ENH: support zone and zones for sampled cutting planes, sampledIsoSurface

- rework to use bitSet for more flexibility

src/sampling/sampledSurface/isoSurface/sampledIsoSurface.C

@@ -108,7 +108,7 @@ void Foam::sampledIsoSurface::getIsoFields() const
                         fvm
                     )
                 );
-                volFieldPtr_ = storedVolFieldPtr_.operator->();
+                volFieldPtr_ = storedVolFieldPtr_.get();
             }
             else
             {
@@ -132,7 +132,7 @@ void Foam::sampledIsoSurface::getIsoFields() const
     // (volPointInterpolation::interpolate with cache=false deletes any
     //  registered one or if mesh.changing())
 
-    if (!subMeshPtr_.valid())
+    if (subMeshPtr_.empty())
     {
         const word pointFldName =
             "volPointInterpolate_"
@@ -200,8 +200,8 @@ void Foam::sampledIsoSurface::getIsoFields() const
         }
 
 
-        // If averaging redo the volField. Can only be done now since needs the
-        // point field.
+        // If averaging redo the volField.
+        // Can only be done now since needs the point field.
         if (average_)
         {
             storedVolFieldPtr_.reset
@@ -261,7 +261,7 @@ void Foam::sampledIsoSurface::getIsoFields() const
         }
 
 
-        // Pointfield on submesh
+        // The point field on subMesh
 
         const word pointFldName =
             "volPointInterpolate_"
@@ -360,30 +360,30 @@ bool Foam::sampledIsoSurface::updateGeometry() const
         return false;
     }
 
-    // Get any subMesh
-    if (zoneID_.index() != -1 && !subMeshPtr_.valid())
+    // Get sub-mesh if any
+    if
+    (
+        (-1 != mesh().cellZones().findIndex(zoneNames_))
+     && subMeshPtr_.empty()
+    )
     {
         const polyBoundaryMesh& patches = mesh().boundaryMesh();
 
         // Patch to put exposed internal faces into
         const label exposedPatchi = patches.findPatchID(exposedPatchName_);
 
-        if (debug)
-        {
-            Info<< "Allocating subset of size "
-                << mesh().cellZones()[zoneID_.index()].size()
-                << " with exposed faces into patch "
-                << patches[exposedPatchi].name() << endl;
-        }
+        DebugInfo
+            << "Allocating subset of size "
+            << mesh().cellZones().selection(zoneNames_).count()
+            << " with exposed faces into patch "
+            << patches[exposedPatchi].name() << endl;
 
-        // Remove old mesh if any
-        subMeshPtr_.clear();
         subMeshPtr_.reset
         (
             new fvMeshSubset
             (
                 fvm,
-                mesh().cellZones()[zoneID_.index()],
+                mesh().cellZones().selection(zoneNames_),
                 exposedPatchi
             )
         );
@@ -474,8 +474,8 @@ Foam::sampledIsoSurface::sampledIsoSurface
     mergeTol_(dict.lookupOrDefault("mergeTol", 1e-6)),
     regularise_(dict.lookupOrDefault("regularise", true)),
     average_(dict.lookupOrDefault("average", false)),
-    zoneID_(dict.lookupOrDefault("zone", word::null), mesh.cellZones()),
-    exposedPatchName_(word::null),
+    zoneNames_(),
+    exposedPatchName_(),
     surfPtr_(nullptr),
     prevTimeIndex_(-1),
     storedVolFieldPtr_(nullptr),
@@ -491,27 +491,30 @@ Foam::sampledIsoSurface::sampledIsoSurface
             << " span across cells." << exit(FatalIOError);
     }
 
-    if (zoneID_.index() != -1)
+
+    if (!dict.readIfPresent("zones", zoneNames_) && dict.found("zone"))
+    {
+        zoneNames_.resize(1);
+        dict.readEntry("zone", zoneNames_.first());
+    }
+
+    if (-1 != mesh.cellZones().findIndex(zoneNames_))
     {
         dict.readEntry("exposedPatchName", exposedPatchName_);
 
         if (mesh.boundaryMesh().findPatchID(exposedPatchName_) == -1)
         {
-            FatalIOErrorInFunction
-            (
-                dict
-            )   << "Cannot find patch " << exposedPatchName_
+            FatalIOErrorInFunction(dict)
+                << "Cannot find patch " << exposedPatchName_
                 << " in which to put exposed faces." << endl
                 << "Valid patches are " << mesh.boundaryMesh().names()
                 << exit(FatalIOError);
         }
 
-        if (debug && zoneID_.index() != -1)
-        {
-            Info<< "Restricting to cellZone " << zoneID_.name()
-                << " with exposed internal faces into patch "
-                << exposedPatchName_ << endl;
-        }
+        DebugInfo
+            << "Restricting to cellZone(s) " << flatOutput(zoneNames_)
+            << " with exposed internal faces into patch "
+            << exposedPatchName_ << endl;
     }
 }
 

src/sampling/sampledSurface/isoSurface/sampledIsoSurface.H

@@ -54,7 +54,8 @@ Usage
         regularise | point snapping                        | yes      |
         average  | cell values from averaged point values  | no       | false
         bounds   | limit with bounding box                 | no       |
-        zone     | limit to specified zone                 | no       |
+        zone     | limit to cell zone (name or regex)      | no       |
+        zones    | limit to cell zones (names, regexs)     | no       |
         exposedPatchName | name for zone subset            | partly   |
     \endtable
 
@@ -68,7 +69,6 @@ SourceFiles
 
 #include "isoSurface.H"
 #include "sampledSurface.H"
-#include "ZoneIDs.H"
 #include "fvMeshSubset.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -104,8 +104,8 @@ class sampledIsoSurface
         //- Whether to recalculate cell values as average of point values
         const bool average_;
 
-        //- Zone name/index (if restricted to zones)
-        mutable cellZoneID zoneID_;
+        //- The zone or zones for the iso-surface
+        wordRes zoneNames_;
 
         //- For zones: patch to put exposed faces into
         mutable word exposedPatchName_;

src/sampling/sampledSurface/isoSurface/sampledIsoSurfaceCell.C

@@ -201,7 +201,6 @@ Foam::sampledIsoSurfaceCell::sampledIsoSurfaceCell
     bounds_(dict.lookupOrDefault("bounds", boundBox::invertedBox)),
     regularise_(dict.lookupOrDefault("regularise", true)),
     average_(dict.lookupOrDefault("average", true)),
-    zoneKey_(keyType::null),
     prevTimeIndex_(-1),
     meshCells_()
 {}

src/sampling/sampledSurface/isoSurface/sampledIsoSurfaceCell.H

@@ -56,6 +56,9 @@ Usage
         bounds   | limit with bounding box                 | no       |
     \endtable
 
+Note
+    Does not currently support cell zones.
+
 SourceFiles
     sampledIsoSurfaceCell.C
 
@@ -102,9 +105,6 @@ class sampledIsoSurfaceCell
         //- Whether to recalculate cell values as average of point values
         const bool average_;
 
-        //- If restricted to zones, name of this zone or a regular expression
-        keyType zoneKey_;
-
 
     // Recreated for every isoSurface
 

src/sampling/sampledSurface/sampledCuttingPlane/sampledCuttingPlane.C

@@ -46,6 +46,51 @@ namespace Foam
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
+void Foam::sampledCuttingPlane::checkBoundsIntersection
+(
+    const plane& pln,
+    const boundBox& meshBb
+) const
+{
+    // Verify specified bounding box
+    if (!bounds_.empty())
+    {
+        // Bounding box does not overlap with (global) mesh!
+        if (!bounds_.overlaps(meshBb))
+        {
+            WarningInFunction
+                << nl
+                << name() << " : "
+                << "Bounds " << bounds_
+                << " do not overlap the mesh bounding box " << meshBb
+                << nl << endl;
+        }
+
+        // Plane does not intersect the bounding box
+        if (!bounds_.intersects(pln))
+        {
+            WarningInFunction
+                << nl
+                << name() << " : "
+                << "Plane "<< pln << " does not intersect the bounds "
+                << bounds_
+                << nl << endl;
+        }
+    }
+
+    // Plane does not intersect the (global) mesh!
+    if (!meshBb.intersects(pln))
+    {
+        WarningInFunction
+            << nl
+            << name() << " : "
+            << "Plane "<< pln << " does not intersect the mesh bounds "
+            << meshBb
+            << nl << endl;
+    }
+}
+
+
 void Foam::sampledCuttingPlane::createGeometry()
 {
     if (debug)
@@ -62,29 +107,51 @@ void Foam::sampledCuttingPlane::createGeometry()
     // Clear derived data
     clearGeom();
 
-    // Get any subMesh
-    if (zoneID_.index() != -1 && !subMeshPtr_.valid())
+    const fvMesh& fvm = static_cast<const fvMesh&>(this->mesh());
+
+    // Get sub-mesh if any
+    if
+    (
+        (-1 != mesh().cellZones().findIndex(zoneNames_))
+     && subMeshPtr_.empty()
+    )
     {
         const polyBoundaryMesh& patches = mesh().boundaryMesh();
 
         // Patch to put exposed internal faces into
         const label exposedPatchi = patches.findPatchID(exposedPatchName_);
 
+        bitSet cellsToSelect = mesh().cellZones().selection(zoneNames_);
+
         DebugInfo
             << "Allocating subset of size "
-            << mesh().cellZones()[zoneID_.index()].size()
+            << cellsToSelect.count()
             << " with exposed faces into patch "
             << patches[exposedPatchi].name() << endl;
 
-        subMeshPtr_.reset
-        (
-            new fvMeshSubset
-            (
-                static_cast<const fvMesh&>(mesh()),
-                mesh().cellZones()[zoneID_.index()],
-                exposedPatchi
-            )
-        );
+
+        // If we will use a fvMeshSubset so can apply bounds as well to make
+        // the initial selection smaller.
+        if (!bounds_.empty() && cellsToSelect.any())
+        {
+            const auto& cellCentres = fvm.C();
+
+            for (const label celli : cellsToSelect)
+            {
+                const point& cc = cellCentres[celli];
+
+                if (!bounds_.contains(cc))
+                {
+                    cellsToSelect.unset(celli);
+                }
+            }
+
+            DebugInfo
+                << "Bounded subset of size "
+                << cellsToSelect.count() << endl;
+        }
+
+        subMeshPtr_.reset(new fvMeshSubset(fvm, cellsToSelect, exposedPatchi));
     }
 
 
@@ -93,9 +160,11 @@ void Foam::sampledCuttingPlane::createGeometry()
     (
         subMeshPtr_.valid()
       ? subMeshPtr_().subMesh()
-      : static_cast<const fvMesh&>(this->mesh())
+      : fvm
     );
 
+    checkBoundsIntersection(plane_, mesh.bounds());
+
 
     // Distance to cell centres
     // ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -121,7 +190,7 @@ void Foam::sampledCuttingPlane::createGeometry()
 
     // Internal field
     {
-        const pointField& cc = mesh.cellCentres();
+        const auto& cc = mesh.cellCentres();
         scalarField& fld = cellDistance.primitiveFieldRef();
 
         forAll(cc, i)
@@ -167,6 +236,7 @@ void Foam::sampledCuttingPlane::createGeometry()
             }
             else
             {
+                // Other side cell centres?
                 const pointField& cc = mesh.C().boundaryField()[patchi];
                 fvPatchScalarField& fld = cellDistanceBf[patchi];
 
@@ -242,43 +312,6 @@ void Foam::sampledCuttingPlane::createGeometry()
         //)
     );
 
-    // Verify specified bounding box
-    if (!bounds_.empty())
-    {
-        // Bounding box does not overlap with (global) mesh!
-        if (!bounds_.overlaps(mesh.bounds()))
-        {
-            WarningInFunction
-                << nl
-                << name() << " : "
-                << "Bounds " << bounds_
-                << " do not overlap the mesh bounding box " << mesh.bounds()
-                << nl << endl;
-        }
-
-        // Plane does not intersect the bounding box
-        if (!bounds_.intersects(plane_))
-        {
-            WarningInFunction
-                << nl
-                << name() << " : "
-                << "Plane "<< plane_ << " does not intersect the bounds "
-                << bounds_
-                << nl << endl;
-        }
-    }
-
-    // Plane does not intersect the (global) mesh!
-    if (!mesh.bounds().intersects(plane_))
-    {
-        WarningInFunction
-            << nl
-            << name() << " : "
-            << "Plane "<< plane_ << " does not intersect the mesh bounds "
-            << mesh.bounds()
-            << nl << endl;
-    }
-
     if (debug)
     {
         print(Pout);
@@ -302,32 +335,36 @@ Foam::sampledCuttingPlane::sampledCuttingPlane
     mergeTol_(dict.lookupOrDefault("mergeTol", 1e-6)),
     regularise_(dict.lookupOrDefault("regularise", true)),
     average_(dict.lookupOrDefault("average", false)),
-    zoneID_(dict.lookupOrDefault("zone", word::null), mesh.cellZones()),
-    exposedPatchName_(word::null),
+    zoneNames_(),
+    exposedPatchName_(),
     needsUpdate_(true),
     subMeshPtr_(nullptr),
     cellDistancePtr_(nullptr),
     isoSurfPtr_(nullptr)
 {
-    if (zoneID_.index() != -1)
+    if (!dict.readIfPresent("zones", zoneNames_) && dict.found("zone"))
+    {
+        zoneNames_.resize(1);
+        dict.readEntry("zone", zoneNames_.first());
+    }
+
+    if (-1 != mesh.cellZones().findIndex(zoneNames_))
     {
         dict.readEntry("exposedPatchName", exposedPatchName_);
 
-        if (mesh.boundaryMesh().findPatchID(exposedPatchName_) == -1)
+        if (-1 == mesh.boundaryMesh().findPatchID(exposedPatchName_))
         {
-            FatalErrorInFunction
+            FatalIOErrorInFunction(dict)
                 << "Cannot find patch " << exposedPatchName_
                 << " in which to put exposed faces." << endl
                 << "Valid patches are " << mesh.boundaryMesh().names()
                 << exit(FatalError);
         }
 
-        if (debug && zoneID_.index() != -1)
-        {
-            Info<< "Restricting to cellZone " << zoneID_.name()
-                << " with exposed internal faces into patch "
-                << exposedPatchName_ << endl;
-        }
+        DebugInfo
+            << "Restricting to cellZone(s) " << flatOutput(zoneNames_)
+            << " with exposed internal faces into patch "
+            << exposedPatchName_ << endl;
     }
 }
 

src/sampling/sampledSurface/sampledCuttingPlane/sampledCuttingPlane.H

@@ -55,10 +55,14 @@ Usage
         mergeTol | tolerance for merging points            | no       | 1e-6
         regularise | point snapping                        | no       | true
         bounds   | limit with bounding box                 | no       |
-        zone     | limit to specified zone                 | no       |
+        zone     | limit to cell zone (name or regex)      | no       |
+        zones    | limit to cell zones (names, regexs)     | no       |
         exposedPatchName | name for zone subset            | partly   |
     \endtable
 
+Note
+    The keyword \c zones has priority over \c zone.
+
 SeeAlso
     Foam::plane
 
@@ -74,7 +78,6 @@ SourceFiles
 #include "isoSurface.H"
 //#include "isoSurfaceCell.H"
 #include "plane.H"
-#include "ZoneIDs.H"
 #include "fvMeshSubset.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -107,8 +110,8 @@ class sampledCuttingPlane
         //- Whether to recalculate cell values as average of point values
         const bool average_;
 
-        //- Zone name/index (if restricted to zones)
-        mutable cellZoneID zoneID_;
+        //- The zone or zones in which cutting is to occur
+        wordRes zoneNames_;
 
         //- For zones: patch to put exposed faces into
         mutable word exposedPatchName_;
@@ -117,7 +120,7 @@ class sampledCuttingPlane
         mutable bool needsUpdate_;
 
 
-        //- Optional subsetted mesh
+        //- Mesh subset (optional: only used with zones)
         autoPtr<fvMeshSubset> subMeshPtr_;
 
         //- Distance to cell centres
@@ -133,6 +136,13 @@ class sampledCuttingPlane
 
     // Private Member Functions
 
+        //- Check and warn if bounding box does not intersect mesh or plane
+        void checkBoundsIntersection
+        (
+            const plane& pln,
+            const boundBox& meshBb
+        ) const;
+
         //- Create iso surface
         void createGeometry();
 

src/sampling/sampledSurface/sampledPlane/sampledPlane.C

@@ -44,6 +44,159 @@ namespace Foam
     );
 }
 
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::sampledPlane::checkBoundsIntersection
+(
+    const plane& pln,
+    const boundBox& meshBb
+) const
+{
+    // Verify specified bounding box
+    if (!bounds_.empty())
+    {
+        // Bounding box does not overlap with (global) mesh!
+        if (!bounds_.overlaps(meshBb))
+        {
+            WarningInFunction
+                << nl
+                << name() << " : "
+                << "Bounds " << bounds_
+                << " do not overlap the mesh bounding box " << meshBb
+                << nl << endl;
+        }
+
+        // Plane does not intersect the bounding box
+        if (!bounds_.intersects(pln))
+        {
+            WarningInFunction
+                << nl
+                << name() << " : "
+                << "Plane "<< pln << " does not intersect the bounds "
+                << bounds_
+                << nl << endl;
+        }
+    }
+
+    // Plane does not intersect the (global) mesh!
+    if (!meshBb.intersects(pln))
+    {
+        WarningInFunction
+            << nl
+            << name() << " : "
+            << "Plane "<< pln << " does not intersect the mesh bounds "
+            << meshBb
+            << nl << endl;
+    }
+}
+
+
+Foam::bitSet Foam::sampledPlane::cellSelection
+(
+    const bool warnIntersect
+) const
+{
+    // Zones requested and in use?
+    const bool hasZones =
+        returnReduce
+        (
+            (-1 != mesh().cellZones().findIndex(zoneNames_)),
+            andOp<bool>()
+        );
+
+
+    bitSet cellsToSelect;
+
+    if (hasZones)
+    {
+        cellsToSelect = mesh().cellZones().selection(zoneNames_);
+    }
+
+
+    // Subset the zoned cells with the bounds_.
+    // For a full mesh, use the bounds to define the cell selection.
+
+    // If there are zones cells, use them to build the effective mesh
+    // bound box.
+    // Note that for convenience we use cell centres here instead of the
+    // cell points, since it will only be used for checking.
+
+    boundBox meshBb;
+
+    if (bounds_.empty())
+    {
+        // No bounds restriction, but will need the effective mesh boundBox
+        // for checking intersections
+
+        if (hasZones && warnIntersect)
+        {
+            const auto& cellCentres = static_cast<const fvMesh&>(mesh()).C();
+
+            for (const label celli : cellsToSelect)
+            {
+                const point& cc = cellCentres[celli];
+
+                meshBb.add(cc);
+            }
+
+            meshBb.reduce();
+        }
+        else
+        {
+            meshBb = mesh().bounds();  // use the regular mesh bounding box
+        }
+    }
+    else
+    {
+        const auto& cellCentres = static_cast<const fvMesh&>(mesh()).C();
+
+        // Only examine cells already set
+        if (hasZones)
+        {
+            for (const label celli : cellsToSelect)
+            {
+                const point& cc = cellCentres[celli];
+
+                meshBb.add(cc);
+