 100644
--- a/channel-transport/transport-openfoam/system/controlDict
+++ b/channel-transport/transport-openfoam/system/controlDict
@@ -6,7 +6,7 @@ FoamFile
     object      controlDict;
 }
 
-application     scalarTransportFoam;
+application     dynamicScalarTransportFoam;
 
 startFrom       startTime;
 
diff --git a/channel-transport/transport-openfoam/system/topoSetDict b/channel-transport/transport-openfoam/system/topoSetDict
deleted file mode 100644
index 0c557f640..000000000
--- a/channel-transport/transport-openfoam/system/topoSetDict
+++ /dev/null
@@ -1,20 +0,0 @@
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      topoSetDict;
-}
-
-actions
-(
-    {
-        name    box1;
-        type    cellSet;
-        action  new;
-        source  boxToCell;
-        box     (0 0 0) (2 2 1);
-    }
-);
-
-

From e103c9a169c03501f1a75c4caa53865c1e28e135 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 10:25:08 +0200
Subject: [PATCH 07/18] Remove U_vol and rename solver

---
 channel-transport/transport-openfoam/clean.sh |  1 +
 .../transport-openfoam/constant/fvOptions     | 44 ------------
 .../dynamicScalarTransportFoam.C              | 70 ++++++++++---------
 .../transport-openfoam/system/preciceDict     |  1 -
 4 files changed, 39 insertions(+), 77 deletions(-)
 delete mode 100644 channel-transport/transport-openfoam/constant/fvOptions

diff --git a/channel-transport/transport-openfoam/clean.sh b/channel-transport/transport-openfoam/clean.sh
index 5120c1355..6ab219250 100755
--- a/channel-transport/transport-openfoam/clean.sh
+++ b/channel-transport/transport-openfoam/clean.sh
@@ -5,3 +5,4 @@ set -e -u
 
 clean_openfoam .
 rm -rf ./0/
+rm -rf ./Make/linux*
diff --git a/channel-transport/transport-openfoam/constant/fvOptions b/channel-transport/transport-openfoam/constant/fvOptions
deleted file mode 100644
index efde08222..000000000
--- a/channel-transport/transport-openfoam/constant/fvOptions
+++ /dev/null
@@ -1,44 +0,0 @@
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      fvOptions;
-}
-
-codedSource
-{
-    type            vectorCodedSource;
-    selectionMode   all;
-
-    fields          (U);
-    name            sourceTime;
-
-    codeConstrain //constrain
-    #{
-        return;
-    #};
-
-    codeCorrect //correct
-    #{
-        const labelList& cells = this->cells();
-        const volVectorField& U_vol = mesh_.lookupObject<volVectorField>("U_vol");
-        for(auto cell : cells)
-        {
-            fld[cell].x() = U_vol[cell].x();
-            fld[cell].y() = U_vol[cell].y();
-            fld[cell].z() = U_vol[cell].z();
-        }
-    #};
-
-    codeAddSup // source term
-    #{
-        return;
-    #};
-
-    codeAddSupRho
-    #{
-        return;
-    #};
-}
-// vim:ft=foam
diff --git a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
index f26165ffd..9ac8e7ba3 100644
--- a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
+++ b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
@@ -63,51 +63,57 @@ Description
 
 int main(int argc, char *argv[])
 {
-  argList::addNote(
-      "Passive scalar transport equation solver.");
+    argList::addNote
+    (
+        "Passive scalar transport equation solver."
+    );
 
-#include "addCheckCaseOptions.H"
-#include "createMesh.H"
-#include "createTime.H"
-#include "setRootCaseLists.H"
+    #include "addCheckCaseOptions.H"
+    #include "setRootCaseLists.H"
+    #include "createTime.H"
+    #include "createMesh.H"
 
-  simpleControl simple(mesh);
+    simpleControl simple(mesh);
 
-#include "createFields.H"
+    #include "createFields.H"
 
-  // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+    // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-  Info << "\nCalculating scalar transport\n"
-       << endl;
+    Info<< "\nCalculating scalar transport\n" << endl;
 
-#include "CourantNo.H"
+    #include "CourantNo.H"
 
-  while (simple.loop()) {
-    Info << "Time = " << runTime.timeName() << nl << endl;
+    while (simple.loop())
+    {
+        Info << "Time = " << runTime.timeName() << nl << endl;
 
-    while (simple.correctNonOrthogonal()) {
-      // TODO directly read from U
-      fvOptions.correct(U);
-      phi = fvc::flux(U);
-      // fvOptions.correct(phi);
+        while (simple.correctNonOrthogonal())
+        {
+            // Update phi as U changes
+            phi = fvc::flux(U);
 
-      fvScalarMatrix TEqn(
-          fvm::ddt(T) + fvm::div(phi, T) - fvm::laplacian(DT, T) ==
-          fvOptions(T));
+            fvScalarMatrix TEqn
+            (
+                fvm::ddt(T)
+              + fvm::div(phi, T)
+              - fvm::laplacian(DT, T)
+             ==
+                fvOptions(T)
+            );
 
-      TEqn.relax();
-      fvOptions.constrain(TEqn);
-      TEqn.solve();
-      fvOptions.correct(T);
-    }
+            TEqn.relax();
+            fvOptions.constrain(TEqn);
+            TEqn.solve();
+            fvOptions.correct(T);
+        }
 
-    runTime.write();
-  }
+        runTime.write();
+    }
 
-  Info << "End\n"
-       << endl;
+    Info<< "End\n" << endl;
 
-  return 0;
+    return 0;
 }
 
+
 // ************************************************************************* //
diff --git a/channel-transport/transport-openfoam/system/preciceDict b/channel-transport/transport-openfoam/system/preciceDict
index 205148959..aca923918 100644
--- a/channel-transport/transport-openfoam/system/preciceDict
+++ b/channel-transport/transport-openfoam/system/preciceDict
@@ -34,5 +34,4 @@ interfaces
 FF
 {
   solverType incompressible;
-  nameU U_vol;
 }

From 38f1424ede691a57fdf70db1b1e78088dbfbc773 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 10:29:07 +0200
Subject: [PATCH 08/18] fix

---
 .../transport-openfoam/.clang-format          | 175 ++++++++++++++++++
 .../transport-openfoam/.gitignore             |   4 +-
 2 files changed, 178 insertions(+), 1 deletion(-)
 create mode 100644 channel-transport/transport-openfoam/.clang-format

diff --git a/channel-transport/transport-openfoam/.clang-format b/channel-transport/transport-openfoam/.clang-format
new file mode 100644
index 000000000..00adea7a3
--- /dev/null
+++ b/channel-transport/transport-openfoam/.clang-format
@@ -0,0 +1,175 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+#
+# Proposed clang-format-11 style for OpenFOAM, trying to follow the OpenFOAM style guide:
+#   https://develop.openfoam.com/Development/openfoam/-/wikis/coding/style/style
+# Configuration developed for the OpenFOAM-preCICE adapter code:
+#   https://github.com/precice/openfoam-adapter
+# Contribute to the discussion at the respective OpenFOAM issue:
+#   https://develop.openfoam.com/Development/openfoam/-/issues/1634
+#
+# Keep `public:` at the first indentation level
+AccessModifierOffset: -4
+# Undocumented guideline: align arguments after an open bracket.
+AlignAfterOpenBracket: Align
+AlignConsecutiveMacros: false
+AlignConsecutiveAssignments: false
+AlignConsecutiveBitFields: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Right
+# Align operands after operators (+,*,<<) (see BreakBeforeBinaryOperators)
+AlignOperands: AlignAfterOperator
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Always
+AllowShortLoopsOnASingleLine: false
+# Guideline: Splitting return type and function name
+# (this guideline is apparently not strictly followed in OpenFOAM)
+# AlwaysBreakAfterReturnType: All
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+# Covered by "BreakBeforeBraces"
+BraceWrapping:
+  AfterCaseLabel:  true
+  AfterClass:      true
+  AfterControlStatement: Always
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: true
+  AfterStruct:     true
+  AfterUnion:      true
+  AfterExternBlock: true
+  BeforeCatch:     true
+  BeforeElse:      true
+  BeforeLambdaBody: true
+  BeforeWhile:     true
+  IndentBraces:    true
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+# Guideline (almost): Splitting long lines at an = sign. Indent after split.
+# Guideline (almost): Splitting formulae over several lines.
+BreakBeforeBinaryOperators: NonAssignment
+# Always break before braces: if, for, functions, classes, etc.
+BreakBeforeBraces: Allman
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+# Guideline (almost): Splitting logical tests over several lines.
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+# Undocumented guideline (almost): Have the initializer : in a new line.
+BreakConstructorInitializers: BeforeColon
+BreakStringLiterals: true
+# Here we could set the 80 charactes limit, but that would lead to more aggressive changes.
+ColumnLimit:     0
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 0
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+# Undocumented guideline: add line after "public:" etc (since clang-format 12)
+# EmptyLineAfterAccessModifier: Always
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: false
+# Guideline: Macro loops are like for loops, but without a space.
+ForEachMacros:
+  - forAllIters
+  - forAllConstIters
+  - forAllReverseIters
+  - forAllConstReverseIters
+  - forAll
+  - forAllReverse
+  - forAllIter
+  - forAllConstIter
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+    SortPriority:    0
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+    SortPriority:    0
+  - Regex:           '.*'
+    Priority:        1
+    SortPriority:    0
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+# Guideline: The normal indentation is 4 spaces per logical level.
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+# Required to not change code following the guidelines
+# "Leave two empty lines between sections" and
+# "Use two empty lines between functions"
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments:  true
+# Do not change the order of include statements (could be catastrophic for OpenFOAM)
+SortIncludes:    false
+SortUsingDeclarations: false
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+# No "template <T>" (guideline already used, but not documented)
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+# No a{1} (no guideline)
+SpaceBeforeCpp11BracedList: true
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+# Guideline: Spaces in "if ()", "for ()", but not "forAll ()".
+SpaceBeforeParens: ControlStatementsExceptForEachMacros
+# Guideline: Range-based for should have a space surrounding the ':'.
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInConditionalStatement: false
+# No "arr[3] = [ 1, 2, 3 ]" (no guideline).
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+# Treat the code as C++11 or later
+Standard:        Latest
+StatementMacros:
+TabWidth:        4
+UseCRLF:         false
+# Guideline: No tab characters - only use spaces for indentation.
+UseTab:          Never
+WhitespaceSensitiveMacros:
+...
+
diff --git a/channel-transport/transport-openfoam/.gitignore b/channel-transport/transport-openfoam/.gitignore
index 52b9cb41a..1f7d5d93a 100644
--- a/channel-transport/transport-openfoam/.gitignore
+++ b/channel-transport/transport-openfoam/.gitignore
@@ -1,2 +1,4 @@
-Make/
+Make/*
+!Make/files
+!Make/options
 0/

From 14db9a1a661779e201bf9c9efae0b6f2b396daa5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 10:41:19 +0200
Subject: [PATCH 09/18] Revert to default schemes

---
 channel-transport/transport-openfoam/system/fvSchemes | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/channel-transport/transport-openfoam/system/fvSchemes b/channel-transport/transport-openfoam/system/fvSchemes
index 6bb4d7d8c..7ffafdece 100644
--- a/channel-transport/transport-openfoam/system/fvSchemes
+++ b/channel-transport/transport-openfoam/system/fvSchemes
@@ -19,14 +19,12 @@ gradSchemes
 divSchemes
 {
     default         none;
-    div(phi,U)      Gauss linear;
-    div(phi,T)      Gauss upwind; //linearUpwind grad(T);
+    div(phi,T)      Gauss linearUpwind grad(T);
 }
 
 laplacianSchemes
 {
     default         none;
-    laplacian(DT,U) Gauss linear corrected;
     laplacian(DT,T) Gauss linear corrected;
 }
 

From a4d0899d04166b23bfce5954ce2f47d224869552 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 11:42:37 +0200
Subject: [PATCH 10/18] Fix dimensions of T

---
 channel-transport/transport-openfoam/0.orig/T | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/channel-transport/transport-openfoam/0.orig/T b/channel-transport/transport-openfoam/0.orig/T
index 3125d4d34..d7a18ffa1 100644
--- a/channel-transport/transport-openfoam/0.orig/T
+++ b/channel-transport/transport-openfoam/0.orig/T
@@ -6,7 +6,7 @@ FoamFile
     object      T;
 }
 
-dimensions      [0 2 -2 0 0 0 0];
+dimensions      [0 0 0 1 0 0 0];
 
 internalField   uniform 0;
 

From 900eef567361a9014917e2bb2d0b20bfb3bfb57b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 11:43:02 +0200
Subject: [PATCH 11/18] Revert to tutorial files

---
 .../transport-openfoam/system/fvSchemes       | 11 ++++++++
 .../transport-openfoam/system/fvSolution      | 28 +++++++++++++------
 2 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/channel-transport/transport-openfoam/system/fvSchemes b/channel-transport/transport-openfoam/system/fvSchemes
index 7ffafdece..f3a636050 100644
--- a/channel-transport/transport-openfoam/system/fvSchemes
+++ b/channel-transport/transport-openfoam/system/fvSchemes
@@ -1,3 +1,10 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2312                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
 FoamFile
 {
     version     2.0;
@@ -5,6 +12,7 @@ FoamFile
     class       dictionary;
     object      fvSchemes;
 }
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 ddtSchemes
 {
@@ -37,3 +45,6 @@ snGradSchemes
 {
     default         corrected;
 }
+
+
+// ************************************************************************* //
diff --git a/channel-transport/transport-openfoam/system/fvSolution b/channel-transport/transport-openfoam/system/fvSolution
index 74640654b..b258c9b1b 100644
--- a/channel-transport/transport-openfoam/system/fvSolution
+++ b/channel-transport/transport-openfoam/system/fvSolution
@@ -1,25 +1,35 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2312                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
 FoamFile
 {
     version     2.0;
     format      ascii;
     class       dictionary;
-    location    "system";
     object      fvSolution;
 }
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 solvers
 {
-  T
-  {
-    solver           PBiCGStab;
-    preconditioner   DILU;
-    tolerance        1e-6;
-    relTol 	         0;
-    norm             default;
-  }
+    T
+    {
+        solver          PBiCGStab;
+        preconditioner  DILU;
+        tolerance       1e-6;
+        relTol          0;
+        norm            default;
+    }
 }
 
 SIMPLE
 {
     nNonOrthogonalCorrectors 0;
 }
+
+
+// ************************************************************************* //

From 759e9e50d7e764f2ff08a1c51b5a260f8058cfe8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 12:45:11 +0200
Subject: [PATCH 12/18] Recompute phi after the preCICE adapter

---
 .../transport-openfoam/dynamicScalarTransportFoam.C    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
index 9ac8e7ba3..f880dd720 100644
--- a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
+++ b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
@@ -81,17 +81,17 @@ int main(int argc, char *argv[])
 
     Info<< "\nCalculating scalar transport\n" << endl;
 
-    #include "CourantNo.H"
-
     while (simple.loop())
     {
         Info << "Time = " << runTime.timeName() << nl << endl;
 
+        Info<< "Recompute phi" << endl;
+        fvOptions.correct(U);
+        phi = fvc::flux(U);
+        #include "CourantNo.H"
+
         while (simple.correctNonOrthogonal())
         {
-            // Update phi as U changes
-            phi = fvc::flux(U);
-
             fvScalarMatrix TEqn
             (
                 fvm::ddt(T)

From 78e47697a821b7e726d339534c61c7c64384ba8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 13:40:30 +0200
Subject: [PATCH 13/18] Correctly set blob

---
 channel-transport/transport-openfoam/run.sh   |  2 +-
 .../system/setExprFieldsDict                  | 29 +++++++++++++++++++
 .../transport-openfoam/system/setFieldsDict   | 28 ------------------
 3 files changed, 30 insertions(+), 29 deletions(-)
 create mode 100644 channel-transport/transport-openfoam/system/setExprFieldsDict
 delete mode 100644 channel-transport/transport-openfoam/system/setFieldsDict

diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
index 3cbec2a56..bf6db3941 100755
--- a/channel-transport/transport-openfoam/run.sh
+++ b/channel-transport/transport-openfoam/run.sh
@@ -6,7 +6,7 @@ exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
 cp -r 0.orig 0
-setFields
+setExprFields
 
 ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
diff --git a/channel-transport/transport-openfoam/system/setExprFieldsDict b/channel-transport/transport-openfoam/system/setExprFieldsDict
new file mode 100644
index 000000000..69f06ed75
--- /dev/null
+++ b/channel-transport/transport-openfoam/system/setExprFieldsDict
@@ -0,0 +1,29 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      setExprFieldsDict;
+}
+
+expressions
+(
+    T
+    {
+        field T;
+
+        variables
+        (
+            "x = pos().x()"
+            "y = pos().y()"
+            "r = 0.5"
+            "bx = 1"
+            "by = 1"
+        );
+
+        expression
+        #{
+            r - r * tanh(((x - bx)*(x - bx) + (y - by)*(y - by) - r) / 0.1)
+        #};
+    }
+);
diff --git a/channel-transport/transport-openfoam/system/setFieldsDict b/channel-transport/transport-openfoam/system/setFieldsDict
deleted file mode 100644
index 245a5ca0e..000000000
--- a/channel-transport/transport-openfoam/system/setFieldsDict
+++ /dev/null
@@ -1,28 +0,0 @@
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      setFieldsDict;
-}
-
-defaultFieldValues
-(
-    volScalarFieldValue T 0
-);
-
-regions
-(
-    cylinderToCell
-    {
-        p1 (1 1 0);
-        p2 (1 1 1);
-        radius 0.5;
-
-        fieldValues
-        (
-            volScalarFieldValue T 1
-            //TODO "0.5 - 0.5 * tanh(((x - 1)*(x - 1) + (y - 1)*(y - 1) - 0.5) / 0.1)"
-        );
-    }
-);

From 3b001ee1b46940aaef0d9839b254593151b3fd42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 26 Jun 2024 13:47:56 +0200
Subject: [PATCH 14/18] Add OpenFOAM transport to README

---
 channel-transport/README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/channel-transport/README.md b/channel-transport/README.md
index 267a70550..da8367ad6 100644
--- a/channel-transport/README.md
+++ b/channel-transport/README.md
@@ -41,6 +41,8 @@ Transport participant:
 
 * Nutils. For more information, have a look at the [Nutils adapter documentation](https://precice.org/adapter-nutils.html). This Nutils solver requires at least Nutils v7.0.
 
+* OpenFOAM. This case uses a modified version of scalarTransportFoam, which recomputes `phi` after the preCICE adapter reads the velocity field. Build it with `wmake`. Read more details in the [OpenFOAM adapter](https://precice.org/adapter-openfoam-overview.html).
+
 ## Running the simulation
 
 Open two separate terminals and start one fluid and one transport participant by calling the respective run scripts `run.sh` located in each of the participants' directory. For example:

From c711cce87b5d1a23ba868c8fc2993a6a11e5cdfd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Thu, 11 Jul 2024 13:09:40 +0200
Subject: [PATCH 15/18] Only set initial condition

---
 channel-transport/transport-openfoam/run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/channel-transport/transport-openfoam/run.sh b/channel-transport/transport-openfoam/run.sh
index bf6db3941..9a8884f2c 100755
--- a/channel-transport/transport-openfoam/run.sh
+++ b/channel-transport/transport-openfoam/run.sh
@@ -6,7 +6,7 @@ exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
 cp -r 0.orig 0
-setExprFields
+setExprFields -time 0
 
 ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs

From 5602cfd397d5ad6ad6c2e2bf41ca0e640cf1fb5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Thu, 11 Jul 2024 13:13:11 +0200
Subject: [PATCH 16/18] Add note about openfoam conserving T

---
 channel-transport/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/channel-transport/README.md b/channel-transport/README.md
index da8367ad6..497bed369 100644
--- a/channel-transport/README.md
+++ b/channel-transport/README.md
@@ -41,7 +41,7 @@ Transport participant:
 
 * Nutils. For more information, have a look at the [Nutils adapter documentation](https://precice.org/adapter-nutils.html). This Nutils solver requires at least Nutils v7.0.
 
-* OpenFOAM. This case uses a modified version of scalarTransportFoam, which recomputes `phi` after the preCICE adapter reads the velocity field. Build it with `wmake`. Read more details in the [OpenFOAM adapter](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM. This case uses a modified version of scalarTransportFoam, which recomputes `phi` after the preCICE adapter reads the velocity field. Build it with `wmake`. Read more details in the [OpenFOAM adapter](https://precice.org/adapter-openfoam-overview.html). Note that T accumulates in front of the outlet as this case conserves overall T.
 
 ## Running the simulation
 

From 9d7249849169963830b61d4423592caca7731a33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Thu, 11 Jul 2024 13:15:08 +0200
Subject: [PATCH 17/18] Fix application name

---
 .../transport-openfoam/dynamicScalarTransportFoam.C             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
index f880dd720..0a3e787ca 100644
--- a/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
+++ b/channel-transport/transport-openfoam/dynamicScalarTransportFoam.C
@@ -24,7 +24,7 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Application
-    scalarTransportFoam
+    dynamicScalarTransportFoam
 
 Group
     grpBasicSolvers

From 7e6502ba4d3dd93bce81ad1db685a3b2091e16f5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Thu, 11 Jul 2024 13:25:55 +0200
Subject: [PATCH 18/18] Add changelog

---
 changelog-entries/551.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 changelog-entries/551.md

diff --git a/changelog-entries/551.md b/changelog-entries/551.md
new file mode 100644
index 000000000..86ff9b8ac
--- /dev/null
+++ b/changelog-entries/551.md
@@ -0,0 +1 @@
+- Added OpenFOAM variant of the transport participant to the channel-transport tutorial.