ENH: surface: various updates to the surface utilities

surfaceBooleanFeatures: use CGAL for intersection
surfaceCheck: write surface zoning as vtk file
surfaceInflate: new utility to offset surface
surfacePatch: replacement for surfaceAutoPatch. Also does cutting of surfaces.

applications/utilities/surface/surfaceBooleanFeatures/PolyhedronReader/Make/files

@@ -0,0 +1,3 @@
+PolyhedronReader.C
+
+LIB = $(FOAM_LIBBIN)/libPolyhedronReader

applications/utilities/surface/surfaceBooleanFeatures/PolyhedronReader/Make/options

@@ -0,0 +1,25 @@
+EXE_NDEBUG = -DNDEBUG
+/* EXE_NDEBUG = -g -O0 -DFULLDEBUG */
+
+
+c++CGALWARN = -Wno-old-style-cast
+
+/*-- Define CGAL_INEXACT to use inexact CGAL constructions */
+
+include $(GENERAL_RULES)/CGAL
+
+EXE_INC = \
+    ${ROUNDING_MATH} \
+    ${EXE_NDEBUG} \
+    ${CGAL_INC} \
+    ${c++CGALWARN} \
+    -I.. \
+    -I$(FOAM_SRC)/surfMesh/lnInclude \
+    -I$(FOAM_SRC)/triSurface/lnInclude \
+    -I$(LIB_SRC)/edgeMesh/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I/usr/include/Qt
+
+LIB_LIBS = \
+    -L${CGAL_ARCH_PATH}/lib \
+    -ltriSurface

applications/utilities/surface/surfaceBooleanFeatures/PolyhedronReader/PolyhedronReader.C

@@ -0,0 +1,49 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
+     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+-------------------------------------------------------------------------------
+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/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "PolyhedronReader.H"
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::PolyhedronReader::PolyhedronReader(const triSurface& s, Polyhedron& p)
+{
+    Build_triangle<HalfedgeDS> triangle(s);
+    p.delegate(triangle);
+    // Populate index and region
+    Foam::label nTris = 0;
+    for
+    (
+        Facet_iterator fi = p.facets_begin();
+        fi != p.facets_end();
+        ++fi
+    )
+    {
+        fi->index = nTris++;
+        fi->region = s[fi->index].region();
+    }
+}
+
+
+// ************************************************************************* //

applications/utilities/surface/surfaceBooleanFeatures/PolyhedronReader/PolyhedronReader.H

@@ -0,0 +1,101 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
+     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+-------------------------------------------------------------------------------
+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/>.
+
+Class
+    Foam::PolyhedronReader
+
+Description
+
+SourceFiles
+    PolyhedronReader.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef PolyhedronReader_H
+#define PolyhedronReader_H
+
+#include "CGALIndexedPolyhedron.H"
+#include "triSurface.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                      Class PolyhedronReader Declaration
+\*---------------------------------------------------------------------------*/
+
+class PolyhedronReader
+{
+    // Private Classes
+
+        template<class HDS>
+        class Build_triangle
+        :
+            public CGAL::Modifier_base<HDS>
+        {
+            const triSurface& s_;
+
+        public:
+
+            Build_triangle(const triSurface& s);
+
+            void operator()(HDS& hds);
+        };
+
+
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct
+        PolyhedronReader(const PolyhedronReader&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const PolyhedronReader&);
+
+
+public:
+
+    // Constructors
+
+        //- Populate polyhedron from surface
+        PolyhedronReader(const triSurface& s, Polyhedron& p);
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#ifdef NoRepository
+#   include "PolyhedronReaderTemplates.C"
+#endif
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

applications/utilities/surface/surfaceBooleanFeatures/PolyhedronReader/PolyhedronReaderTemplates.C

@@ -0,0 +1,72 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
+     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+-------------------------------------------------------------------------------
+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/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "PolyhedronReader.H"
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+template<class HDS>
+Foam::PolyhedronReader::Build_triangle<HDS>::Build_triangle
+(
+    const triSurface& s
+)
+:
+    s_(s)
+{}
+
+
+// * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * * //
+
+template<class HDS>
+void Foam::PolyhedronReader::Build_triangle<HDS>::operator()(HDS& hds)
+{
+    // Postcondition: hds is a valid polyhedral surface.
+    CGAL::Polyhedron_incremental_builder_3<HDS> B(hds, true);
+
+    B.begin_surface(s_.nPoints(), s_.size());
+
+    typedef typename HDS::Vertex Vertex;
+    typedef typename Vertex::Point Point;
+
+    const Foam::pointField& pts = s_.points();
+    forAll(pts, i)
+    {
+        const Foam::point& pt = pts[i];
+        B.add_vertex(Point(pt.x(), pt.y(), pt.z()));
+    }
+    forAll(s_, i)
+    {
+        const Foam::labelledTri& t = s_[i];
+        B.begin_facet();
+        B.add_vertex_to_facet(t[0]);
+        B.add_vertex_to_facet(t[1]);
+        B.add_vertex_to_facet(t[2]);
+        B.end_facet();
+    }
+    B.end_surface();
+}
+
+
+// ************************************************************************* //