From 26aa427dd3842bdbfd507451ca64a1d95cc8c637 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 15 Nov 2011 16:48:59 +0000
Subject: [PATCH 1/5] ENH: addPatchCellLayer: avoid use of mesh.edgeFaces()

---
 .../polyTopoChange/addPatchCellLayer.C            | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C b/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
index d70c2794c8..0029fbe56e 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C
@@ -650,6 +650,9 @@ void Foam::addPatchCellLayer::calcSidePatch
     // ------------------------------------------------------
 
     const labelListList& edgeFaces = pp.edgeFaces();
+
+    DynamicList<label> dynMeshEdgeFaces;
+
     forAll(edgeFaces, edgeI)
     {
         if (edgeFaces[edgeI].size() == 1 && sidePatchID[edgeI] == -1)
@@ -660,7 +663,11 @@ void Foam::addPatchCellLayer::calcSidePatch
 
             // Pick up any boundary face on this edge and use its properties
             label meshEdgeI = meshEdges[edgeI];
-            const labelList& meshFaces = mesh.edgeFaces()[meshEdgeI];
+            const labelList& meshFaces = mesh.edgeFaces
+            (
+                meshEdgeI,
+                dynMeshEdgeFaces
+            );
 
             forAll(meshFaces, k)
             {
@@ -716,7 +723,11 @@ void Foam::addPatchCellLayer::calcSidePatch
 
             // Pick up any boundary face on this edge and use its properties
             label meshEdgeI = meshEdges[edgeI];
-            const labelList& meshFaces = mesh.edgeFaces()[meshEdgeI];
+            const labelList& meshFaces = mesh.edgeFaces
+            (
+                meshEdgeI,
+                dynMeshEdgeFaces
+            );
 
             forAll(meshFaces, k)
             {

From f1aa8b5f2ad9ec0952639f83263841fbf00407d5 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 15 Nov 2011 17:58:10 +0000
Subject: [PATCH 2/5] ENH: topoSet: add remove support

---
 .../mesh/manipulation/topoSet/topoSet.C       | 100 ++++++++++++++++++
 .../mesh/manipulation/topoSet/topoSetDict     |  10 +-
 2 files changed, 109 insertions(+), 1 deletion(-)

diff --git a/applications/utilities/mesh/manipulation/topoSet/topoSet.C b/applications/utilities/mesh/manipulation/topoSet/topoSet.C
index 5e5c15426c..5aedbdc775 100644
--- a/applications/utilities/mesh/manipulation/topoSet/topoSet.C
+++ b/applications/utilities/mesh/manipulation/topoSet/topoSet.C
@@ -35,6 +35,10 @@ Description
 #include "pointSet.H"
 #include "globalMeshData.H"
 #include "timeSelector.H"
+#include "IOobjectList.H"
+#include "cellZoneSet.H"
+#include "faceZoneSet.H"
+#include "pointZoneSet.H"
 
 using namespace Foam;
 
@@ -51,6 +55,96 @@ void printMesh(const Time& runTime, const polyMesh& mesh)
 }
 
 
+template<class ZoneType>
+void removeZone
+(
+    ZoneMesh<ZoneType, polyMesh>& zones,
+    const word& setName
+)
+{
+    label zoneID = zones.findZoneID(setName);
+
+    if (zoneID != -1)
+    {
+        Info<< "Removing zone " << setName << " at index " << zoneID << endl;
+        // Shuffle to last position
+        labelList oldToNew(zones.size());
+        label newI = 0;
+        forAll(oldToNew, i)
+        {
+            if (i != zoneID)
+            {
+                oldToNew[i] = newI++;
+            }
+        }
+        oldToNew[zoneID] = newI;
+        zones.reorder(oldToNew);
+        // Remove last element
+        zones.setSize(zones.size()-1);
+        zones.clearAddressing();
+        zones.write();
+    }
+}
+
+
+// Physically remove a set
+void removeSet
+(
+    const polyMesh& mesh,
+    const word& setType,
+    const word& setName
+)
+{
+    // Remove the file
+    IOobjectList objects
+    (
+        mesh,
+        mesh.time().findInstance
+        (
+            polyMesh::meshSubDir/"sets",
+            word::null,
+            IOobject::READ_IF_PRESENT,
+            mesh.facesInstance()
+        ),
+        polyMesh::meshSubDir/"sets"
+    );
+
+    if (objects.found(setName))
+    {
+        // Remove file
+        fileName object = objects[setName]->objectPath();
+        Info<< "Removing file " << object << endl;
+        rm(object);
+    }
+
+    // See if zone
+    if (setType == cellZoneSet::typeName)
+    {
+        removeZone
+        (
+            const_cast<cellZoneMesh&>(mesh.cellZones()),
+            setName
+        );
+    }
+    else if (setType == faceZoneSet::typeName)
+    {
+        removeZone
+        (
+            const_cast<faceZoneMesh&>(mesh.faceZones()),
+            setName
+        );
+    }
+    else if (setType == pointZoneSet::typeName)
+    {
+        removeZone
+        (
+            const_cast<pointZoneMesh&>(mesh.pointZones()),
+            setName
+        );
+    }
+}
+
+
 polyMesh::readUpdateState meshReadUpdate(polyMesh& mesh)
 {
     polyMesh::readUpdateState stat = mesh.readUpdate();
@@ -284,6 +378,12 @@ int main(int argc, char *argv[])
                     currentSet().write();
                 break;
 
+                case topoSetSource::REMOVE:
+                    Info<< "    Removing set" << endl;
+                    removeSet(mesh, setType, setName);
+                break;
+
+
                 default:
                     WarningIn(args.executable())
                         << "Unhandled action " << action << endl;
diff --git a/applications/utilities/mesh/manipulation/topoSet/topoSetDict b/applications/utilities/mesh/manipulation/topoSet/topoSetDict
index 86e5b98f1c..9c910aa7ec 100644
--- a/applications/utilities/mesh/manipulation/topoSet/topoSetDict
+++ b/applications/utilities/mesh/manipulation/topoSet/topoSetDict
@@ -22,8 +22,15 @@ FoamFile
 //     type    cellSet;
 //
 //     // action to perform on set. Two types:
-//     // - require no source : clear/invert
+//     // - require no source : clear/invert/remove
+//     //       clear  : clears set or zone
+//     //       invert : select all currently non-selected elements
+//     //       remove : removes set or zone
 //     // - require source    : new/add/delete/subset
+//     //       new    : create new set or zone from source
+//     //       add    : add source to contents
+//     //       delete : deletes source from contents
+//     //       subset : keeps elements both in contents and source
 //     action  new;
 //
 // The source entry varies according to the type of set:
@@ -329,6 +336,7 @@ FoamFile
 //        faceSet f0;       // name of faceSet
 //        cellSet c0;       // name of cellSet of slave side
 //    }
+//
 
 actions
 (

From d1dc882633c9cbf87132d567c5ad2e2242e8461a Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 15 Nov 2011 17:58:43 +0000
Subject: [PATCH 3/5] BUG: ZoneSet: fix inverting functionality

---
 src/meshTools/sets/topoSets/cellZoneSet.C  | 15 ++++++++++++++-
 src/meshTools/sets/topoSets/faceZoneSet.C  | 16 ++++++++++++++--
 src/meshTools/sets/topoSets/pointZoneSet.C | 14 +++++++++++++-
 3 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/src/meshTools/sets/topoSets/cellZoneSet.C b/src/meshTools/sets/topoSets/cellZoneSet.C
index d3498f1998..80528e3192 100644
--- a/src/meshTools/sets/topoSets/cellZoneSet.C
+++ b/src/meshTools/sets/topoSets/cellZoneSet.C
@@ -136,8 +136,21 @@ cellZoneSet::~cellZoneSet()
 
 void cellZoneSet::invert(const label maxLen)
 {
+    // Count
     label n = 0;
 
+    for (label cellI = 0; cellI < maxLen; cellI++)
+    {
+        if (!found(cellI))
+        {
+            n++;
+        }
+    }
+
+    // Fill
+    addressing_.setSize(n);
+    n = 0;
+
     for (label cellI = 0; cellI < maxLen; cellI++)
     {
         if (!found(cellI))
@@ -146,7 +159,7 @@ void cellZoneSet::invert(const label maxLen)
             n++;
         }
     }
-    addressing_.setSize(n);
+
     updateSet();
 }
 
diff --git a/src/meshTools/sets/topoSets/faceZoneSet.C b/src/meshTools/sets/topoSets/faceZoneSet.C
index 5d7cd831db..10d9c0b9bf 100644
--- a/src/meshTools/sets/topoSets/faceZoneSet.C
+++ b/src/meshTools/sets/topoSets/faceZoneSet.C
@@ -141,8 +141,22 @@ faceZoneSet::~faceZoneSet()
 
 void faceZoneSet::invert(const label maxLen)
 {
+    // Count
     label n = 0;
 
+    for (label faceI = 0; faceI < maxLen; faceI++)
+    {
+        if (!found(faceI))
+        {
+            n++;
+        }
+    }
+
+    // Fill
+    addressing_.setSize(n);
+    flipMap_.setSize(n);
+    n = 0;
+
     for (label faceI = 0; faceI < maxLen; faceI++)
     {
         if (!found(faceI))
@@ -152,8 +166,6 @@ void faceZoneSet::invert(const label maxLen)
             n++;
         }
     }
-    addressing_.setSize(n);
-    flipMap_.setSize(n);
     updateSet();
 }
 
diff --git a/src/meshTools/sets/topoSets/pointZoneSet.C b/src/meshTools/sets/topoSets/pointZoneSet.C
index 783cd78431..8a02f718a2 100644
--- a/src/meshTools/sets/topoSets/pointZoneSet.C
+++ b/src/meshTools/sets/topoSets/pointZoneSet.C
@@ -138,8 +138,21 @@ pointZoneSet::~pointZoneSet()
 
 void pointZoneSet::invert(const label maxLen)
 {
+    // Count
     label n = 0;
 
+    for (label pointI = 0; pointI < maxLen; pointI++)
+    {
+        if (!found(pointI))
+        {
+            n++;
+        }
+    }
+
+    // Fill
+    addressing_.setSize(n);
+    n = 0;
+
     for (label pointI = 0; pointI < maxLen; pointI++)
     {
         if (!found(pointI))
@@ -148,7 +161,6 @@ void pointZoneSet::invert(const label maxLen)
             n++;
         }
     }
-    addressing_.setSize(n);
     updateSet();
 }
 

From d6ef1ac9d1090acc7a3e8fa388f1ab71db343291 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 15 Nov 2011 18:18:25 +0000
Subject: [PATCH 4/5] STYLE: snappyHexMeshDict: changed default

---
 .../utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
index 2bbc9b42fc..74d24954aa 100644
--- a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
+++ b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict
@@ -212,7 +212,7 @@ snapControls
     //- 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 1.0;
+    tolerance 2.0;
 
     //- Number of mesh displacement relaxation iterations.
     nSolveIter 30;

From acba38b8aa8cbec73106064d51fb767ed15d6a99 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 16 Nov 2011 11:52:40 +0000
Subject: [PATCH 5/5] ENH: setSet: do not exit upon error if in interactive
 mode

---
 applications/utilities/mesh/manipulation/setSet/setSet.C | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/utilities/mesh/manipulation/setSet/setSet.C b/applications/utilities/mesh/manipulation/setSet/setSet.C
index f512561058..1a47854895 100644
--- a/applications/utilities/mesh/manipulation/setSet/setSet.C
+++ b/applications/utilities/mesh/manipulation/setSet/setSet.C
@@ -1018,7 +1018,7 @@ int main(int argc, char *argv[])
                     is
                 );
 
-                if (!ok)
+                if (!ok && batch)
                 {
                     // Exit with error.
                     quit = true;