Merge branch 'surface-declutter' into 'develop'

Surface declutter - issue #294

Removing various clutter from surfMesh and triSurface
- unused classes/files (backup copies on non-release repo)
- relocate some triSurface-related classes to where they make more sense, and where they can be reused.
- improve handling of various face types in MeshedSurface and UnsortedMeshedSurface (to bridge the gap to triSurface)
- improve transfer methods for reclaiming/reusing surface allocations

See merge request !77

applications/test/faces/Make/files

+Test-faces.C
+
+EXE = $(FOAM_USER_APPBIN)/Test-faces

src/triSurface/tools/hashSignedLabel/hashSignedLabel.H → applications/test/faces/Test-faces.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,47 +21,64 @@ License
     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::hashSignedLabel
+Application
+    Test-faces
 
 Description
-    hash for signed integers (Hash\<label\> only works for unsigned ints)
+    Simple tests for various faces
 
 \*---------------------------------------------------------------------------*/
 
-#ifndef HashSignedLabel_H
-#define HashSignedLabel_H
+#include "argList.H"
+#include "labelledTri.H"
 
-#include "List.H"
-#include "word.H"
+using namespace Foam;
 
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class hashSignedLabel Declaration
-\*---------------------------------------------------------------------------*/
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
 
-class hashSignedLabel
+int main(int argc, char *argv[])
 {
+    face f1{ 1, 2, 3, 4 };
+    Info<< "face:" << f1 << nl;
 
-public:
+    triFace t1{ 1, 2, 3 };
+    Info<< "triFace:" << t1 << nl;
 
-    hashSignedLabel()
-    {}
+    f1 = t1;
+    Info<< "face:" << f1 << nl;
 
+    f1 = t1.triFaceFace();
+    Info<< "face:" << f1 << nl;
 
-    label operator()(const label key, const label tableSize) const
+    // expect these to fail
+    FatalError.throwExceptions();
+    try
+    {
+        labelledTri l1{ 1, 2, 3, 10, 24 };
+        Info<< "labelled:" << l1 << nl;
+    }
+    catch (Foam::error& err)
     {
-        return mag(key)%tableSize;
+        WarningInFunction
+            << "Caught FatalError " << err << nl << endl;
     }
-};
+    FatalError.dontThrowExceptions();
 
-} // End namespace Foam
+    labelledTri l2{ 1, 2, 3 };
+    Info<< "labelled:" << l2 << nl;
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+    labelledTri l3{ 1, 2, 3, 10 };
+    Info<< "labelled:" << l3 << nl;
 
-#endif
+    t1.flip();
+    l3.flip();
 
-// ************************************************************************* //
+    Info<< "flip:" << t1 << nl;
+    Info<< "flip:" << l3 << nl;
 
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/surface/surfaceMeshConvertTesting/surfaceMeshConvertTesting.C

@@ -41,6 +41,9 @@ Usage
       - \par -orient
         Check face orientation on the input surface
 
+      - \par -testModify
+        Test modification mechanism
+
       - \par -scale \<scale\>
         Specify a scaling factor for writing the files
 
@@ -65,6 +68,7 @@ Note
 #include "PackedBoolList.H"
 
 #include "MeshedSurfaces.H"
+#include "ModifiableMeshedSurface.H"
 #include "UnsortedMeshedSurfaces.H"
 
 #include "IStringStream.H"
@@ -93,6 +97,13 @@ int main(int argc, char *argv[])
         "orient",
         "check surface orientation"
     );
+
+    argList::addBoolOption
+    (
+        "testModify",
+        "Test modification mechanism (MeshedSurface)"
+    );
+
     argList::addBoolOption
     (
         "surfMesh",
@@ -389,6 +400,34 @@ int main(int argc, char *argv[])
             Info<< endl;
         }
 
+        if (args.optionFound("testModify"))
+        {
+            Info<< "Use ModifiableMeshedSurface to shift (1, 0, 0)" << endl;
+            Info<< "original" << nl;
+            surf.writeStats(Info);
+            Info<< endl;
+
+            ModifiableMeshedSurface<face> tsurf(surf.xfer());
+            // ModifiableMeshedSurface<face> tsurf;
+            // tsurf.reset(surf.xfer());
+
+            Info<< "in-progress" << nl;
+            surf.writeStats(Info);
+            Info<< endl;
+
+            tsurf.storedPoints() += vector(1, 0, 0);
+
+            surf.transfer(tsurf);
+
+            Info<< "updated" << nl;
+            surf.writeStats(Info);
+            Info<< endl;
+
+            Info<< "modifier" << nl;
+            tsurf.writeStats(Info);
+            Info<< endl;
+        }
+
         Info<< "writing " << exportName;
         if (scaleFactor <= 0)
         {

etc/controlDict

@@ -794,7 +794,6 @@ DebugSwitches
     surfaceIntersection 0;
     surfaceNormalFixedValue 0;
     surfacePatch        0;
-    surfacePatchIOList  0;
     surfaceScalarField  0;
     surfaceScalarField::Internal 0;
     surfaceSlipDisplacement 0;

src/OpenFOAM/Make/files

@@ -418,6 +418,7 @@ $(cellShape)/cellShapeIOList.C
 
 meshes/Identifiers/patch/patchIdentifier.C
 meshes/Identifiers/patch/coupleGroupIdentifier.C
+meshes/Identifiers/surface/surfZoneIdentifier.C
 
 meshes/MeshObject/meshObject.C
 

src/surfMesh/surfZone/surfZoneIdentifier/surfZoneIdentifier.C → src/OpenFOAM/meshes/Identifiers/surface/surfZoneIdentifier.C

@@ -97,14 +97,11 @@ Foam::surfZoneIdentifier::~surfZoneIdentifier()
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-
 void Foam::surfZoneIdentifier::write(Ostream& os) const
 {
     if (geometricType_.size())
     {
-        os.writeKeyword("geometricType")
-            << geometricType_
-            << token::END_STATEMENT << nl;
+        os.writeEntry("geometricType", geometricType_);
     }
 }
 
@@ -112,7 +109,6 @@ void Foam::surfZoneIdentifier::write(Ostream& os) const
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 // needed for list output
-
 bool Foam::surfZoneIdentifier::operator!=
 (
     const surfZoneIdentifier& rhs
@@ -129,8 +125,9 @@ bool Foam::surfZoneIdentifier::operator==
 {
     return
     (
-        name() == rhs.name()
-     && geometricType() == rhs.geometricType()
+        (index() == rhs.index())
+     && (name()  == rhs.name())
+     && (geometricType() == rhs.geometricType())
     );
 }
 
@@ -139,8 +136,7 @@ bool Foam::surfZoneIdentifier::operator==
 
 Foam::Istream& Foam::operator>>(Istream& is, surfZoneIdentifier& obj)
 {
-    is  >> obj.name_
-        >> obj.geometricType_;
+    is >> obj.name_ >> obj.geometricType_;
 
     return is;
 }
@@ -148,7 +144,8 @@ Foam::Istream& Foam::operator>>(Istream& is, surfZoneIdentifier& obj)
 
 Foam::Ostream& Foam::operator<<(Ostream& os, const surfZoneIdentifier& obj)
 {
-    os  << obj.name_ << ' ' << obj.geometricType_;
+    // newlines to separate, since that is what triSurface currently expects
+    os  << nl << obj.name_ << nl << obj.geometricType_;
 
     os.check("Ostream& operator<<(Ostream&, const surfZoneIdentifier&)");
     return os;

src/surfMesh/surfZone/surfZoneIdentifier/surfZoneIdentifier.H → src/OpenFOAM/meshes/Identifiers/surface/surfZoneIdentifier.H

@@ -40,7 +40,6 @@ SourceFiles
 
 #include "word.H"
 #include "label.H"
-#include "typeInfo.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -56,7 +55,7 @@ Istream& operator>>(Istream&, surfZoneIdentifier&);
 Ostream& operator<<(Ostream&, const surfZoneIdentifier&);
 
 /*---------------------------------------------------------------------------*\
-                    Class surfZoneIdentifier Declaration
+                     Class surfZoneIdentifier Declaration
 \*---------------------------------------------------------------------------*/
 
 class surfZoneIdentifier

src/OpenFOAM/meshes/meshShapes/face/face.H

@@ -155,8 +155,8 @@ public:
         //- Construct from list of labels
         explicit inline face(const labelUList&);
 
-        //- Construct from list of labels
-        explicit inline face(const labelList&);
+        //- Construct from an initializer list of labels
+        explicit inline face(std::initializer_list<label>);
 
         //- Construct by transferring the parameter contents
         explicit inline face(const Xfer<labelList>&);

src/OpenFOAM/meshes/meshShapes/face/faceI.H

@@ -57,7 +57,7 @@ inline Foam::face::face(const labelUList& lst)
 {}
 
 
-inline Foam::face::face(const labelList& lst)
+inline Foam::face::face(std::initializer_list<label> lst)
 :
     labelList(lst)
 {}
@@ -79,7 +79,7 @@ inline Foam::face::face(Istream& is)
 
 inline Foam::pointField Foam::face::points(const pointField& meshPoints) const
 {
-    // There are as many points as there labels for them
+    // There are as many points as there are labels for them
     pointField p(size());
 
     // For each point in list, set it to the point in 'pnts' addressed

src/OpenFOAM/meshes/meshShapes/face/faceListFwd.H

@@ -43,8 +43,6 @@ namespace Foam
     typedef List<face> faceList;
     typedef SubList<face> faceSubList;
     typedef List<faceList> faceListList;
-    // same as faceUList:
-    typedef UList<face> unallocFaceList;
 }
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

src/triSurface/tools/labelledTri/labelledTri.H → src/OpenFOAM/meshes/meshShapes/labelledTri/labelledTri.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -64,29 +64,44 @@ class labelledTri
         label region_;
 
 
+    // Private Member Functions
+
+        //- Assign from a list of 3 or 4 labels.
+        //  Default region is 0.
+        inline void assign(const labelUList&);
+
 public:
 
     // Constructors
 
-        //- Construct null
+        //- Construct null with invalid point labels and region (-1).
         inline labelledTri();
 
-        //- Construct from triFace and a region label
+        //- Construct from triFace and region label.
+        //  Default region is 0 if not specified.
         inline labelledTri
         (
             const triFace&,
-            const label region
+            const label region = 0
         );
 
-        //- Construct from three point labels and a region label
+        //- Construct from three point labels and a region label.
+        //  Default region is 0 if not specified.
         inline labelledTri
         (
             const label a,
             const label b,
             const label c,
-            const label region
+            const label region = 0
         );
 
+        //- Construct from a list of 3 or 4 labels.
+        //  Default region is 0.
+        explicit inline labelledTri(const labelUList&);
+
+        //- Construct from an initializer list of 3 or 4 labels.
+        explicit inline labelledTri(std::initializer_list<label>);
+
         //- Construct from Istream
         inline labelledTri(Istream&);
 
@@ -102,17 +117,6 @@ public:
             inline label& region();
 
 
-        // Check
-
-        // Edit
-
-        // Write
-
-
-    // Friend Functions
-
-    // Friend Operators
-
     // IOstream Operators
 
         inline friend Istream& operator>>(Istream&, labelledTri&);

src/triSurface/tools/labelledTri/labelledTriI.H → src/OpenFOAM/meshes/meshShapes/labelledTri/labelledTriI.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -25,10 +25,34 @@ License
 
 #include "IOstreams.H"
 
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+inline void Foam::labelledTri::assign(const labelUList& lst)
+{
+    const label sz = lst.size();
+
+    // checkSize
+    if (sz < 3 || sz > 4)
+    {
+         FatalErrorInFunction
+            << "size " << sz << " != (3 or 4)"
+            << abort(FatalError);
+    }
+
+    for (label i=0; i<3; ++i)
+    {
+        operator[](i) = lst[i];
+    }
+
+    region_ = (sz > 3 ? lst[3] : 0);
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 inline Foam::labelledTri::labelledTri()
 :
+    triFace(),
     region_(-1)
 {}
 
@@ -57,6 +81,24 @@ inline Foam::labelledTri::labelledTri
 {}
 
 
+inline Foam::labelledTri::labelledTri(const labelUList& lst)
+:
+    triFace(),
+    region_(0)
+{
+    assign(lst);
+}
+
+
+inline Foam::labelledTri::labelledTri(std::initializer_list<label> initLst)
+:
+    triFace(),
+    region_(0)
+{
+    assign(labelList(initLst));
+}
+
+
 inline Foam::labelledTri::labelledTri(Istream& is)
 {
     operator>>(is, *this);

src/OpenFOAM/meshes/meshShapes/triFace/triFace.H

@@ -75,7 +75,7 @@ public:
 
     // Constructors
 
-        //- Construct null
+        //- Construct null with invalid point labels (-1)
         inline triFace();
 
         //- Construct from three point labels
@@ -86,9 +86,12 @@ public:
             const label c
         );
 
-        //- Construct from a list of labels
+        //- Construct from a list of 3 labels.
         explicit inline triFace(const labelUList&);
 
+        //- Construct from an initializer list of 3 labels
+        explicit inline triFace(std::initializer_list<label>);
+
         //- Construct from Istream
         inline triFace(Istream&);
 

src/OpenFOAM/meshes/meshShapes/triFace/triFaceI.H

@@ -62,6 +62,8 @@ inline int Foam::triFace::compare(const triFace& a, const triFace& b)
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 inline Foam::triFace::triFace()
+:
+    FixedList<label, 3>(-1)
 {}
 
 
@@ -84,6 +86,12 @@ inline Foam::triFace::triFace(const labelUList& lst)
 {}
 
 
+inline Foam::triFace::triFace(std::initializer_list<label> lst)
+:
+    FixedList<label, 3>(lst)
+{}
+
+
 inline Foam::triFace::triFace(Istream& is)
 :
     FixedList<label, 3>(is)

src/fileFormats/Make/files

@@ -10,6 +10,9 @@ ensight/type/ensightPTraits.C
 nas/NASCore.C
 fire/FIRECore.C
 starcd/STARCDCore.C
+stl/STLCore.C
+stl/STLReader.C
+stl/STLReaderASCII.L
 
 vtk/foamVtkCore.C
 vtk/format/foamVtkAppendBase64Formatter.C

src/surfMesh/surfaceFormats/stl/STLsurfaceFormatCore.C → src/fileFormats/stl/STLCore.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -23,36 +23,75 @@ License
 
 \*---------------------------------------------------------------------------*/
 
-#include "STLsurfaceFormatCore.H"
+#include "STLCore.H"
 #include "gzstream.h"
 #include "OSspecific.H"
-#include "Map.H"
 #include "IFstream.H"
-#include "Ostream.H"
 
-#undef DEBUG_STLBINARY
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+//! \cond fileScope
 
-// check binary by getting the header and number of facets
+//  The number of bytes in the STL binary header
+static const unsigned STLHeaderSize = 80;
+
+//! \endcond
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::fileFormats::STLCore::STLCore()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+bool Foam::fileFormats::STLCore::isBinaryName
+(
+    const fileName& filename,
+    const STLFormat& format
+)
+{
+    return (format == DETECT ? (filename.ext() == "stlb") : format == BINARY);
+}
+
+
+// Check binary by getting the header and number of facets
 // this seems to work better than the old token-based method
 // - some programs (eg, pro-STAR) have 'solid' as the first word in
 //   the binary header.
 // - using wordToken can cause an abort if non-word (binary) content
 //   is detected ... this is not exactly what we want.
-int Foam::fileFormats::STLsurfaceFormatCore::detectBINARY
+int Foam::fileFormats::STLCore::detectBinaryHeader
 (
     const fileName& filename
 )
 {
-    off_t dataFileSize = Foam::fileSize(filename);
+    bool compressed = false;
+    autoPtr<istream> streamPtr
+    (
+        new ifstream(filename.c_str(), std::ios::binary)
+    );
+
+    // If the file is compressed, decompress it before further checking.
+    if (!streamPtr->good() && isFile(filename + ".gz", false))
+    {
+        compressed = true;
+        streamPtr.reset(new igzstream((filename + ".gz").c_str()));
+    }
+    istream& is = streamPtr();
 
-    IFstream str(filename, IOstream::BINARY);
-    istream& is = str().stdStream();
+    if (!is.good())
+    {
+        FatalErrorInFunction
+            << "Cannot read file " << filename
+            << " or file " << filename + ".gz"
+            << exit(FatalError);
+    }
 
     // Read the STL header
-    char header[headerSize];
-    is.read(header, headerSize);
+    char header[STLHeaderSize];
+    is.read(header, STLHeaderSize);
 
     // Check that stream is OK, if not this may be an ASCII file
     if (!is.good())
@@ -60,7 +99,7 @@ int Foam::fileFormats::STLsurfaceFormatCore::detectBINARY
         return 0;
     }
 
-    // Read the number of triangles in the STl file
+    // Read the number of triangles in the STL file
     // (note: read as int so we can check whether >2^31)
     int nTris;
     is.read(reinterpret_cast<char*>(&nTris), sizeof(unsigned int));
@@ -74,33 +113,73 @@ int Foam::fileFormats::STLsurfaceFormatCore::detectBINARY
     (
         !is
      || nTris < 0
-     || nTris < (dataFileSize - headerSize)/50
-     || nTris > (dataFileSize - headerSize)/25