/*--------------------------------*- C++ -*----------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  dev
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
FoamFile
{
    format      ascii;
    class       dictionary;
    object      snappyHexMeshDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

// Which of the steps to run
castellatedMesh true;
snap            true;
addLayers       false;


//Optional: single region surfaces get patch names according to
//          surface only. Multi-region surfaces get patch name
//          surface "_ "region. Default is true
//singleRegionName false;


//Optional: preserve all generated patches. Default is to remove
//          zero-sized patches.
//keepPatches true;


// Geometry. Definition of all surfaces. All surfaces are of class
// searchableSurface.
// Surfaces are used
// - to specify refinement for any mesh cell intersecting it
// - to specify refinement for any mesh cell inside/outside/near
// - to 'snap' the mesh boundary to the surface
geometry
{
    box1x1x1
    {
        type searchableBox;
        min (1.5 1 -0.5);
        max (3.5 2 0.5);
    }

    sphere
    {
        type triSurfaceMesh;
        file "sphere.stl"

        // Optional: non-default tolerance on intersections
        // tolerance 1e-5;

        // Optional: depth of octree. Decrease only in case of memory
        // limitations.
        // maxTreeDepth 10;

        // Optional: scaling factor, e.g. unit conversion
        // scale 1;

        // Optional: discard triangles with low quality when getting normal
        // minQuality -1;

        // Per region the patchname. If not provided will be <surface>_<region>.
        // Note: this name cannot be used to identity this region in any
        //       other part of this dictionary; it is only a name
        //       for the combination of surface+region (which is only used
        //       when creating patches)
        regions
        {
            secondSolid
            {
                name mySecondPatch;
            }
        }
    }

    sphere2
    {
        type searchableSphere;
        centre  (1.5 1.5 1.5);
        radius  1.03;
    }
};

// Settings for the castellatedMesh generation.
castellatedMeshControls
{

    // Refinement parameters
    // ~~~~~~~~~~~~~~~~~~~~~

    // If local number of cells is >= maxLocalCells on any processor
    // switches from from refinement followed by balancing
    // (current method) to (weighted) balancing before refinement.
    maxLocalCells 100000;

    // Overall cell limit (approximately). Refinement will stop immediately
    // upon reaching this number so a refinement level might not complete.
    // Note that this is the number of cells before removing the part which
    // is not 'visible' from the keepPoint. The final number of cells might
    // actually be a lot less.
    maxGlobalCells 2000000;

    // The surface refinement loop might spend lots of iterations refining just a
    // few cells. This setting will cause refinement to stop if <= minimumRefine
    // are selected for refinement. Note: it will at least do one iteration
    // (unless the number of cells to refine is 0)
    minRefinementCells 0;

    // Allow a certain level of imbalance during refining
    // (since balancing is quite expensive)
    // Expressed as fraction of perfect balance (= overall number of cells /
    // nProcs). 0=balance always.
    maxLoadUnbalance 0.10;

    // Number of buffer layers between different levels.
    // 1 means normal 2:1 refinement restriction, larger means slower
    // refinement.
    nCellsBetweenLevels 1;


    // Explicit feature edge refinement
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    // Specifies a level for any cell intersected by explicitly provided
    // edges.
    // This is a featureEdgeMesh, read from constant/geometry for now.
    // Specify 'levels' in the same way as the 'distance' mode in the
    // refinementRegions (see below). The old specification
    //      level   2;
    // is equivalent to
    //      levels  ((0 2));

    features
    (
        //{
        //    file "someLine.eMesh";
        //    // level 2;
        //    levels ((0.0 2) (1.0 3));
        //}
    );


    // Surface based refinement
    // ~~~~~~~~~~~~~~~~~~~~~~~~

    // Specifies two levels for every surface. The first is the minimum level,
    // every cell intersecting a surface gets refined up to the minimum level.
    // The second level is the maximum level. Cells that 'see' multiple
    // intersections where the intersections make an
    // angle > resolveFeatureAngle get refined up to the maximum level.

    refinementSurfaces
    {
        sphere
        {
            // Surface-wise min and max refinement level
            level (2 2);

            // Optional region-wise level specification
            regions
            {
                secondSolid
                {
                    level (3 3);
                }
            }

            // Optional specification of patch type (default is wall). No
            // constraint types (cyclic, symmetry) etc. are allowed.
            patchInfo
            {
                type patch;
                inGroups (meshedPatches);
            }


            //- Optional increment (on top of max level) in small gaps
            // gapLevelIncrement 2;

            //- Optional angle to detect small-large cell situation
            //  perpendicular to the surface. Is the angle of face w.r.t.
            //  the local surface normal. Use on flat(ish) surfaces only.
            //  Otherwise leave out or set to negative number.
            // perpendicularAngle 10;

            //- Optional faceZone and (for closed surface) cellZone with
            //  how to select the cells that are in the cellZone
            //  (inside / outside / specified insidePoint)
            //  The orientation of the faceZone is
            //  - if on cellZone(s) : point out of (maximum) cellZone
            //  - if freestanding   : oriented according to surface

            // faceZone sphere;
            // cellZone sphere;
            // mode        inside;  // outside/insidePoint

            //- Optional specification of what to do with faceZone faces:
            //      internal : keep them as internal faces (default)
            //      baffle   : create baffles from them. This gives more
            //                 freedom in mesh motion
            //      boundary : create free-standing boundary faces (baffles
            //                 but without the shared points)
            // faceType baffle;
        }
    }

    // Feature angle:
    // - used if min and max refinement level of a surface differ
    // - used if feature snapping (see snapControls below) is used
    resolveFeatureAngle 30;

    //- Optional increment (on top of max level) in small gaps
    // gapLevelIncrement 2;


    // Planar angle:
    // - used to determine if surface normals
    //   are roughly the same or opposite. Used
    //      - in proximity refinement
    //      - to decide when to merge free-standing baffles
    //        (if e.g. running in surfaceSimplify mode set this to 180 to
    //         merge all baffles)
    //      - in snapping to avoid snapping to nearest on 'wrong' side
    //        of thin gap
    //
    // If not specified same as resolveFeatureAngle
    planarAngle 30;


    // Region-wise refinement
    // ~~~~~~~~~~~~~~~~~~~~~~

    // Specifies refinement level for cells in relation to a surface. One of
    // three modes
    // - distance. 'levels' specifies per distance to the surface the
    //   wanted refinement level. The distances need to be specified in
    //   increasing order.
    // - inside. 'levels' is only one entry and only the level is used. All
    //   cells inside the surface get refined up to the level. The surface
    //   needs to be closed for this to be possible.
    // - outside. Same but cells outside.

    refinementRegions
    {
        box1x1x1
        {
            mode inside;
            levels ((1.0 4));
        }
        // sphere
        //{
        //    mode distance;
        //    levels ((1.0 5) (2.0 3));
        //}
    }

    // Mesh selection
    // ~~~~~~~~~~~~~~

    // After refinement patches get added for all refinementSurfaces and
    // all cells intersecting the surfaces get put into these patches. The
    // section reachable from the insidePoint is kept.
    // NOTE: This point should never be on a face, always inside a cell, even
    // after refinement.
    insidePoint (5 0.28 0.43);

    // Whether any faceZones (as specified in the refinementSurfaces)
    // are only on the boundary of corresponding cellZones or also allow
    // free-standing zone faces. Not used if there are no faceZones.
    allowFreeStandingZoneFaces true;


    // Optional: do not remove cells likely to give snapping problems
    // handleSnapProblems false;

    // Optional: switch off topological test for cells to-be-squashed
    //           and use geometric test instead
    // useTopologicalSnapDetection false;

    // Extend refinement regions to the span of the surface facet/triangles
    extendedRefinementSpan true;
}

// Settings for the snapping.
snapControls
{
    // Number of patch smoothing iterations before finding correspondence
    // to surface
    nSmoothPatch 3;

    // Maximum relative distance for points to be attracted by surface.
    // True distance is this factor times local maximum edge length.
    // Note: changed(corrected) w.r.t 17x! (17x used 2* tolerance)
    tolerance 2.0;

    // Number of mesh displacement relaxation iterations.
    nSolveIter 30;

    // Maximum number of snapping relaxation iterations. Should stop
    // before upon reaching a correct mesh.
    nRelaxIter 5;

    // Feature snapping

        // Number of feature edge snapping iterations.
        // Leave out altogether to disable.
        nFeatureSnapIter 10;

        // Detect (geometric only) features by sampling the surface
        // (default=false).
        implicitFeatureSnap false;

        // Use castellatedMeshControls::features (default = true)
        explicitFeatureSnap true;

        // Detect features between multiple surfaces
        // (only for explicitFeatureSnap, default = false)
        multiRegionFeatureSnap false;


    // wip: disable snapping to opposite near surfaces (revert to 22x behaviour)
    // detectNearSurfacesSnap false;
}

// Settings for the layer addition.
addLayersControls
{
    // Are the thickness parameters below relative to the undistorted
    // size of the refined cell outside layer (true) or absolute sizes (false).
    relativeSizes true;

    // Layer thickness specification. This can be specified in one of following
    // ways:
    // - expansionRatio and finalLayerThickness (cell nearest internal mesh)
    // - expansionRatio and firstLayerThickness (cell on surface)
    // - overall thickness and firstLayerThickness
    // - overall thickness and finalLayerThickness
    // - overall thickness and expansionRatio
    //
    // Note: the mode thus selected is global, i.e. one cannot override the
    //       mode on a per-patch basis (only the values can be overridden)

        // Expansion factor for layer mesh
        expansionRatio 1.0;

        // Wanted thickness of the layer furthest away from the wall.
        // If relativeSizes this is relative to undistorted size of cell
        // outside layer.
        finalLayerThickness 0.3;

        // Wanted thickness of the layer next to the wall.
        // If relativeSizes this is relative to undistorted size of cell
        // outside layer.
        // firstLayerThickness 0.3;

        // Wanted overall thickness of layers.
        // If relativeSizes this is relative to undistorted size of cell
        // outside layer.
        // thickness 0.5


    // Minimum overall thickness of total layers. If for any reason layer
    // cannot be above minThickness do not add layer.
    // If relativeSizes this is relative to undistorted size of cell
    // outside layer..
    minThickness 0.25;


    // Per final patch (so not geometry!) the layer information
    // Note: This behaviour changed after 21x. Any non-mentioned patches
    //       now slide unless:
    //          - nSurfaceLayers is explicitly mentioned to be 0.
    //          - angle to nearest surface < slipFeatureAngle (see below)
    layers
    {
        sphere_firstSolid
        {
            nSurfaceLayers 1;

        }
        maxY
        {
            nSurfaceLayers 1;
            // Per patch layer data
            expansionRatio      1.3;
            finalLayerThickness 0.3;
            minThickness        0.1;
        }

        // Disable any mesh shrinking and layer addition on any point of
        // a patch by setting nSurfaceLayers to 0
        frozenPatches
        {
            nSurfaceLayers 0;
        }
    }

    // If points get not extruded do nGrow layers of connected faces that are
    // also not grown. This helps convergence of the layer addition process
    // close to features.
    // Note: changed(corrected) w.r.t 17x! (didn't do anything in 17x)
    nGrow 0;

    // Advanced settings


    // Static analysis of starting mesh

        // When not to extrude surface. 0 is flat surface, 90 is when two faces
        // are perpendicular
        featureAngle 130;

        // Stop layer growth on highly warped cells
        maxFaceThicknessRatio 0.5;


    // Patch displacement

        // Number of smoothing iterations of surface normals
        nSmoothSurfaceNormals 1;

        // Smooth layer thickness over surface patches
        nSmoothThickness 10;



    // Medial axis analysis

        // Angle used to pick up medial axis points
        // Note: changed(corrected) w.r.t 17x! 90 degrees corresponds to 130
        // in 17x.
        minMedialAxisAngle 90;

        // Reduce layer growth where ratio thickness to medial
        // distance is large
        maxThicknessToMedialRatio 0.3;

        // Number of smoothing iterations of interior mesh movement direction
        nSmoothNormals 3;

        // Optional: limit the number of steps walking away from the surface.
        // Default is unlimited.
        // nMedialAxisIter 10;

        // Optional: smooth displacement after medial axis determination.
        // default is 0.
        // nSmoothDisplacement 90;

        // (wip)Optional: do not extrude a point if none of the surrounding points is
        // not extruded. Default is false.
        // detectExtrusionIsland true;


    // Mesh shrinking

        // Optional: at non-patched sides allow mesh to slip if extrusion
        // direction makes angle larger than slipFeatureAngle. Default is
        // 0.5*featureAngle.
        slipFeatureAngle 30;

        // Maximum number of snapping relaxation iterations. Should stop
        // before upon reaching a correct mesh.
        nRelaxIter 5;

        // Create buffer region for new layer terminations
        nBufferCellsNoExtrude 0;

        // Overall max number of layer addition iterations. The mesher will
        // exit if it reaches this number of iterations; possibly with an
        // illegal mesh.
        nLayerIter 50;

        // Max number of iterations after which relaxed meshQuality controls
        // get used. Up to nRelaxedIter it uses the settings in
        // meshQualityControls,
        // after nRelaxedIter it uses the values in
        // meshQualityControls::relaxed.
        nRelaxedIter 20;

        // Additional reporting: if there are just a few faces where there
        // are mesh errors (after adding the layers) print their face centres.
        // This helps in tracking down problematic mesh areas.
        // additionalReporting true;
}

// Generic mesh quality settings. At any undoable phase these determine
// where to undo.
meshQualityControls
{
    // Specify mesh quality constraints in separate dictionary so can
    // be reused (e.g. checkMesh -meshQuality)
    #include "meshQualityDict"


    // Optional : some meshing phases allow usage of relaxed rules.
    // See e.g. addLayersControls::nRelaxedIter.
    relaxed
    {
        // Maximum non-orthogonality allowed. Set to 180 to disable.
        maxNonOrtho 75;
    }
}

// Advanced

//// Debug flags
//debugFlags
//(
//    mesh            // write intermediate meshes
//    intersections   // write current mesh intersections as .obj files
//    featureSeeds    // write information about explicit feature edge
//                    // refinement
//    attraction      // write attraction as .obj files
//    layerInfo       // write information about layers
//);
//
//// Write flags
//writeFlags
//(
//    scalarLevels    // write volScalarField with cellLevel for postprocessing
//    layerSets       // write cellSets, faceSets of faces in layer
//    layerFields     // write volScalarField for layer coverage
//);

// Merge tolerance. Is fraction of overall bounding box of initial mesh.
// Note: the write tolerance needs to be higher than this.
mergeTolerance 1e-6;

// ************************************************************************* //

diff --git a/etc/caseDicts/annotated/snappyHexMeshDict b/etc/caseDicts/annotated/snappyHexMeshDict
index 0407691..cb98025 100644
--- a/etc/caseDicts/annotated/snappyHexMeshDict
+++ b/etc/caseDicts/annotated/snappyHexMeshDict
@@ -50,9 +50,18 @@ geometry
         type triSurfaceMesh;
         file "sphere.stl"
 
-        // tolerance   1e-5;   // optional:non-default tolerance on intersections
-        // maxTreeDepth 10;    // optional:depth of octree. Decrease only in case
-                              // of memory limitations.
+        // Optional: non-default tolerance on intersections
+        // tolerance 1e-5;
+
+        // Optional: depth of octree. Decrease only in case of memory
+        // limitations.
+        // maxTreeDepth 10;
+
+        // Optional: scaling factor, e.g. unit conversion
+        // scale 1;
+
+        // Optional: discard triangles with low quality when getting normal
+        // minQuality -1;
 
         // Per region the patchname. If not provided will be <surface>_<region>.
         // Note: this name cannot be used to identity this region in any
diff --git a/src/mesh/snappyHexMesh/meshRefinement/meshRefinementRefine.C b/src/mesh/snappyHexMesh/meshRefinement/meshRefinementRefine.C
index fea1f26..d65cb97 100644
--- a/src/mesh/snappyHexMesh/meshRefinement/meshRefinementRefine.C
+++ b/src/mesh/snappyHexMesh/meshRefinement/meshRefinementRefine.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2021 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2022 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -707,7 +707,7 @@ Foam::label Foam::meshRefinement::markInternalDistanceToFeatureRefinement
     const labelList& cellLevel = meshCutter_.cellLevel();
     const pointField& cellCentres = mesh_.cellCentres();
 
-    // Detect if there are any distance shells
+    // Detect if there are any distance features
     if (features_.maxDistance() <= 0.0)
     {
         return 0;
@@ -730,7 +730,7 @@ Foam::label Foam::meshRefinement::markInternalDistanceToFeatureRefinement
         }
     }
 
-    // Do test to see whether cells is inside/outside shell with higher level
+    // Do test to see whether cells are in/near features with higher level
     labelList maxLevel;
     features_.findHigherLevel(testCc, testLevels, maxLevel);
 
@@ -2086,7 +2086,7 @@ Foam::labelList Foam::meshRefinement::refineCandidates
 
 
 
-        // Cells pierced by feature lines
+        // Cells pierced by feature edges
         // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
         if (featureRefinement)
@@ -2104,12 +2104,12 @@ Foam::labelList Foam::meshRefinement::refineCandidates
                 << ": " << nFeatures << " cells."  << endl;
         }
 
-        // Inside distance-to-feature shells
-        // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+        // Inside distance-to-feature
+        // ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
         if (featureDistanceRefinement)
         {
-            const label nShell = markInternalDistanceToFeatureRefinement
+            const label nCellsFeat = markInternalDistanceToFeatureRefinement
             (
                 nAllowRefine,
 
@@ -2117,7 +2117,7 @@ Foam::labelList Foam::meshRefinement::refineCandidates
                 nRefine
             );
             Info<< "Marked for refinement due to distance to explicit features "
-                ": " << nShell << " cells."  << endl;
+                ": " << nCellsFeat << " cells."  << endl;
         }
 
         // Inside refinement shells
diff --git a/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.C b/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.C
index 2acdbf1..60289d9 100644
--- a/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.C
+++ b/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2021 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2022 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -295,7 +295,7 @@ void Foam::refinementFeatures::buildTrees(const label feati)
 }
 
 
-// Find maximum level of a shell.
+// Find maximum level of a feature edge.
 void Foam::refinementFeatures::findHigherLevel
 (
     const pointField& pt,
@@ -308,8 +308,8 @@ void Foam::refinementFeatures::findHigherLevel
     const scalarField& distances = distances_[feati];
 
     // Collect all those points that have a current maxLevel less than
-    // (any of) the shell. Also collect the furthest distance allowable
-    // to any shell with a higher level.
+    // (any of) the feature edge. Also collect the furthest distance allowable
+    // to any feature edge with a higher level.
 
     pointField candidates(pt.size());
     labelList candidateMap(pt.size());
@@ -361,7 +361,7 @@ void Foam::refinementFeatures::findHigherLevel
 
             label pointi = candidateMap[candidatei];
 
-            // pt is in between shell[minDistI] and shell[minDistI+1]
+            // pt is in between feature[minDistI] and feature[minDistI+1]
             maxLevel[pointi] = levels[minDistI+1];
         }
     }
@@ -747,7 +747,7 @@ void Foam::refinementFeatures::findHigherLevel
     labelList& maxLevel
 ) const
 {
-    // Maximum level of any shell. Start off with level of point.
+    // Maximum level of any feature edge. Start off with level of point.
     maxLevel = ptLevel;
 
     forAll(*this, feati)
diff --git a/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.H b/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.H
index a7c8286..1343004 100644
--- a/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.H
+++ b/src/mesh/snappyHexMesh/refinementFeatures/refinementFeatures.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2021 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2022 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -55,10 +55,10 @@ class refinementFeatures
 {
     // Private Data
 
-        //- Per shell the list of ranges
+        //- Per feature the list of ranges
         List<scalarField> distances_;
 
-        //- Per shell per distance the refinement level
+        //- Per feature per distance the refinement level
         labelListList levels_;
 
         //- Edge
@@ -80,7 +80,7 @@ class refinementFeatures
         //- Build edge tree and feature point tree
         void buildTrees(const label);
 
-        //- Find shell level higher than ptLevel
+        //- Find feature level higher than ptLevel
         void findHigherLevel
         (
             const pointField& pt,
@@ -184,7 +184,7 @@ public:
                 List<pointIndexHit>& nearInfo
             ) const;
 
-            //- Find shell level higher than ptLevel
+            //- Find feature level higher than ptLevel
             void findHigherLevel
             (
                 const pointField& pt,