Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

.gitignore

@@ -49,6 +49,9 @@ doc/[Dd]oxygen/man
 *.tar.gz
 *.tgz
 
+# ignore the persistent .build tag in the main directory
+/.build
+
 # ignore .timeStamp in the main directory
 /.timeStamp
 

applications/solvers/combustion/PDRFoam/PDRModels/XiEqModels/basicXiSubXiEq/basicXiSubXiEq.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    basicSubGrid
+    Foam::XiEqModels::basicSubGrid
 
 Description
     Basic sub-grid obstacle flame-wrinking enhancement factor model.

applications/solvers/combustion/PDRFoam/PDRModels/XiGModels/basicXiSubG/basicXiSubG.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    basicSubGrid
+    Foam::XiGModel::basicSubGrid
 
 
 Description

applications/solvers/combustion/PDRFoam/PDRModels/dragModels/PDRDragModel/PDRDragModel.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    PDRDragModel
+    Foam::PDRDragModel
 
 Description
     Base-class for sub-grid obstacle drag models.

applications/solvers/combustion/PDRFoam/PDRModels/dragModels/basic/basic.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    basic
+    Foam::PDRDragModels::basic
 
 Description
     Basic sub-grid obstacle drag model.

applications/solvers/combustion/PDRFoam/PDRModels/turbulence/PDRkEpsilon/PDRkEpsilon.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    PDRkEpsilon
+    Foam::compressible::RASModels::PDRkEpsilon
 
 Description
     Standard k-epsilon turbulence model with additional source terms

applications/solvers/combustion/PDRFoam/XiModels/XiEqModels/Gulder/Gulder.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Gulder
+    Foam::XiEqModels::Gulder
 
 Description
     Simple Gulder model for XiEq based on Gulders correlation

applications/solvers/combustion/PDRFoam/XiModels/XiEqModels/SCOPEBlendXiEq/SCOPEBlendXiEq.H

@@ -23,10 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    SCOPEBlend
+    Foam::XiEqModels::SCOPEBlend
 
 Description
-    
+
 SourceFiles
     SCOPEBlend.C
 

applications/solvers/combustion/PDRFoam/XiModels/XiEqModels/SCOPEXiEq/SCOPEXiEq.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    SCOPEXiEq
+    Foam::XiEqModel::SCOPEXiEq
 
 Description
     Simple SCOPEXiEq model for XiEq based on SCOPEXiEqs correlation

applications/solvers/combustion/PDRFoam/XiModels/XiEqModels/XiEqModel/XiEqModel.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    XiEqModel
+    Foam::XiEqModel
 
 Description
     Base-class for all XiEq models used by the b-XiEq combustion model.

applications/solvers/combustion/PDRFoam/XiModels/XiEqModels/instabilityXiEq/instabilityXiEq.H

@@ -23,10 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    instability
+    Foam::XiEqModels::instability
 
 Description
-    
+
 SourceFiles
     instability.C
 

applications/solvers/combustion/PDRFoam/XiModels/XiGModels/KTS/KTS.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    KTS
+    Foam::XiGModels::KTS
 
 Description
     Simple Kolmogorov time-scale model for the flame-wrinling generation rate.

applications/solvers/combustion/PDRFoam/XiModels/XiGModels/XiGModel/XiGModel.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    XiGModel
+    Foam::XiGModel
 
 Description
     Base-class for all Xi generation models used by the b-Xi combustion model.

applications/solvers/combustion/PDRFoam/XiModels/XiGModels/instabilityG/instabilityG.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    instabilityG
+    Foam::XiGModels::instabilityG
 
 Description
     Flame-surface instabilityG flame-wrinking generation rate coefficient model.

applications/solvers/combustion/PDRFoam/XiModels/XiModel/XiModel.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    XiModel
+    Foam::XiModel
 
 Description
     Base-class for all Xi models used by the b-Xi combustion model.
@@ -102,8 +102,6 @@ namespace Foam
                           Class XiModel Declaration
 \*---------------------------------------------------------------------------*/
 
-
-
 class XiModel
 {
 

applications/solvers/combustion/PDRFoam/XiModels/algebraic/algebraic.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    algebraic
+    Foam::XiModels::algebraic
 
 Description
     Simple algebraic model for Xi based on Gulders correlation

applications/solvers/combustion/PDRFoam/XiModels/fixed/fixed.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    fixed
+    Foam::XiModels::fixed
 
 Description
     Fixed value model for Xi.

applications/solvers/combustion/PDRFoam/XiModels/transport/transport.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    transport
+    Foam::XiModels::transport
 
 Description
     Simple transport model for Xi based on Gulders correlation

applications/solvers/combustion/PDRFoam/laminarFlameSpeed/SCOPE/SCOPELaminarFlameSpeed.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    SCOPE
+    Foam::laminarFlameSpeedModels::SCOPE
 
 Description
     Laminar flame speed obtained from the SCOPE correlation.

applications/solvers/multiphase/compressibleInterDyMFoam/compressibleInterDyMFoam.C

@@ -74,24 +74,26 @@ int main(int argc, char *argv[])
 
         Info<< "Time = " << runTime.timeName() << nl << endl;
 
-        scalar timeBeforeMeshUpdate = runTime.elapsedCpuTime();
-
-        // Do any mesh changes
-        mesh.update();
-
-        if (mesh.changing())
         {
-            Info<< "Execution time for mesh.update() = "
+            // Store divU from the previous mesh for the correctPhi
-                << runTime.elapsedCpuTime() - timeBeforeMeshUpdate
+            volScalarField divU = fvc::div(phi);
-                << " s" << endl;
 
-            gh = g & mesh.C();
+            scalar timeBeforeMeshUpdate = runTime.elapsedCpuTime();
-            ghf = g & mesh.Cf();
-        }
 
-        if (mesh.changing() && correctPhi)
+            // Do any mesh changes
-        {
+            mesh.update();
-            //***HGW#include "correctPhi.H"
+
+            if (mesh.changing())
+            {
+                Info<< "Execution time for mesh.update() = "
+                    << runTime.elapsedCpuTime() - timeBeforeMeshUpdate
+                    << " s" << endl;
+            }
+
+            if (mesh.changing() && correctPhi)
+            {
+                #include "correctPhi.H"
+            }
         }
 
         // Make the fluxes relative to the mesh motion
@@ -102,6 +104,12 @@ int main(int argc, char *argv[])
             #include "meshCourantNo.H"
         }
 
+        if (mesh.changing())
+        {
+            gh = g & mesh.C();
+            ghf = g & mesh.Cf();
+        }
+
         turbulence->correct();
 
         // --- Outer-corrector loop

applications/solvers/multiphase/compressibleInterDyMFoam/correctPhi.H

@@ -0,0 +1,39 @@
+{
+    #include "continuityErrs.H"
+
+    volScalarField pcorr
+    (
+        IOobject
+        (
+            "pcorr",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
+        mesh,
+        dimensionedScalar("pcorr", pd.dimensions(), 0.0),
+        pcorrTypes
+    );
+
+    dimensionedScalar rAUf("(1|A(U))", dimTime/rho.dimensions(), 1.0);
+
+    adjustPhi(phi, U, pcorr);
+
+    for(int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
+    {
+        fvScalarMatrix pcorrEqn
+        (
+            fvm::laplacian(rAUf, pcorr) == fvc::div(phi) - divU
+        );
+
+        pcorrEqn.solve();
+
+        if (nonOrth == nNonOrthCorr)
+        {
+            phi -= pcorrEqn.flux();
+        }
+    }
+
+    #include "continuityErrs.H"
+}

applications/solvers/multiphase/compressibleInterDyMFoam/createFields.H

@@ -150,3 +150,14 @@
     (
         incompressible::turbulenceModel::New(U, phi, twoPhaseProperties)
     );
+
+
+    wordList pcorrTypes(pd.boundaryField().types());
+
+    for (label i=0; i<pd.boundaryField().size(); i++)
+    {
+        if (pd.boundaryField()[i].fixesValue())
+        {
+            pcorrTypes[i] = fixedValueFvPatchScalarField::typeName;
+        }
+    }

applications/solvers/multiphase/compressibleInterDyMFoam/pEqn.H

@@ -21,7 +21,7 @@
     surfaceScalarField phiU
     (
         "phiU",
-        (fvc::interpolate(U) & mesh.Sf()) + fvc::ddtPhiCorr(rUA, rho, U, phi)
+        (fvc::interpolate(U) & mesh.Sf())
     );
 
     phi = phiU +

applications/test/DLList/DLListTest.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    
+
 Description
 
 \*---------------------------------------------------------------------------*/
@@ -48,7 +48,6 @@ int main(int argc, char *argv[])
     }
 
     myList.append(100.3);
-
     myList.append(500.3);
 
     Info<< nl << "And again using STL iterator: " << nl << endl;
@@ -120,7 +119,18 @@ int main(int argc, char *argv[])
         Info<< "element:" << *iter << endl;
     }
 
-    Info<< nl << "Bye." << endl;
+
+    Info<< nl << "Testing transfer: " << nl << endl;
+    Info<< "original: " << myList << endl;
+
+    DLList<scalar> newList;
+    newList.transfer(myList);
+
+    Info<< nl << "source: " << myList << nl
+        << nl << "target: " << newList << endl;
+
+
+    Info<< nl << "Done." << endl;
     return 0;
 }
 

applications/test/Dictionary/DictionaryTest.C

@@ -23,15 +23,18 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    
+
 Description
 
 \*---------------------------------------------------------------------------*/
 
 #include "OSspecific.H"
 
+#include "scalar.H"
+
 #include "IOstreams.H"
 #include "Dictionary.H"
+#include "PtrDictionary.H"
 
 using namespace Foam;
 
@@ -63,6 +66,36 @@ public:
 };
 
 
+class Scalar
+{
+    scalar data_;
+
+public:
+
+    Scalar()
+    :
+        data_(0)
+    {}
+
+    Scalar(scalar val)
+    :
+        data_(val)
+    {}
+
+    ~Scalar()
+    {
+        Info <<"delete Scalar: " << data_ << endl;
+    }
+
+    friend Ostream& operator<<(Ostream& os, const Scalar& val)
+    {
+        os << val.data_;
+        return os;
+    }
+};
+
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 //  Main program:
 
@@ -92,12 +125,11 @@ int main(int argc, char *argv[])
         Info<< "element : " << *iter;
     }
 
-    Info<< dict.toc() << endl;
+    Info<< "keys: " << dict.toc() << endl;
 
     delete dictPtr;
 
-    dictPtr = new Dictionary<ent>;
+    Dictionary<ent> dict2;
-    Dictionary<ent>& dict2 = *dictPtr;
 
     for (int i = 0; i<10; i++)
     {
@@ -106,9 +138,79 @@ int main(int argc, char *argv[])
         dict2.swapUp(ePtr);
     }
 
-    Info<< dict2 << endl;
+    Info<< "dict:\n" << dict2 << endl;
 
-    Info<< nl << "Bye." << endl;
+    Info<< nl << "Testing transfer: " << nl << endl;
+    Info<< "original: " << dict2 << endl;
+
+    Dictionary<ent> newDict;
+    newDict.transfer(dict2);
+
+    Info<< nl << "source: " << dict2 << nl
+        << "keys: " << dict2.toc() << nl
+        << "target: " << newDict << nl
+        << "keys: " << newDict.toc() << endl;
+
+
+    PtrDictionary<Scalar> scalarDict;
+    for (int i = 0; i<10; i++)
+    {
+        word key("ent" + name(i));
+        scalarDict.insert(key, new Scalar(1.3*i));
+    }
+
+    Info<< nl << "scalarDict1: " << endl;
+    for
+    (
+        PtrDictionary<Scalar>::const_iterator iter = scalarDict.begin();
+        iter != scalarDict.end();
+        ++iter
+    )
+    {
+        Info<< " = " << iter() << endl;
+    }
+    
+    PtrDictionary<Scalar> scalarDict2;
+    for (int i = 8; i<15; i++)
+    {
+        word key("ent" + name(i));
+        scalarDict2.insert(key, new Scalar(1.3*i));
+    }
+    Info<< nl << "scalarDict2: " << endl;
+    for
+    (
+        PtrDictionary<Scalar>::const_iterator iter = scalarDict2.begin();
+        iter != scalarDict2.end();
+        ++iter
+    )
+    {
+        Info<< "elem = " << *iter << endl;
+    }
+    
+    scalarDict.transfer(scalarDict2);
+
+    
+    Scalar* p = scalarDict.lookupPtr("ent8");
+    
+    // This does not (yet) work
+    // Scalar* q = scalarDict.remove("ent10");
+
+    if (p)
+    {
+        Info << "found: " << *p << endl;
+    }
+    else
+    {
+        Info << "no p: " << endl;
+    }
+
+    scalarDict.clear();
+
+    // Info<< " = " << *iter << endl;
+
+
+
+    Info<< nl << "Done." << endl;
     return 0;
 }
 

applications/test/ISLList/ISLListTest.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    
+
 Description
 
 \*---------------------------------------------------------------------------*/
@@ -52,6 +52,13 @@ public:
     :
         data_(s)
     {}
+
+    friend Ostream& operator<<(Ostream& os, const Scalar& s)
+    {
+        os << s.data_;
+        return os;
+    }
+
 };
 
 
@@ -68,10 +75,8 @@ int main(int argc, char *argv[])
     }
 
     myList.append(new Scalar(100.3));
-
     myList.append(new Scalar(500.3));
 
-
     Info<< nl << "And again using STL iterator: " << nl << endl;
 
     for
@@ -99,6 +104,15 @@ int main(int argc, char *argv[])
     }
 
 
+    Info<< nl << "Testing transfer: " << nl << endl;
+    Info<< "original: " << myList << endl;
+
+    ISLList<Scalar> newList;
+    newList.transfer(myList);
+
+    Info<< nl << "source: " << myList << nl
+        << nl << "target: " << newList << endl;
+
     Info<< nl << "Bye." << endl;
     return 0;
 }

applications/test/NamedEnum/Make/files

@@ -1,4 +1,3 @@
-
 namedEnumTest.C
 
-EXE = $(FOAM_APPBIN)/NamedEnum
+EXE = $(FOAM_USER_APPBIN)/NamedEnum

applications/test/PtrList/Make/files

@@ -0,0 +1,3 @@
+PtrListTest.C
+
+EXE = $(FOAM_USER_APPBIN)/PtrListTest

applications/test/PtrList/PtrListTest.C

@@ -0,0 +1,112 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+
+Description
+
+\*---------------------------------------------------------------------------*/
+
+#include "OSspecific.H"
+
+#include "scalar.H"
+#include "IOstreams.H"
+#include "PtrList.H"
+
+using namespace Foam;
+
+class Scalar
+{
+    scalar data_;
+
+public:
+
+    Scalar()
+    :
+        data_(0)
+    {}
+
+    Scalar(scalar val)
+    :
+        data_(val)
+    {}
+
+    ~Scalar()
+    {
+        Info <<"delete Scalar: " << data_ << endl;
+    }
+
+    friend Ostream& operator<<(Ostream& os, const Scalar& val)
+    {
+        os << val.data_;
+        return os;
+    }
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    PtrList<Scalar> list1(10);
+    PtrList<Scalar> list2(15);
+
+    forAll(list1, i)
+    {
+        list1.set(i, new Scalar(1.3*i));
+    }
+
+    forAll(list2, i)
+    {
+        list2.set(i, new Scalar(10 + 1.3*i));
+    }
+
+
+    Info<<"list1: " << list1 << endl;
+    Info<<"list2: " << list2 << endl;
+
+    Info<<"indirectly delete some items via set(.., 0) :" << endl;
+    for (label i = 0; i < 3; i++)
+    {
+        list1.set(i, 0);
+    }
+
+    Info<<"transfer list2 -> list1:" << endl;
+    list1.transfer(list2);
+
+    Info<<"list1: " << list1 << endl;
+    Info<<"list2: " << list2 << endl;
+
+    Info<<"indirectly delete some items via setSize :" << endl;
+    list1.setSize(4);
+
+    Info<<"list1: " << list1 << endl;
+
+    Info<< nl << "Done." << endl;
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/test/SLList/SLListTest.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    
+
 Description
 
 \*---------------------------------------------------------------------------*/
@@ -48,10 +48,8 @@ int main(int argc, char *argv[])
     }
 
     myList.append(100.3);
-
     myList.append(500.3);
 
-
     Info<< nl << "And again using STL iterator: " << nl << endl;
 
     for
@@ -99,7 +97,27 @@ int main(int argc, char *argv[])
         Info<< "element:" << *iter2 << endl;
     }
 
-    Info<< nl << "Bye." << endl;
+
+
+    for (int i = 0; i<10; i++)
+    {
+        myList.append(1.3*i);
+    }
+
+    myList.append(100.3);
+    myList.append(500.3);
+
+    Info<< nl << "Testing transfer: " << nl << endl;
+    Info<< "original: " << myList << endl;
+
+    SLList<scalar> newList;
+    newList.transfer(myList);
+
+    Info<< nl << "source: " << myList << nl
+        << nl << "target: " << newList << endl;
+
+
+    Info<< nl << "Done." << endl;
     return 0;
 }
 

applications/test/UDictionary/UDictionaryTest.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    
+
 Description
 
 \*---------------------------------------------------------------------------*/
@@ -113,7 +113,20 @@ int main(int argc, char *argv[])
 
     Info<< dict2 << endl;
 
-    Info<< nl << "Bye." << endl;
+
+    Info<< nl << "Testing transfer: " << nl << endl;
+    Info<< "original: " << dict2 << endl;
+
+    UDictionary<ent> newDict;
+    newDict.transfer(dict2);
+
+    Info<< nl << "source: " << dict2 << nl
+        << "keys: " << dict2.toc() << nl
+        << "target: " << newDict << nl
+        << "keys: " << newDict.toc() << endl;
+
+    Info<< nl << "Done." << endl;
+
     return 0;
 }
 

applications/test/callback/Make/files

@@ -1,3 +1,3 @@
 callbackTest.C
 
-EXE = $(FOAM_APPBIN)/callbackTest
+EXE = $(FOAM_USER_APPBIN)/callbackTest

applications/test/dataEntry/Make/files

@@ -1,3 +1,3 @@
 testDataEntry.C
 
-EXE = $(FOAM_APPBIN)/testDataEntry
+EXE = $(FOAM_USER_APPBIN)/testDataEntry

applications/test/dictionary/dictionaryTest.C

@@ -30,6 +30,7 @@ Description
 \*---------------------------------------------------------------------------*/
 
 #include "IOstreams.H"
+#include "IOobject.H"
 #include "IFstream.H"
 #include "dictionary.H"
 
@@ -40,30 +41,46 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    IFstream dictStream("testDict");
+    {
-    dictionary testDict(dictStream);
+        dictionary dict(IFstream("testDict")());
+        Info<< "dict: " << dict << nl
+            << "toc: " << dict.toc() << nl
+            << "keys: " << dict.keys() << nl
+            << "patterns: " << dict.keys(true) << endl;
+    }
 
-    Info<< testDict << endl;
+
+    IOobject::writeDivider(Info);
 
     {
-        dictionary someDict;
+        dictionary dict(IFstream("testDictRegex")());
-        someDict.add(keyType("a.*", true), "subdictValue");
+        dict.add(keyType("fooba[rz]", true), "anything");
 
-        dictionary dict;
+        Info<< "dict:" << dict << nl
-        dict.add("someDict", someDict);
+            << "toc: " << dict.toc() << nl
-        dict.add(keyType(".*", true), "parentValue");
+            << "keys: " << dict.keys() << nl
+            << "patterns: " << dict.keys(true) << endl;
 
-        Info<< "dict:" << dict << endl;
+        Info<< "Pattern find \"abc\" in top directory : "
-
-        // Wildcard find.
-        Info<< "Wildcard find \"abc\" in top directory : "
             << dict.lookup("abc") << endl;
-        Info<< "Wildcard find \"abc\" in sub directory : "
+        Info<< "Pattern find \"abc\" in sub directory : "
             << dict.subDict("someDict").lookup("abc")
             << endl;
-        Info<< "Recursive wildcard find \"def\" in sub directory : "
+        Info<< "Recursive pattern find \"def\" in sub directory : "
             << dict.subDict("someDict").lookup("def", true)
             << endl;
+        Info<< "Recursive pattern find \"foo\" in sub directory : "
+            << dict.subDict("someDict").lookup("foo", true)
+            << endl;
+        Info<< "Recursive pattern find \"fooz\" in sub directory : "
+            << dict.subDict("someDict").lookup("fooz", true)
+            << endl;
+        Info<< "Recursive pattern find \"bar\" in sub directory : "
+            << dict.subDict("someDict").lookup("bar", true)
+            << endl;
+        Info<< "Recursive pattern find \"xxx\" in sub directory : "
+            << dict.subDict("someDict").lookup("xxx", true)
+            << endl;
     }
 
     return 0;

applications/test/dictionary/testDictRegex

@@ -0,0 +1,36 @@
+/*-------------------------------*- C++ -*---------------------------------*\
+|    =========                                                              |
+|    \\      /     OpenFOAM                                                 |
+|     \\    /                                                               |
+|      \\  /       The Open Source CFD Toolbox                              |
+|       \\/                                        http://www.OpenFOAM.org  |
+\*-------------------------------------------------------------------------*/
+FoamFile
+{
+    version         2.0;
+    format          ascii;
+    class           dictionary;
+    object          testDictRegex;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+#inputMode  merge
+
+".*"        parentValue1;
+"[n-z].*"   parentValue2;
+"f.*"       parentValue3;
+keyX        parentValue4;
+keyY        parentValue5;
+
+"(.*)Dict"
+{
+    foo         subdictValue0;
+    bar         $f.*;         // should this really match 'foo'?
+
+    // result is dependent on insert order!
+    "a.*c"      subdictValue3;
+    "ab.*"      subdictValue2;
+    "a.*"       subdictValue1;
+    abcd        \1;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/test/fileName/fileNameTest.C

@@ -32,6 +32,7 @@ Description
 
 #include "fileName.H"
 #include "IOstreams.H"
+#include "OSspecific.H"
 
 using namespace Foam;
 
@@ -57,7 +58,16 @@ int main()
     Info<< "pathName.components() = " << pathName.components() << endl;
     Info<< "pathName.component(2) = " << pathName.component(2) << endl;
 
-    Info<< "end" << endl;
+
+    // test findEtcFile
+    Info<< "\n\nfindEtcFile tests:" << nl
+        << " controlDict => " << findEtcFile("controlDict") << nl
+        << " badName => " << findEtcFile("badName") << endl;
+    Info<< "This should emit a fatal error:" << endl;
+    Info<< " badName(die) => " << findEtcFile("badName", true) << nl
+        << endl;
+
+    Info<< "\nEnd" << endl;
 
     return 0;
 }

applications/test/findTimes/findTimes.C

@@ -28,6 +28,7 @@ Description
 
 #include "argList.H"
 #include "Time.H"
+#include "timeSelector.H"
 
 using namespace Foam;
 
@@ -36,13 +37,19 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
+    argList::noParallel();
+    // timeSelector::addOptions();
+    timeSelector::addOptions(true, true);
 
 #   include "setRootCase.H"
 #   include "createTime.H"
 
-    Info<< runTime.times() << endl;
+    Info<< "Times found:" << runTime.times() << endl;
 
-    Info << "End\n" << endl;
+    instantList timeDirs = timeSelector::select0(runTime, args);
+
+    Info<< "Times selected:" << timeDirs << endl;
+    Info<< "\nEnd\n" << endl;
 
     return 0;
 }

applications/test/getRoots/Make/files

@@ -1,2 +0,0 @@
-getRoots.C
-EXE = $(FOAM_USER_APPBIN)/getRoots

applications/test/getRoots/Make/options

@@ -1,2 +0,0 @@
-/* EXE_INC = -I$(LIB_SRC)/finiteVolume/lnInclude */
-/* EXE_LIBS = -lfiniteVolume */

applications/test/getRoots/getRoots.C

@@ -1,30 +0,0 @@
-#include "dictionary.H"
-#include "fileNameList.H"
-#include "IFstream.H"
-#include "OSspecific.H"
-
-using namespace Foam;
-
-int main()
-{
-    Info << "\nReading Roots" << endl;
-
-    IFstream rootsFile(home()/".foam/apps/openDX/roots");
-    fileNameList rootsList(dictionary(rootsFile).lookup("roots"));
-
-    char** rootsStrings = new char*[rootsList.size() + 1];
-    rootsStrings[rootsList.size()] = 0;
-
-    if (rootsList.size())
-    {
-        for (int i=0; i<rootsList.size(); i++)
-        {
-            rootsStrings[i] = new char[rootsList[i].size() + 1];
-            strcpy(rootsStrings[i], rootsList[i].c_str());
-
-            Info<< rootsStrings[i] << endl;
-        }
-    }
-
-    return 0;
-}

applications/test/hmm/Make/files

@@ -1,4 +0,0 @@
-calcEntry/calcEntry.C
-dictionaryTest.C
-
-EXE = $(FOAM_USER_APPBIN)/dictionaryTest

applications/test/hmm/testDict

@@ -1,55 +0,0 @@
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          testDict;
-}
-
-
-dimensions      [ 0 2 -2 0 0 0 0 ];
-internalField   uniform 1;
-
-active
-{
-    type            turbulentIntensityKineticEnergyInlet;
-    intensity       0.1;
-    value           $internalField;
-}
-
-
-inactive
-{
-    type            zeroGradient;
-}
-
-
-boundaryField
-{
-    Default_Boundary_Region
-    {
-        type            zeroGradient;
-    }
-
-    inlet_1  { $active }
-    inlet_2  { $inactive }
-    inlet_3  { $inactive }
-
-    #include "testDictInc"
-
-    outlet
-    {
-        type            inletOutlet;
-        inletValue      $internalField;
-        value           #include "value";
-        x               5;
-        y               6;
-        another         #calc{x $x; y $y;};
-    }
-}

applications/test/hmm/testDictInc

@@ -1,6 +0,0 @@
-    inlet_4
-    {
-        type            inletOutlet;
-        inletValue      $internalField;
-        value           $internalField;
-    }

applications/test/hmm/value

@@ -1 +0,0 @@
-uniform 2

applications/test/regex/Make/files

@@ -0,0 +1,3 @@
+regexTest.C
+
+EXE = $(FOAM_USER_APPBIN)/regexTest

applications/test/regex/regexTest.C

@@ -0,0 +1,115 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Description
+
+\*---------------------------------------------------------------------------*/
+
+#include "IOstreams.H"
+#include "IOobject.H"
+#include "IFstream.H"
+#include "regExp.H"
+#include "List.H"
+#include "Tuple2.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Main program:
+
+int main(int argc, char *argv[])
+{
+
+    List<Tuple2<string, string> > rawList(IFstream("testRegexps")());
+    Info<< "input list:" << rawList << endl;
+    IOobject::writeDivider(Info);
+    Info<< endl;
+
+    List<string> groups;
+
+    // report matches:
+    forAll(rawList, elemI)
+    {
+        const string& pat = rawList[elemI].first();
+        const string& str = rawList[elemI].second();
+        regExp re(pat);
+
+        Info<< str << " =~ m/" << pat.c_str() << "/ == ";
+
+        if (re.match(str, groups))
+        {
+            Info<< "true";
+            if (re.ngroups())
+            {
+                Info<< groups;
+            }
+        }
+        else
+        {
+            Info<< "false";
+            if (re.match(str, true))
+            {
+                Info<< " partial match";
+            }
+        }
+        Info << endl;
+    }
+
+    Info<<"test regExp(const char*) ..." << endl;
+    string me("Mark");
+
+    if (regExp("[Mm]ar[ck]").match(me))
+    {
+        Info<< "matched: " << me << endl;
+    }
+    else
+    {
+        Info<< "no match" << endl;
+    }
+
+    if (regExp("").match(me))
+    {
+        Info<< "matched: " << me << endl;
+    }
+    else
+    {
+        Info<< "no match" << endl;
+    }
+
+    if (regExp(NULL).match(me))
+    {
+        Info<< "matched: " << me << endl;
+    }
+    else
+    {
+        Info<< "no match" << endl;
+    }
+
+    Info<< endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/test/regex/testRegexps

@@ -0,0 +1,20 @@
+/*-------------------------------*- C++ -*---------------------------------*\
+|    =========                                                              |
+|    \\      /     OpenFOAM                                                 |
+|     \\    /                                                               |
+|      \\  /       The Open Source CFD Toolbox                              |
+|       \\/                                        http://www.OpenFOAM.org  |
+\*-------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// pattern, string
+(
+    ( "a.*" "abc" )
+    ( "a.*" "bac" )
+    ( "a.*" "abcd" )
+    ( "a.*" "def" )
+    ( "d(.*)f" "def" )
+)
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/test/router/Gather/Gather.C

@@ -59,23 +59,24 @@ Gather<T0>::Gather(const T0& localData, const bool redistribute)
             // Receive data
             for
             (
-                int slave=Pstream::firstSlave(), procIndex = 1;
+                int slave = Pstream::firstSlave(), procIndex = 1;
-                slave<=Pstream::lastSlave();
+                slave <= Pstream::lastSlave();
                 slave++, procIndex++
             )
             {
-                IPstream fromSlave(slave);
+                IPstream fromSlave(Pstream::scheduled, slave);
                 fromSlave >> this->operator[](procIndex);
             }
+
             // Send data
             for
             (
-                int slave=Pstream::firstSlave(), procIndex = 1;
+                int slave = Pstream::firstSlave(), procIndex = 1;
-                slave<=Pstream::lastSlave();
+                slave <= Pstream::lastSlave();
                 slave++, procIndex++
             )
             {
-                OPstream toSlave(slave);
+                OPstream toSlave(Pstream::scheduled, slave);
 
                 if (redistribute)
                 {
@@ -92,12 +93,13 @@ Gather<T0>::Gather(const T0& localData, const bool redistribute)
         {
             // Slave: send my local data to master
             {
-                OPstream toMaster(Pstream::masterNo());
+                OPstream toMaster(Pstream::scheduled, Pstream::masterNo());
                 toMaster << localData;
             }
+
             // Receive data from master
             {
-                IPstream fromMaster(Pstream::masterNo());
+                IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
                 if (redistribute)
                 {
                     fromMaster >> *this;

applications/test/stringList/stringListTest.C

@@ -26,7 +26,7 @@ Description
 
 \*---------------------------------------------------------------------------*/
 
-#include "stringList.H"
+#include "stringListOps.H"
 #include "IOstreams.H"
 
 using namespace Foam;

applications/test/xfer/Make/files

@@ -1,4 +1,3 @@
 xferListTest.C
 
-/* EXE = $(FOAM_USER_APPBIN)/xferListTest */
+EXE = $(FOAM_USER_APPBIN)/xferListTest
-EXE = ./xferListTest

applications/utilities/mesh/conversion/netgenNeutralToFoam/netgenNeutralToFoam.C

@@ -289,9 +289,7 @@ int main(int argc, char *argv[])
                 << patchNames[patchI] << "\t\t"
                 << allPatchFaces[patchI].size() << endl;
 
-            allPatchFaces[patchI].shrink();
             patchFaces[patchI].transfer(allPatchFaces[patchI]);
-            allPatchFaces[patchI].clear();
         }
 
         Info<< endl;

applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C

@@ -461,7 +461,7 @@ int main(int argc, char *argv[])
             }
         }
 
-   
+
         // Trim
         boundaryFaces.setSize(faceI);
         boundaryPatch.setSize(faceI);
@@ -515,7 +515,7 @@ int main(int argc, char *argv[])
             Info<< "    " << patchNames[patchI] << " : "
                 << allPatchFaces[patchI].size() << endl;
 
-            patchFaces[patchI].transfer(allPatchFaces[patchI].shrink());
+            patchFaces[patchI].transfer(allPatchFaces[patchI]);
         }
 
         Info<< endl;
@@ -548,7 +548,6 @@ int main(int argc, char *argv[])
 
     meshPtr().write();
 
-
     Info<< "End\n" << endl;
 
     return 0;

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -292,6 +292,7 @@ meshQualityControls
     minFlatness 0.5;
 
     //- Minimum pyramid volume. Is absolute volume of cell pyramid.
+    //  Set to a sensible fraction of the smallest cell volume expected.
     //  Set to very negative number (e.g. -1E30) to disable.
     minVol 1e-13;
 

applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C

@@ -45,8 +45,10 @@ Description
 
 int main(int argc, char *argv[])
 {
+    // enable -constant ... if someone really wants it
+    // enable -zeroTime to prevent accidentally trashing the initial fields
+    timeSelector::addOptions(true, true);
     argList::noParallel();
-    timeSelector::addOptions();
 #   include "addRegionOption.H"
     argList::validOptions.insert("fields", "\"(list of fields)\"");
 

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/foamToEnsightParts.C

@@ -74,7 +74,9 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    // with -constant and -zeroTime
+    // enable -constant
+    // probably don't need -zeroTime though, since the fields are vetted
+    // afterwards anyhow
     timeSelector::addOptions(true, false);
     argList::noParallel();
     argList::validOptions.insert("ascii", "");

applications/utilities/postProcessing/graphics/PV3FoamReader/PV3FoamReader/CMakeLists.txt

@@ -7,6 +7,8 @@
 # the pqReader.xml file contains xml defining readers with their
 # file extensions and descriptions.
 
+cmake_minimum_required(VERSION 2.4)
+
 FIND_PACKAGE(ParaView REQUIRED)
 INCLUDE(${PARAVIEW_USE_FILE})
 

applications/utilities/postProcessing/graphics/fieldview9Reader/readerDatabase.C

@@ -74,10 +74,7 @@ void Foam::readerDatabase::getPolyHedra()
         }
     }
 
-    polys.shrink();
-
     Info<< "Found " << polys.size() << " polyhedral cells " << endl;
-
     polys_.transfer(polys);
 }
 

applications/utilities/preProcessing/foamUpgradeFvSolution/Make/files

@@ -0,0 +1,3 @@
+foamUpgradeFvSolution.C
+
+EXE = $(FOAM_APPBIN)/foamUpgradeFvSolution

applications/utilities/preProcessing/foamUpgradeFvSolution/foamUpgradeFvSolution.C

@@ -0,0 +1,109 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    foamUpgradeFvSolution
+
+Description
+    Simple tool to upgrade the syntax of system/fvSolution::solvers
+
+Usage
+
+    - foamUpgradeFvSolution [OPTION]
+
+    @param -test \n
+    Suppress writing the updated fvSolution file
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "Time.H"
+#include "IOdictionary.H"
+#include "solution.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::noParallel();
+    argList::validOptions.insert("test", "");
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+
+    IOdictionary solutionDict
+    (
+        IOobject
+        (
+            "fvSolution",
+            runTime.system(),
+            runTime,
+            IOobject::MUST_READ,
+            IOobject::NO_WRITE,
+            false
+        )
+    );
+
+    label nChanged = 0;
+    entry* e = solutionDict.lookupEntryPtr("solvers", false, false);
+    if (e && e->isDict())
+    {
+        nChanged = solution::upgradeSolverDict(e->dict(), true);
+    }
+
+    Info<< nChanged << " solver settings changed" << nl << endl;
+    if (nChanged)
+    {
+        if (args.options().found("test"))
+        {
+            Info<< "-test option: no changes made" << nl << endl;
+        }
+        else
+        {
+            mv
+            (
+                solutionDict.objectPath(),
+                solutionDict.objectPath() + ".old"
+            );
+
+            solutionDict.writeObject
+            (
+                IOstream::ASCII,
+                IOstream::currentVersion,
+                IOstream::UNCOMPRESSED
+            );
+
+            Info<< "Backup to    " << (solutionDict.objectPath() + ".old") << nl
+                << "Write  to    " << solutionDict.objectPath() << nl << endl;
+        }
+    }
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/thermophysical/adiabaticFlameT/adiabaticFlameT.C

@@ -78,7 +78,7 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Reading Burcat data dictionary" << endl;
 
-    fileName BurcatCpDataFileName(dotFoam("thermoData/BurcatCpData"));
+    fileName BurcatCpDataFileName(findEtcFile("thermoData/BurcatCpData"));
 
     // Construct control dictionary
     IFstream BurcatCpDataFile(BurcatCpDataFileName);

applications/utilities/thermophysical/equilibriumFlameT/equilibriumFlameT.C

@@ -79,7 +79,7 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Reading Burcat data dictionary" << endl;
 
-    fileName BurcatCpDataFileName(dotFoam("thermoData/BurcatCpData"));
+    fileName BurcatCpDataFileName(findEtcFile("thermoData/BurcatCpData"));
 
     // Construct control dictionary
     IFstream BurcatCpDataFile(BurcatCpDataFileName);

applications/utilities/thermophysical/mixtureAdiabaticFlameT/mixtureAdiabaticFlameT.C

@@ -77,7 +77,7 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Reading Burcat data dictionary" << endl;
 
-    fileName BurcatCpDataFileName(dotFoam("thermoData/BurcatCpData"));
+    fileName BurcatCpDataFileName(findEtcFile("thermoData/BurcatCpData"));
 
     // Construct control dictionary
     IFstream BurcatCpDataFile(BurcatCpDataFileName);

bin/buildParaView3.3-cvs-python

@@ -1 +0,0 @@
-buildParaView3.3-cvs

bin/buildParaView3.5-cvs

@@ -0,0 +1,192 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# 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 2 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, write to the Free Software Foundation,
+#     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+#
+# Script
+#     buildParaView3.5-cvs
+#
+# Description
+#     Build and install ParaView
+#     - run from folder above ParaView source folder or place the
+#       ParaView source under $WM_THIRD_PARTY_DIR
+#
+#------------------------------------------------------------------------------
+. $WM_PROJECT_DIR/bin/tools/buildParaViewFunctions
+
+PARAVIEW_SRC=paraview-3.5-cvs
+PARAVIEW_MAJOR_VERSION=3.5
+
+# User options:
+# ~~~~~~~~~~~~~
+
+# MPI support:
+WITH_MPI=OFF
+MPI_MAX_PROCS=32
+
+# Python support:
+# note: script will try to determine the appropriate python library.
+#       If it fails, specify the path using the PYTHON_LIBRARY variable
+WITH_PYTHON=OFF
+PYTHON_LIBRARY=""
+# PYTHON_LIBRARY="/usr/lib64/libpython2.5.so.1.0"
+
+# MESA graphics support:
+WITH_MESA=OFF
+
+#
+# No further editing below this line
+#------------------------------------------------------------------------------
+Script=${0##*/}
+
+usage() {
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    cat<<USAGE
+
+usage: ${0##*/} [OPTION]
+options:
+  -fast      for repeated builds (-make -install) *use with caution*
+  -mpi       with mpi (if not already enabled)
+  -python    with python (if not already enabled)
+  -mesa      with mesa (if not already enabled)
+  -verbose   verbose output in Makefiles
+  -help
+
+For finer control, the build stages can be also selected individually
+(mutually exclusive)
+  -config
+  -make
+  -makedoc
+  -install
+  [-envpath]    alter absolute paths in CMake files to use env variables
+
+Build and install $PARAVIEW_SRC
+  - run from folder above the ParaView source folder or place the
+    ParaView source under \$WM_THIRD_PARTY_DIR
+
+USAGE
+   exit 1
+}
+
+# add options based on script name:
+case "$Script" in *-mpi*)    WITH_MPI=ON;; esac
+case "$Script" in *-python*) WITH_PYTHON=ON;; esac
+case "$Script" in *-mesa*)   WITH_MESA=ON;; esac
+
+runCONFIG=true
+runMAKE=true
+runMAKEDOC=true
+runINSTALL=true
+runENVPATH=false
+
+# parse options
+while [ "$#" -gt 0 ]
+do
+    case "$1" in
+    -h | -help)
+        usage
+        ;;
+    -config)             # stage 1: config only
+        runCONFIG=true
+        runMAKE=false
+        runMAKEDOC=false
+        runINSTALL=false
+        shift
+        ;;
+    -make)               # stage 2: make only
+        runCONFIG=false
+        runMAKE=true
+        runMAKEDOC=false
+        runINSTALL=false
+        shift
+        ;;
+    -makedoc)            # stage 3: generate html documentation
+        runCONFIG=false
+        runMAKE=false
+        runMAKEDOC=true
+        runINSTALL=false
+        shift
+        ;;
+    -install)            # stage 4: install only
+        runCONFIG=false
+        runMAKE=false
+        runMAKEDOC=false
+        runINSTALL=true
+        shift
+        ;;
+    -envpath)            # optional: change cmake files to use env variables
+        runCONFIG=false
+        runMAKE=false
+        runMAKEDOC=false
+        runINSTALL=false
+        runENVPATH=true
+        shift
+        ;;
+    -fast)               # shortcut for rebuild
+        runCONFIG=false
+        runMAKE=true
+        runMAKEDOC=false
+        runINSTALL=true
+        shift
+        ;;
+    -mpi)
+        WITH_MPI=ON
+        shift
+        ;;
+    -python)
+        WITH_PYTHON=ON
+        shift
+        ;;
+    -mesa)
+        WITH_MESA=ON
+        shift
+        ;;
+    -verbose)
+        VERBOSE=ON
+        shift
+        ;;
+    *)
+        usage "unknown option/argument: '$*'"
+        ;;
+    esac
+done
+
+# Set configure options
+#~~~~~~~~~~~~~~~~~~~~~~
+addVerbosity        # verbose makefiles
+addMpiSupport       # set MPI-specific options
+addPythonSupport    # set Python-specific options
+addMesaSupport      # set MESA-specific options
+
+getPaths            # discover where things are or should be put
+
+# Build and install
+# ~~~~~~~~~~~~~~~~~
+[ $runCONFIG  = true ] && configParaView
+[ $runMAKE    = true ] && makeParaView
+[ $runMAKEDOC = true ] && makeDocs
+[ $runINSTALL = true ] && installParaView
+[ $runENVPATH = true ] && fixCMakeFiles
+
+echo "done"
+#------------------------------------------------------------------------------

bin/buildParaView3.5-cvs-python

@@ -0,0 +1 @@
+buildParaView3.5-cvs

bin/foamUpdateCaseFileHeader

@@ -45,8 +45,8 @@ options:
   -h      help
 
   Updates the header of application files and removes consecutive blank lines.
-  By default, writes current version in the header.
+  By default, writes current OpenFOAM version in the header.
-  An alternative version can be specified with -v option.
+  An alternative version can be specified with the -v option.
 
 USAGE
     exit 1
@@ -59,8 +59,8 @@ printHeader() {
 | =========                 |                                                 |
 | \\\\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
 |  \\\\    /   O peration     | Version:  ${foamVersion}  |
-|   \\\\  /    A nd           | Web:      http://www.OpenFOAM.org               |
+|   \\\\  /    A nd           |                                                 |
-|    \\\\/     M anipulation  |                                                 |
+|    \\\\/     M anipulation  |                                www.OpenFOAM.org |
 \\*---------------------------------------------------------------------------*/
 FoamFile
 {
@@ -84,13 +84,13 @@ FoamFileAttribute() {
 #
 # OPTIONS
 #
-OPTS=`getopt hv: $*`
+opts=$(getopt hv: $*)
 if [ $? -ne 0 ]
 then
     echo "Aborting due to invalid option"
     usage
 fi
-eval set -- '$OPTS'
+eval set -- '$opts'
 while [ "$1" != "--" ]
 do
     case $1 in
@@ -110,11 +110,13 @@ shift
 
 
 # constant width for version
-foamVersion=`printf %-36s $foamVersion`
+foamVersion=$(printf %-36s $foamVersion)
 
 #
 # MAIN
 #
+unset NOTE
+
 for caseFile
 do
     if grep FoamFile $caseFile >/dev/null 2>&1
@@ -122,16 +124,17 @@ do
         echo "Updating case file: $caseFile"
         sed -n '/FoamFile/,/}/p' $caseFile > FoamFile.tmp
 
-        CLASS=`FoamFileAttribute class FoamFile.tmp`
+        FORMAT=$(FoamFileAttribute format FoamFile.tmp)
-        OBJECT=`FoamFileAttribute object FoamFile.tmp`
+        CLASS=$(FoamFileAttribute  class  FoamFile.tmp)
-        FORMAT=`FoamFileAttribute format FoamFile.tmp`
+        OBJECT=$(FoamFileAttribute object FoamFile.tmp)
+        # extract NOTE?
 
         printHeader $FORMAT $CLASS $OBJECT $NOTE > FoamFile.tmp
         sed '1,/}/d' $caseFile | sed '/./,/^$/!d' >> FoamFile.tmp
 
         # use cat to avoid removing/replace soft-links
         [ -s FoamFile.tmp ] && cat FoamFile.tmp >| $caseFile
-        rm FoamFile.tmp
+        rm -f FoamFile.tmp 2>/dev/null
     else
         echo " Invalid case file: $caseFile" 1>&2
     fi

bin/paraFoam

@@ -31,19 +31,19 @@
 #
 #------------------------------------------------------------------------------
 usage() {
-   while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
-   cat<<USAGE
+    cat<<USAGE
 
 usage: ${0##*/} [OPTION]
 options:
   -case   dir    specify alternative case directory
   -region name   specify mesh region name
-  -touch         create the .OpenFOAM file only and exit
+  -touch         only create the .OpenFOAM file
 
 * start paraview $ParaView_VERSION with the OpenFOAM libraries
 
 USAGE
-   exit 1
+    exit 1
 }
 
 unset regionName touchOnly
@@ -51,81 +51,83 @@ unset regionName touchOnly
 # parse options
 while [ "$#" -gt 0 ]
 do
-   case "$1" in
+    case "$1" in
-   -h | -help)
+    -h | -help)
-      usage
+        usage
-      ;;
+        ;;
-   -case)
+    -case)
-      [ "$#" -ge 2 ] || usage "'-case' option requires an argument"
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
-      caseDir=$2
+        cd "$2" 2>/dev/null || usage "directory does not exist:  '$2'"
-      shift 2
+        shift 2
-      cd "$caseDir" 2>/dev/null || usage "directory does not exist:  '$caseDir'"
+        ;;
-      ;;
+    -region)
-   -region)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
-      [ "$#" -ge 2 ] || usage "'-region' option requires an argument"
+        regionName=$2
-      regionName=$2
+        shift 2
-      shift 2
+        ;;
-      ;;
+    -touch)
-   -touch)
+        touchOnly=true
-      touchOnly=1
+        shift
-      shift
+        ;;
-      ;;
+    *)
-   *)
+        usage "unknown option/argument: '$*'"
-      usage "unknown option/argument: '$*'"
+        ;;
-      ;;
+    esac
-   esac
 done
 
 # get a sensible caseName
 caseName=${PWD##*/}
 caseFile="$caseName.OpenFOAM"
+fvControls="system"
+
 if [ -n "$regionName" ]
 then
-   caseFile="$caseName{$regionName}.OpenFOAM"
+    caseFile="$caseName{$regionName}.OpenFOAM"
+    fvControls="$fvControls/$regionName"
 fi
 
-if [ -n "$touchOnly" ];
+if [ -n "$touchOnly" ]
 then
-   touch "$caseFile"
+    touch "$caseFile"
-   echo "created '$caseFile'"
+    echo "created '$caseFile'"
-   exit 0
+    exit 0
 fi
 
 # parent directory for normal or parallel results
 case "$caseName" in
-   processor*) parentDir=".." ;;
+    processor*) parentDir=".." ;;
-   *)          parentDir="."  ;;
+    *)          parentDir="."  ;;
 esac
 
 # check existence of essential files
-for check in system/controlDict system/fvSchemes system/fvSolution
+for check in system/controlDict $fvControls/fvSchemes $fvControls/fvSolution
 do
-   [ -s "$parentDir/$check" ] || usage "file does not exist:  '$parentDir/$check'"
+    [ -s "$parentDir/$check" ] || usage "file does not exist:  '$parentDir/$check'"
 done
 
 
 case "$ParaView_VERSION" in
 2*)
-   trap "rm -f paraFoam.pvs $caseFile 2>/dev/null; exit 0" EXIT TERM INT
+    trap "rm -f paraFoam.pvs $caseFile 2>/dev/null; exit 0" EXIT TERM INT
-   touch $caseFile
+    touch "$caseFile"
 
-   # since we are now in the cwd, %CASE% is '$PWD/$caseFile'
+    # since we are now in the cwd, %CASE% is '$PWD/$caseFile'
-   sed -e s@%CASE%@$PWD/$caseFile@g \
+    sed -e s@%CASE%@$PWD/$caseFile@g \
-       $WM_PROJECT_DIR/bin/paraFoam.pvs > paraFoam.pvs
+        $WM_PROJECT_DIR/bin/tools/paraFoam.pvs > paraFoam.pvs
 
-   paraview paraFoam.pvs
+    paraview paraFoam.pvs
-   ;;
+    ;;
 
 *)
-   # only create/remove caseFile if it doesn't exist
+    # only create/remove caseFile if it didn't already exist
-   [ -e $caseFile ] || {
+    [ -e $caseFile ] || {
-      trap "rm -f $caseFile 2>/dev/null; exit 0" EXIT TERM INT
+        trap "rm -f $caseFile 2>/dev/null; exit 0" EXIT TERM INT
-      touch "$caseFile"
+        touch "$caseFile"
-      echo "created temporary '$caseFile'"
+        echo "created temporary '$caseFile'"
-   }
+    }
 
-   paraview --data="$caseFile"
+    paraview --data="$caseFile"
-   ;;
+    ;;
 
 esac
 #------------------------------------------------------------------------------

bin/tools/README

@@ -1,2 +1,2 @@
-Misc. tools for building applications, etc that are useful to have
+Misc. tools, scripts, templates that are useful (eg, for building applications)
-but which don't really need to be in the PATH.
+but don't need to be in the PATH.

bin/tools/buildParaView3.4

@@ -34,8 +34,8 @@
 #------------------------------------------------------------------------------
 . $WM_PROJECT_DIR/bin/tools/buildParaViewFunctions
 
-PARAVIEW_SRC="ParaView3.3-cvs"
+PARAVIEW_SRC=paraview-3.4
-PARAVIEW_MAJOR_VERSION="3.3"
+PARAVIEW_MAJOR_VERSION=3.4
 
 # User options:
 # ~~~~~~~~~~~~~
@@ -45,7 +45,7 @@ WITH_MPI=OFF
 MPI_MAX_PROCS=32
 
 # Python support:
-# note: script will try to determine python library.
+# note: script will try to determine the appropriate python library.
 #       If it fails, specify the path using the PYTHON_LIBRARY variable
 WITH_PYTHON=OFF
 PYTHON_LIBRARY=""
@@ -60,18 +60,26 @@ WITH_MESA=OFF
 Script=${0##*/}
 
 usage() {
-   while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
-   cat<<USAGE
+    cat<<USAGE
 
 usage: ${0##*/} [OPTION]
 options:
-  -fast      skip cmake for repeated builds - use with caution
+  -fast      for repeated builds (-make -install) *use with caution*
   -mpi       with mpi (if not already enabled)
   -python    with python (if not already enabled)
   -mesa      with mesa (if not already enabled)
-  -verbose   verbose cmake output
+  -verbose   verbose output in Makefiles
   -help
 
+For finer control, the build stages can be also selected individually
+(mutually exclusive)
+  -config
+  -make
+  -makedoc
+  -install
+  [-envpath]    alter absolute paths in CMake files to use env variables
+
 Build and install $PARAVIEW_SRC
   - run from folder above the ParaView source folder or place the
     ParaView source under \$WM_THIRD_PARTY_DIR
@@ -80,57 +88,105 @@ USAGE
    exit 1
 }
 
-# options based on the script name:
+# add options based on script name:
-case "$Script" in *-fast*)   CMAKE_SKIP=ON;; esac
 case "$Script" in *-mpi*)    WITH_MPI=ON;; esac
 case "$Script" in *-python*) WITH_PYTHON=ON;; esac
 case "$Script" in *-mesa*)   WITH_MESA=ON;; esac
 
+runCONFIG=true
+runMAKE=true
+runMAKEDOC=true
+runINSTALL=true
+runENVPATH=false
+
 # parse options
 while [ "$#" -gt 0 ]
 do
-   case "$1" in
+    case "$1" in
-   -h | -help)
+    -h | -help)
-      usage
+        usage
-      ;;
+        ;;
-   -fast)
+    -config)             # stage 1: config only
-      CMAKE_SKIP=YES
+        runCONFIG=true
-      shift
+        runMAKE=false
-      ;;
+        runMAKEDOC=false
-   -mpi)
+        runINSTALL=false
-      WITH_MPI=ON
+        shift
-      shift
+        ;;
-      ;;
+    -make)               # stage 2: make only
-   -python)
+        runCONFIG=false
-      WITH_PYTHON=ON
+        runMAKE=true
-      shift
+        runMAKEDOC=false
-      ;;
+        runINSTALL=false
-   -mesa)
+        shift
-      WITH_MESA=ON
+        ;;
-      shift
+    -makedoc)            # stage 3: generate html documentation
-      ;;
+        runCONFIG=false
-   -verbose)
+        runMAKE=false
-      VERBOSE=ON
+        runMAKEDOC=true
-      shift
+        runINSTALL=false
-      ;;
+        shift
-   *)
+        ;;
-      usage "unknown option/argument: '$*'"
+    -install)            # stage 4: install only
-      ;;
+        runCONFIG=false
-   esac
+        runMAKE=false
+        runMAKEDOC=false
+        runINSTALL=true
+        shift
+        ;;
+    -envpath)            # optional: change cmake files to use env variables
+        runCONFIG=false
+        runMAKE=false
+        runMAKEDOC=false
+        runINSTALL=false
+        runENVPATH=true
+        shift
+        ;;
+    -fast)               # shortcut for rebuild
+        runCONFIG=false
+        runMAKE=true
+        runMAKEDOC=false
+        runINSTALL=true
+        shift
+        ;;
+    -mpi)
+        WITH_MPI=ON
+        shift
+        ;;
+    -python)
+        WITH_PYTHON=ON
+        shift
+        ;;
+    -mesa)
+        WITH_MESA=ON
+        shift
+        ;;
+    -verbose)
+        VERBOSE=ON
+        shift
+        ;;
+    *)
+        usage "unknown option/argument: '$*'"
+        ;;
+    esac
 done
 
 # Set configure options
 #~~~~~~~~~~~~~~~~~~~~~~
-addVerbosity        # set CMake verbosity
+addVerbosity        # verbose makefiles
 addMpiSupport       # set MPI-specific options
 addPythonSupport    # set Python-specific options
 addMesaSupport      # set MESA-specific options
 
+getPaths            # discover where things are or should be put
+
 # Build and install
 # ~~~~~~~~~~~~~~~~~
-buildParaView
+[ $runCONFIG  = true ] && configParaView
-installParaView
+[ $runMAKE    = true ] && makeParaView
+[ $runENVPATH = true ] && fixCMakeFiles
+[ $runMAKEDOC = true ] && makeDocs
+[ $runINSTALL = true ] && installParaView
 
 echo "done"
-
 #------------------------------------------------------------------------------

bin/tools/buildParaViewFunctions

@@ -31,299 +31,366 @@
 #------------------------------------------------------------------------------
 
 # ParaView_INST_DIR  : location of the original sources
-# ParaView_DIR       : location of the compiled output
+# ParaView_DIR       : location of the build (for the ParaViewConfig.cmake)
+#                      and the installed program
 
+
+#
+# set CMake cache variables
+#
 addCMakeVariable()
 {
-   while [ -n "$1" ]
+    while [ -n "$1" ]
-   do
+    do
-      CMAKE_VARIABLES="$CMAKE_VARIABLES -D$1"
+        CMAKE_VARIABLES="$CMAKE_VARIABLES -D$1"
-      shift
+        shift
-   done
+    done
 }
 
 
+#
+# verbose makefiles
+#
 addVerbosity()
 {
-   [ "$VERBOSE" = ON ] && addCMakeVariable  CMAKE_VERBOSE_MAKEFILE=TRUE
+    [ "$VERBOSE" = ON ] && addCMakeVariable  CMAKE_VERBOSE_MAKEFILE=TRUE
 }
 
 
+#
+# define options for mpi support
+#
 addMpiSupport()
 {
-   [ "$WITH_MPI" = ON ] || return
+    [ "$WITH_MPI" = ON ] || return
-   OBJ_ADD="$OBJ_ADD-mpi"
+    OBJ_ADD="$OBJ_ADD-mpi"
 
-   addCMakeVariable  PARAVIEW_USE_MPI=ON
+    addCMakeVariable  PARAVIEW_USE_MPI=ON VTK_USE_MPI=ON
-   addCMakeVariable  VTK_USE_MPI=ON
+    addCMakeVariable  MPI_INCLUDE_PATH=$MPI_ARCH_PATH/include
-   addCMakeVariable  MPI_INCLUDE_PATH=$MPI_ARCH_PATH/include
+    addCMakeVariable  MPI_LIBRARY=$MPI_ARCH_PATH/lib/libmpi.so
-   addCMakeVariable  MPI_LIBRARY=$MPI_ARCH_PATH/lib/libmpi.so
+    addCMakeVariable  VTK_MPIRUN_EXE=$MPI_ARCH_PATH/bin/mpirun
-   addCMakeVariable  VTK_MPIRUN_EXE=$MPI_ARCH_PATH/bin/mpirun
+    addCMakeVariable  VTK_MPI_MAX_NUMPROCS=$MPI_MAX_PROCS
-   addCMakeVariable  VTK_MPI_MAX_NUMPROCS=$MPI_MAX_PROCS
 }
 
 
+#
+# define options for python support
+#
 addPythonSupport()
 {
-   [ "$WITH_PYTHON" = ON ] || return
+    [ "$WITH_PYTHON" = ON ] || return
-   OBJ_ADD="$OBJ_ADD-py"
+    OBJ_ADD="$OBJ_ADD-py"
 
-   if pythonBin=$(which python 2>/dev/null)
+    if pythonBin=$(which python 2>/dev/null)
-   then
+    then
-      if [ -n "$PYTHON_LIBRARY" ]
+        if [ -n "$PYTHON_LIBRARY" ]
-      then
+        then
-         # check $PYTHON_LIBRARY if it has been set
+            # check $PYTHON_LIBRARY if it has been set
-         if [ ! -e "$PYTHON_LIBRARY" ]
+            if [ ! -e "$PYTHON_LIBRARY" ]
-         then
+            then
-            echo "*** Error: libpython not found at location specified " \
+                echo "*** Error: libpython not found at location specified " \
-                 "by PYTHON_LIBRARY=$PYTHON_LIBRARY"
+                     "by PYTHON_LIBRARY=$PYTHON_LIBRARY"
-         fi
+            fi
-      else
+        else
-         # Try to get $PYTHON_LIBRARY from dynamically linked binary
+            # Try to get $PYTHON_LIBRARY from dynamically linked binary
-         PYTHON_LIBRARY=$(ldd $pythonBin | \
+            PYTHON_LIBRARY=$(ldd $pythonBin | \
-            sed -ne '/libpython/s/.* => \(.*\) (.*/\1/p')
+                sed -ne '/libpython/s/.* => \(.*\) (.*/\1/p')
 
-         if [ ! -e "$PYTHON_LIBRARY" ]
+           if [ ! -e "$PYTHON_LIBRARY" ]
-         then
+           then
-            echo "*** Error: Unable to determine path to python library."
+               echo "*** Error: Unable to determine path to python library."
-         fi
+           fi
-      fi
+        fi
 
-      [ -e "$PYTHON_LIBRARY" ] || {
+        [ -e "$PYTHON_LIBRARY" ] || {
-         echo "    Please set the variable PYTHON_LIBRARY to the full"
+            echo "    Please set the variable PYTHON_LIBRARY to the full"
-         echo "    path to (and including) libpython, or deactivate"
+            echo "    path to (and including) libpython, or deactivate"
-         echo "    python support by setting WITH_PYTHON=OFF"
+            echo "    python support by setting WITH_PYTHON=OFF"
-         exit 1
+            exit 1
-      }
+        }
 
-      pythonMajor=$(echo $PYTHON_LIBRARY | sed 's/.*libpython\(.*\)\.so.*/\1/')
+        pythonMajor=$(echo $PYTHON_LIBRARY | sed 's/.*libpython\(.*\)\.so.*/\1/')
-      pythonInclude=/usr/include/python$pythonMajor
+        pythonInclude=/usr/include/python$pythonMajor
 
-      [ -e "$PYTHON_LIBRARY" ] || {
+        [ -e "$PYTHON_LIBRARY" ] || {
-         echo "    Please set the variable PYTHON_LIBRARY to the full"
+            echo "    Please set the variable PYTHON_LIBRARY to the full"
-         echo "    path to (and including) libpython, or deactivate"
+            echo "    path to (and including) libpython, or deactivate"
-         echo "    python support by setting WITH_PYTHON=OFF"
+            echo "    python support by setting WITH_PYTHON=OFF"
-         exit 1
+            exit 1
-      }
+        }
 
-      # note - we could also allow for a PYTHON_INCLUDE variable ...
+        # note - we could also allow for a PYTHON_INCLUDE variable ...
-      [ -e "$pythonInclude" ] || {
+        [ -e "$pythonInclude" ] || {
-         echo "    No python include headers found"
+            echo "    No python include headers found"
-         echo "    Please install python headers or deactivate "
+            echo "    Please install python headers or deactivate "
-         echo "    python support by setting WITH_PYTHON=OFF"
+            echo "    python support by setting WITH_PYTHON=OFF"
-         exit 1
+            exit 1
-      }
+        }
 
-      addCMakeVariable  PARAVIEW_ENABLE_PYTHON=ON
+        addCMakeVariable  PARAVIEW_ENABLE_PYTHON=ON
-      addCMakeVariable  PYTHON_INCLUDE_PATH=$pythonInclude
+        addCMakeVariable  PYTHON_INCLUDE_PATH=$pythonInclude
-      addCMakeVariable  PYTHON_LIBRARY=$PYTHON_LIBRARY
+        addCMakeVariable  PYTHON_LIBRARY=$PYTHON_LIBRARY
 
-      echo "----"
+        echo "----"
-      echo "Python information:"
+        echo "Python information:"
-      echo "    executable     : $pythonBin"
+        echo "    executable     : $pythonBin"
-      echo "    version        : $pythonMajor"
+        echo "    version        : $pythonMajor"
-      echo "    include path   : $pythonInclude"
+        echo "    include path   : $pythonInclude"
-      echo "    library        : $PYTHON_LIBRARY"
+        echo "    library        : $PYTHON_LIBRARY"
 
-      unset pythonBin pythonInclude pythonMajor
+        unset pythonBin pythonInclude pythonMajor
-   else
+    else
-      echo "*** Error: python not installed"
+        echo "*** Error: python not installed"
-      echo "***        Deactivate python support by setting WITH_PYTHON=OFF"
+        echo "***        Deactivate python support by setting WITH_PYTHON=OFF"
-      exit 1
+        exit 1
-   fi
+    fi
 }
 
 
+#
+# define options for mesa support
+#
 addMesaSupport()
 {
-   [ "$WITH_MESA" = ON ] || return
+    [ "$WITH_MESA" = ON ] || return
 
-   MESA_INCLUDE_DIR=/usr/include/GL
+    MESA_INCLUDE_DIR=/usr/include/GL
-   MESA_LIBRARY=/usr/lib$WM_COMPILER_LIB_ARCH/libOSMesa.so
+    MESA_LIBRARY=/usr/lib$WM_COMPILER_LIB_ARCH/libOSMesa.so
 
-   if [ -d "$MESA_INCLUDE_DIR" -a -f "$MESA_LIBRARY" ]
+    if [ -d "$MESA_INCLUDE_DIR" -a -f "$MESA_LIBRARY" ]
-   then
+    then
-      OBJ_ADD="$OBJ_ADD-mesa"
+        OBJ_ADD="$OBJ_ADD-mesa"
 
-      addCMakeVariable  VTK_OPENGL_HAS_OSMESA=ON
+        addCMakeVariable  VTK_OPENGL_HAS_OSMESA=ON
-      addCMakeVariable  OSMESA_INCLUDE_DIR=$MESA_INCLUDE_DIR
+        addCMakeVariable  OSMESA_INCLUDE_DIR=$MESA_INCLUDE_DIR
-      addCMakeVariable  OSMESA_LIBRARY=$MESA_LIBRARY
+        addCMakeVariable  OSMESA_LIBRARY=$MESA_LIBRARY
 
-   else
+    else
-      echo "*** Error: no MESA information found"
+       echo "*** Error: no MESA information found"
-      exit 1
+       exit 1
-   fi
+    fi
 }
 
 
-buildParaView()
+#
+# discover where things are or should be put
+#
+getPaths()
 {
-   # set paraview environment
+    # set paraview environment
-   for i in $PWD $WM_THIRD_PARTY_DIR
+    for i in $PWD $WM_THIRD_PARTY_DIR
-   do
+    do
-      ParaView_INST_DIR=$i/$PARAVIEW_SRC
+        ParaView_INST_DIR=$i/$PARAVIEW_SRC
-      [ -d $ParaView_INST_DIR ] && break
+        [ -d $ParaView_INST_DIR ] && break
-   done
+    done
 
-   if [ ! -d "$ParaView_INST_DIR" ]
+    if [ ! -d "$ParaView_INST_DIR" ]
-   then
+    then
-      # last chance: maybe already in the paraview directory
+        # last chance: maybe already in the paraview directory
-      [ "${PWD##*/}" = $PARAVIEW_SRC ] && ParaView_INST_DIR=$PWD
+        [ "${PWD##*/}" = $PARAVIEW_SRC ] && ParaView_INST_DIR=$PWD
 
-      [ -d "$ParaView_INST_DIR" ] || {
+        [ -d "$ParaView_INST_DIR" ] || {
-         echo "did not find $PARAVIEW_SRC in these directories:"
+            echo "did not find $PARAVIEW_SRC in these directories:"
-         echo "  PWD=$PWD"
+            echo "  PWD=$PWD"
-         echo "  WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR"
+            echo "  WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR"
-         echo "abort build"
+            echo "abort build"
-         exit 1
+            exit 1
-      }
+        }
-   fi
+    fi
 
-
+    # ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER$OBJ_ADD
-   # ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER$OBJ_ADD
+    ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
-   ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
+    echo "ParaView_DIR=$ParaView_DIR"
-
-   # shortcut for repeated builds - use with caution
-   if [ "$CMAKE_SKIP" = YES ]
-   then
-
-      # change to build/install folder
-      cd $ParaView_DIR || exit 1
-
-   else
-
-      # remove any existing build folder and recreate
-      rm -rf $ParaView_DIR
-      mkdir -p $ParaView_DIR
-      cd $ParaView_DIR
-
-      echo "----"
-      echo "Building $PARAVIEW_SRC"
-      echo "    MPI support    : $WITH_MPI"
-      echo "    Python support : $WITH_PYTHON"
-      echo "    MESA support   : $WITH_MESA"
-      echo "    Source         : $ParaView_INST_DIR"
-      echo "    Target         : $ParaView_DIR"
-      echo "----"
-
-      # make paraview
-      cmake \
-         -DCMAKE_INSTALL_PREFIX=$PARAVIEW_APP_DIR \
-         $CMAKE_VARIABLES \
-         $ParaView_INST_DIR
-   fi
-
-   # change to build folder
-   echo "    Starting make"
-
-   if [ -r /proc/cpuinfo ]
-   then
-      WM_NCOMPPROCS=$(egrep "^processor" /proc/cpuinfo | wc -l)
-
-      if [ $WM_NCOMPPROCS -gt 8 ]
-      then
-         WM_NCOMPPROCS=8
-      fi
-
-      make -j $WM_NCOMPPROCS
-   else
-      make
-   fi
 }
 
 
-# adjust hard-links
+#
+# configure via cmake, but don't actually build anything
+#
+configParaView()
+{
+    # remove any existing build folder and recreate
+    if [ -d $ParaView_DIR ]
+    then
+        echo "removing old build/install directory"
+        rm -rf $ParaView_DIR
+    fi
+    mkdir -p $ParaView_DIR
+
+    cd $ParaView_DIR
+
+    echo "----"
+    echo "Configuring $PARAVIEW_SRC"
+    echo "    MPI support    : $WITH_MPI"
+    echo "    Python support : $WITH_PYTHON"
+    echo "    MESA support   : $WITH_MESA"
+    echo "    Source         : $ParaView_INST_DIR"
+    echo "    Target         : $ParaView_DIR"
+    echo "----"
+    echo
+    echo cmake \
+        -DCMAKE_INSTALL_PREFIX:PATH=$ParaView_DIR \
+        $CMAKE_VARIABLES \
+        ../..
+    echo
+    echo "----"
+    echo
+
+    # run cmake to create Makefiles
+    cmake \
+        -DCMAKE_INSTALL_PREFIX:PATH=$ParaView_DIR \
+        $CMAKE_VARIABLES \
+        ../..
+
+}
+
+
+#
+# invoke make
+# also link bin/ to lib/paraview-* for development without installation
+#
+makeParaView()
+{
+    cd $ParaView_DIR || exit 1  # change to build folder
+    echo "    Starting make"
+
+    if [ -r /proc/cpuinfo ]
+    then
+        WM_NCOMPPROCS=$(egrep "^processor" /proc/cpuinfo | wc -l)
+        [ $WM_NCOMPPROCS -le 8 ] || WM_NCOMPPROCS=8
+
+        time make -j $WM_NCOMPPROCS
+    else
+        time make
+    fi
+    echo "    Done make"
+
+    echo "    For quicker development, linking lib/paraview-$PARAVIEW_MAJOR_VERSION/ -> bin/"
+    rm -rf lib/paraview-$PARAVIEW_MAJOR_VERSION
+    mkdir lib 2>/dev/null
+    ( cd lib && ln -s ../bin paraview-$PARAVIEW_MAJOR_VERSION )
+}
+
+
+#
+# adjust hard-links (internal function)
 # Note: use loop with grep to avoid touching too many files
-fixCMakeHardLinks()
+#
+fixHardLinks()
 {
-   fileSpec=$1
+    envName=$1
-   string=$2
+    string=$2
-   envName=$3
+    shift 2
 
-   echo -n "    for \$$envName "
+    echo "-- Replacing path hard links for \$$envName"
-   for i in $(find . -type f -iname "$fileSpec")
+
-   do
+    for fileSpec
-      if grep -q "$string" $i
+    do
-      then
+        echo -n "   $fileSpec: "
-         echo -n "#"
+        for i in $(find . -type f -iname "$fileSpec")
-         sed -i "s,$string,\$ENV{$envName},g" $i
+        do
-      fi
+            if grep -q "$string" $i
-   done
+            then
-   echo
+                echo -n "#"
+                sed -i "s,$string,\$ENV{$envName},g" $i
+            fi
+        done
+        echo
+    done
 }
 
 
+#
+# replace absolute paths with environment variables
+# This triggers a partial (or even a full) rebuild, but might let us
+# find our files later if we relocate the build
+#
+fixCMakeFiles()
+{
+    cd $ParaView_DIR || exit 1  # change to build folder
+
+    # Replace path with env variable: ParaView_DIR
+    fixHardLinks ParaView_DIR "$ParaView_DIR" '*.cmake'
+
+    # Replace path with env variable: ParaView_INST_DIR
+    fixHardLinks ParaView_INST_DIR "$ParaView_INST_DIR" '*.cmake'
+
+    # Replace path with env variable: MPI_ARCH_PATH
+    if [ "$WITH_MPI" = ON ]
+    then
+        fixHardLinks MPI_ARCH_PATH "$MPI_ARCH_PATH" '*.cmake'
+    fi
+
+    # Replace path with env variable: CMAKE_HOME
+    if [ -r "$CMAKE_HOME" ]
+    then
+        fixHardLinks CMAKE_HOME "$CMAKE_HOME" '*cmake*'
+    fi
+
+    # Replace path with env variable: WM_COMPILER_DIR
+    # (include cmake.check_cache)
+    # This triggers a complete rebuild (with cmake-2.6.2), but is likely
+    # needed when redistributing files
+    fixHardLinks WM_COMPILER_DIR "$WM_COMPILER_DIR" '*cmake*'
+}
+
+
+#
+# make html documentation (mostly just for the readers/writers)
+#
+makeDocs()
+{
+    cd $ParaView_DIR || exit 1  # change to build folder
+    echo "    Creating html documentation"
+
+    make HTMLDocumentation
+}
+
+
+#
+# actually install the program
+#
 installParaView()
 {
-   if [ ! -e "$ParaView_DIR/bin/paraview" ]
+    cd $ParaView_DIR || exit 1  # change to build folder
-   then
+    echo "    Installing ParaView to $ParaView_DIR"
-      echo "    Cannot install - no paraview binary found"
-      return
-   fi
-   echo "    Build complete"
 
-   cd $ParaView_DIR
+    echo "disabled 'make install' for now, just use links"
 
-   echo "    Replacing path hard links"
+    # about.txt may be missing
+    paraviewLibDir="$ParaView_DIR/lib/paraview-$PARAVIEW_MAJOR_VERSION"
+    if [ -d "$paraviewLibDir" -a ! -e "$paraviewLibDir/about.txt" ]
+    then
+        echo "paraview-$PARAVIEW_MAJOR_VERSION installed - $(date)" > $paraviewLibDir/about.txt
+    fi
 
-   # Replace local ParaView_INST_DIR path with ParaView_INST_DIR
+cat<< INFO
-   # environment variable
+    ---
-   fixCMakeHardLinks '*.cmake' "$ParaView_INST_DIR" ParaView_INST_DIR
+    Installation complete
+    Set environment variables:
 
-   # Replace local MPI_ARCH_PATH path with MPI_ARCH_PATH
+        export ParaView_INST_DIR=$ParaView_INST_DIR
-   # environment variable
+        export ParaView_DIR=$ParaView_DIR
-   if [ "$WITH_MPI" = ON ]
+        export PV_PLUGIN_PATH=$FOAM_LIBBIN
-   then
+        export PATH=\$ParaView_DIR/bin:\$PATH
-      fixCMakeHardLinks '*.cmake' "$MPI_ARCH_PATH" MPI_ARCH_PATH
+    ---
-   fi
+INFO
-
-   # Replace local CMAKE_HOME path with CMAKE_HOME
-   # environment variable
-   if [ -r "$CMAKE_HOME" ]
-   then
-      fixCMakeHardLinks '*cmake*' "$CMAKE_HOME" CMAKE_HOME
-   fi
-
-   # Replace local WM_COMPILER_DIR path with WM_COMPILER_DIR
-   # environment variable
-   fixCMakeHardLinks '*cmake*' "$WM_COMPILER_DIR" WM_COMPILER_DIR
-
-   # create a softlink to the $ParaView_DIR/bin folder
-   # - workaround for chosen install location
-   echo "    Creating lib/paraview-$PARAVIEW_MAJOR_VERSION soft link to 'bin'"
-   rm -rf lib/paraview-$PARAVIEW_MAJOR_VERSION
-   [ -d lib ] || mkdir lib
-   ( cd lib && ln -s ../bin paraview-$PARAVIEW_MAJOR_VERSION )
-
-   # info on symlinks to screen
-   echo ""
-   echo "    ---"
-   echo "    Installation complete"
-   echo "    Set environment variables:"
-   echo "    - ParaView_INST_DIR to $ParaView_INST_DIR"
-   echo "    - ParaView_DIR to $ParaView_DIR"
-   echo "    - PV_PLUGIN_PATH to $FOAM_LIBBIN"
-   echo "    Add $ParaView_DIR/bin to PATH"
-   # echo "   Add $ParaView_INST_DIR/lib to LD_LIBRARY_PATH"
-   echo "    ---"
 }
 
 
 # clear all the variables used before using any of the functions
-
 unset VERBOSE
-unset WITH_MPI
+unset WITH_MPI WITH_MESA
-unset WITH_MESA
+unset WITH_PYTHON PYTHON_LIBRARY
-unset WITH_PYTHON
-unset PYTHON_LIBRARY
 unset CMAKE_VARIABLES
-unset CMAKE_SKIP
 unset OBJ_ADD
 
 # start with these general settings
 addCMakeVariable  VTK_USE_TK=FALSE
-addCMakeVariable  BUILD_SHARED_LIBS:BOOL=ON
+addCMakeVariable  BUILD_SHARED_LIBS:BOOL=ON VTK_USE_RPATH:BOOL=OFF
-addCMakeVariable  VTK_USE_RPATH:BOOL=OFF
 addCMakeVariable  CMAKE_BUILD_TYPE:STRING=Release
 
+# include development files in "make install"
+addCMakeVariable  PARAVIEW_INSTALL_DEVELOPMENT:BOOL=ON
+
 # ----------------------------------------------------------------- end-of-file

etc/apps/paraview3/bashrc

@@ -26,38 +26,49 @@
 #     paraview3/bashrc
 #
 # Description
-#     Setup file for ParaView3.
+#     Setup file for paraview-3.x
 #     Sourced from OpenFOAM-?.?/etc/bashrc
 #
+# Note
+#     The env. variable 'ParaView_DIR' is required for building plugins
 #------------------------------------------------------------------------------
 
-export CMAKE_HOME=$WM_THIRD_PARTY_DIR/cmake-2.4.6/platforms/$WM_ARCH
+# determine the cmake to be used
+unset CMAKE_HOME
+for cmake in cmake-2.6.2 cmake-2.4.6
+do
+    cmake=$WM_THIRD_PARTY_DIR/$cmake/platforms/$WM_ARCH
+    if [ -r $cmake ]
+    then
+        export CMAKE_HOME=$cmake
+        export PATH=$CMAKE_HOME/bin:$PATH
+        break
+    fi
+done
 
-if [ -r $CMAKE_HOME ]
+paraviewMajor=paraview-3.5
-then
+export ParaView_VERSION=3.5-cvs
-    export PATH=$CMAKE_HOME/bin:$PATH
-else
-    unset CMAKE_HOME
-fi
 
-export ParaView_VERSION="3.3-cvs"
+export ParaView_INST_DIR=$WM_THIRD_PARTY_DIR/paraview-$ParaView_VERSION
-
-export ParaView_INST_DIR=$WM_THIRD_PARTY_DIR/ParaView$ParaView_VERSION
 export ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
 
-if [ "$PYTHONPATH" ]
+# add in python libraries if required
+paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping
+if [ -r $paraviewPython ]
 then
-    export PYTHONPATH=$PYTHONPATH:$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
+    if [ "$PYTHONPATH" ]
-else
+    then
-    export PYTHONPATH=$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
+        export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_DIR/lib/$paraviewMajor
+    else
+        export PYTHONPATH=$paraviewPython:$ParaView_DIR/lib/$paraviewMajor
+    fi
 fi
 
-
 if [ -r $ParaView_DIR ]
 then
     export PATH=$ParaView_DIR/bin:$PATH
-    export LD_LIBRARY_PATH=$ParaView_DIR/bin:$LD_LIBRARY_PATH
     export PV_PLUGIN_PATH=$FOAM_LIBBIN
 fi
 
+unset cmake paraviewMajor paraviewPython
 # -----------------------------------------------------------------------------

etc/apps/paraview3/cshrc

@@ -26,34 +26,44 @@
 #     paraview3/cshrc
 #
 # Description
-#     Startup File for Paraview3
+#     Startup File for paraview-3.x
 #     Sourced from OpenFOAM-?.?/etc/cshrc
 #
+# Note
+#     The env. variable 'ParaView_DIR' is required for building plugins
 #------------------------------------------------------------------------------
 
-setenv CMAKE_HOME $WM_THIRD_PARTY_DIR/cmake-2.4.6/platforms/$WM_ARCH
+# determine the cmake to be used
+unsetenv CMAKE_HOME
+foreach cmake ( cmake-2.6.2 cmake-2.4.6 )
+    set cmake=$WM_THIRD_PARTY_DIR/$cmake/platforms/$WM_ARCH
+    if ( -r $cmake ) then
+        setenv CMAKE_HOME $cmake
+        set path=($CMAKE_HOME/bin $path)
+        break
+    endif
+end
 
-if ( -r $CMAKE_HOME ) then
+set paraviewMajor=paraview-3.5
-    set path=($CMAKE_HOME/bin $path)
+setenv ParaView_VERSION 3.5-cvs
-else
-    unsetenv CMAKE_HOME
-endif
 
-setenv ParaView_VERSION 3.3-cvs
+setenv ParaView_INST_DIR $WM_THIRD_PARTY_DIR/paraview-$ParaView_VERSION
-
-setenv ParaView_INST_DIR $WM_THIRD_PARTY_DIR/ParaView$ParaView_VERSION
 setenv ParaView_DIR $ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
 
-if ($?PYTHONPATH) then
+# add in python libraries if required
-    setenv PYTHONPATH ${PYTHONPATH}:$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
+set paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping
-else
+if ( -r $paraviewPython ) then
-    setenv PYTHONPATH $ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
+    if ($?PYTHONPATH) then
+        setenv PYTHONPATH ${PYTHONPATH}:$paraviewPython:$ParaView_DIR/lib/${paraviewMajor}
+    else
+        setenv PYTHONPATH $paraviewPython:$ParaView_DIR/lib/${paraviewMajor}
+    endif
 endif
 
 if ( -r $ParaView_INST_DIR ) then
     set path=($ParaView_DIR/bin $path)
-    setenv LD_LIBRARY_PATH $ParaView_DIR/bin:$LD_LIBRARY_PATH
     setenv PV_PLUGIN_PATH $FOAM_LIBBIN
 endif
 
+unset cmake paraviewMajor paraviewPython
 # -----------------------------------------------------------------------------

etc/bashrc

@@ -91,7 +91,7 @@ export WM_COMPILER_LIB_ARCH=
 # WM_JAVAC_OPTION = Opt | Debug
 : ${WM_JAVAC_OPTION:=Opt}; export WM_JAVAC_OPTION
 
-# WM_MPLIB = | OPENMPI| LAM | MPICH | MPICH-GM | HPMPI | GAMMA | MPI
+# WM_MPLIB = | OPENMPI | LAM | MPICH | MPICH-GM | HPMPI | GAMMA | MPI
 : ${WM_MPLIB:=OPENMPI}; export WM_MPLIB
 
 

src/Allwmake

@@ -2,6 +2,9 @@
 cd ${0%/*} || exit 1    # run from this directory
 set -x
 
+# force update of Foam::FOAMversion string (git tag or $WM_PROJECT_VERSION)
+/bin/rm -f OpenFOAM/Make/$WM_OPTIONS/global.? 2>/dev/null
+
 wmakeLnInclude -f OpenFOAM
 wmakeLnInclude -f OSspecific/$WM_OS
 Pstream/Allwmake

src/OSspecific/Unix/Make/files

@@ -2,6 +2,7 @@ signals/sigFpe.C
 signals/sigSegv.C
 signals/sigInt.C
 signals/sigQuit.C
+regExp.C
 timer.C
 fileStat.C
 Unix.C

src/OSspecific/Unix/Unix.C

@@ -211,7 +211,7 @@ bool Foam::chDir(const fileName& dir)
 }
 
 
-Foam::fileName Foam::dotFoam(const fileName& name)
+Foam::fileName Foam::findEtcFile(const fileName& name, bool mandatory)
 {
     // Search user files:
     // ~~~~~~~~~~~~~~~~~~
@@ -268,6 +268,15 @@ Foam::fileName Foam::dotFoam(const fileName& name)
     }
 
     // Not found
+    // abort if the file is mandatory, otherwise return null
+    if (mandatory)
+    {
+        cerr<< "--> FOAM FATAL ERROR in Foam::findEtcFile() :"
+               " could not find mandatory file\n    '"
+            << name.c_str() << "'\n\n" << std::endl;
+        ::exit(1);
+    }
+
     return fileName::null;
 }
 

src/OSspecific/Unix/regExp.C

@@ -0,0 +1,208 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include <sys/types.h>
+#include "regExp.H"
+#include "label.H"
+#include "string.H"
+#include "List.H"
+#include "IOstreams.H"
+
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+void Foam::regExp::compile(const char* pat) const
+{
+    clear();
+
+    // avoid NULL and zero-length patterns
+    if (pat && *pat)
+    {
+        preg_ = new regex_t;
+
+        if (regcomp(preg_, pat, REG_EXTENDED) != 0)
+        {
+            FatalErrorIn
+            (
+                "regExp::compile(const char*)"
+            )   << "Failed to compile regular expression '" << pat << "'"
+                << exit(FatalError);
+        }
+    }
+}
+
+
+void Foam::regExp::clear() const
+{
+    if (preg_)
+    {
+        regfree(preg_);
+        delete preg_;
+        preg_ = 0;
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::regExp::regExp()
+:
+    preg_(0)
+{}
+
+
+Foam::regExp::regExp(const string& pat)
+:
+    preg_(0)
+{
+    compile(pat.c_str());
+}
+
+
+Foam::regExp::regExp(const char* pat)
+:
+    preg_(0)
+{
+    compile(pat);
+}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+Foam::regExp::~regExp()
+{
+    clear();
+}
+
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+int Foam::regExp::ngroups() const
+{
+    return preg_ ? preg_->re_nsub : 0;
+}
+
+
+bool Foam::regExp::match
+(
+    const string& str,
+    bool partialMatch
+) const
+{
+    if (preg_ && str.size())
+    {
+        size_t nmatch = 1;
+        regmatch_t pmatch[1];
+
+        // match and also verify that the entire string was matched
+        // pmatch[0] is the entire match
+        if
+        (
+            regexec(preg_, str.c_str(), nmatch, pmatch, 0) == 0
+         &&
+            (
+                partialMatch
+             || (pmatch[0].rm_so == 0 && pmatch[0].rm_eo == label(str.size()))
+            )
+        )
+        {
+            return true;
+        }
+    }
+
+    return false;
+}
+
+
+bool Foam::regExp::match
+(
+    const string& str,
+    List<string>& groups,
+    bool partialMatch
+) const
+{
+    if (preg_ && str.size())
+    {
+        size_t nmatch = ngroups() + 1;
+        regmatch_t pmatch[nmatch];
+
+        // match and also verify that the entire string was matched
+        // pmatch[0] is the entire match
+        // pmatch[1..] are the (...) sub-groups
+        if
+        (
+            regexec(preg_, str.c_str(), nmatch, pmatch, 0) == 0
+         &&
+            (
+                partialMatch
+             || (pmatch[0].rm_so == 0 && pmatch[0].rm_eo == label(str.size()))
+            )
+        )
+        {
+            groups.setSize(ngroups());
+            label groupI = 0;
+
+            for (size_t matchI = 1; matchI < nmatch; matchI++)
+            {
+                if (pmatch[matchI].rm_so != -1 && pmatch[matchI].rm_eo != -1)
+                {
+                    groups[groupI] = str.substr
+                    (
+                        pmatch[matchI].rm_so,
+                        pmatch[matchI].rm_eo - pmatch[matchI].rm_so
+                    );
+                }
+                else
+                {
+                    groups[groupI].clear();
+                }
+                groupI++;
+            }
+
+            return true;
+        }
+    }
+
+    groups.clear();
+    return false;
+}
+
+
+// * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * * //
+
+void Foam::regExp::operator=(const string& pat)
+{
+    compile(pat.c_str());
+}
+
+
+void Foam::regExp::operator=(const char* pat)
+{
+    compile(pat);
+}
+
+
+// ************************************************************************* //

src/OSspecific/Unix/regExp.H

@@ -23,94 +23,108 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::regularExpression
+    Foam::regExp
 
 Description
-    Wrapper around regular expressions.
+    Wrapper around POSIX extended regular expressions.
+
+    The beginning-of-line (^) and the end-of-line ($) anchors are implicit
+    by default.
+
+SeeAlso
+    The manpage regex(7) for more information about POSIX regular expressions.
+    These differ somewhat from @c Perl and @c sed regular expressions.
 
 SourceFiles
+    regExp.C
 
 \*---------------------------------------------------------------------------*/
 
-#ifndef regularExpression_H
+#ifndef regExp_H
-#define regularExpression_H
+#define regExp_H
 
-#include <sys/types.h>
 #include <regex.h>
-#include "string.H"
-#include "IOstreams.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
 {
 
+// Forward declaration of classes
+class string;
+template<class T> class List;
+
 /*---------------------------------------------------------------------------*\
-                           Class regularExpression Declaration
+                          Class regExp Declaration
 \*---------------------------------------------------------------------------*/
 
-class regularExpression
+class regExp
 {
     // Private data
 
         //- Precompiled regular expression
-        regex_t* preg_;
+        mutable regex_t* preg_;
-
 
     // Private member functions
 
+        //- release allocated space
+        void clear() const;
+
+        //- compile into a regular expression
+        void compile(const char*) const;
+
         //- Disallow default bitwise copy construct
-        regularExpression(const regularExpression&);
+        regExp(const regExp&);
 
         //- Disallow default bitwise assignment
-        void operator=(const regularExpression&);
+        void operator=(const regExp&);
 
 public:
 
-
     // Constructors
 
+        //- Construct null
+        regExp();
+
         //- Construct from string
-        inline regularExpression(const string& s)
+        regExp(const string&);
-        {
-            preg_ = new regex_t;
-
-            if (regcomp(preg_, s.c_str(), REG_EXTENDED) != 0)
-            {
-                FatalErrorIn
-                (
-                    "regularExpression::regularExpression(const char*)"
-                )   << "Failed to compile regular expression " << s
-                    << exit(FatalError);
-            }
-        }
 
+        //- Construct from character array
+        regExp(const char*);
 
     // Destructor
 
-        //- Construct from string
+        ~regExp();
-        inline ~regularExpression()
-        {
-            if (preg_)
-            {
-                regfree(preg_);
-                delete preg_;
-            }
-        }
-
 
     // Member functions
 
-        //- Matches?
+        //- Return the number of (groups)
-        inline bool matches(const string& s) const
+        int ngroups() const;
-        {
-            size_t nmatch = 1;
-            regmatch_t pmatch[1];
 
-            int errVal = regexec(preg_, s.c_str(), nmatch, pmatch, 0);
+        //- Return true if it matches, partial matches are optional
+        bool match
+        (
+            const string&,
+            bool partialMatch=false
+        ) const;
+
+        //- Return true if it matches and sets the sub-groups matched,
+        //  partial matches are optional
+        bool match
+        (
+            const string&,
+            List<string>& groups,
+            bool partialMatch=false
+        ) const;
+
+    // Member Operators
+
+        //- Assign from a string
+        void operator=(const string&);
+
+        //- Assign from a character array
+        void operator=(const char*);
 
-            return (errVal == 0 && pmatch[0].rm_eo == label(s.size()));
-        }
 };
 
 

src/OpenFOAM/Make/files

@@ -289,7 +289,6 @@ $(tetCell)/tetCell.C
 
 cellModeller = $(meshShapes)/cellModeller
 $(cellModeller)/cellModeller.C
-$(cellModeller)/cellModellerIO.C
 
 cellModel = $(meshShapes)/cellModel
 $(cellModel)/cellModel.C

src/OpenFOAM/containers/Dictionaries/Dictionary/Dictionary.C

@@ -28,22 +28,15 @@ Description
 
 #include "Dictionary.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-// Null constructor
 template<class T>
-Dictionary<T>::Dictionary()
+Foam::Dictionary<T>::Dictionary()
 {}
 
 
-// Copy constructor
 template<class T>
-Dictionary<T>::Dictionary(const Dictionary& dict)
+Foam::Dictionary<T>::Dictionary(const Dictionary& dict)
 :
     DictionaryBase<IDLList<T>, T>(dict)
 {}
@@ -52,10 +45,10 @@ Dictionary<T>::Dictionary(const Dictionary& dict)
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 template<class T>
-bool Dictionary<T>::erase(const word& Keyword)
+bool Foam::Dictionary<T>::erase(const word& keyword)
 {
     T* tPtr;
-    if ((tPtr = this->remove(Keyword)))
+    if (tPtr = this->remove(keyword))
     {
         delete tPtr;
         return true;
@@ -69,6 +62,4 @@ bool Dictionary<T>::erase(const word& Keyword)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/Dictionaries/Dictionary/Dictionary.H

@@ -27,8 +27,10 @@ Class
 
 Description
     Gerneral purpose template dictionary class which manages the storage
-    associated with it.  It is derived from DictionaryBase instantiated on
+    associated with it.
-    a memory managed form of intrusive doubly-linked list of \<T\>.
+
+    It is derived from DictionaryBase instantiated on a memory managed form
+    of intrusive doubly-linked list of \<T\>.
 
 SourceFiles
     Dictionary.C
@@ -47,7 +49,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class Dictionary Declaration
+                         Class Dictionary Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class T>
@@ -69,11 +71,9 @@ public:
 
     // Member functions
 
-        // Editing
+        //- Remove an entry specified by keyword and delete the pointer.
-
+        //  Returns true if the keyword was found
-            //- Remove an entry specified by keyword from the dictionary
+        bool erase(const word& keyword);
-            //  and delete it
-            bool erase(const word& keyword);
 };
 
 

src/OpenFOAM/containers/Dictionaries/DictionaryBase/DictionaryBase.C

@@ -26,15 +26,10 @@ License
 
 #include "DictionaryBase.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
 template<class IDLListType, class T>
-void DictionaryBase<IDLListType, T>::addEntries()
+void Foam::DictionaryBase<IDLListType, T>::addEntries()
 {
     for
     (
@@ -51,12 +46,15 @@ void DictionaryBase<IDLListType, T>::addEntries()
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class IDLListType, class T>
-DictionaryBase<IDLListType, T>::DictionaryBase()
+Foam::DictionaryBase<IDLListType, T>::DictionaryBase()
 {}
 
 
 template<class IDLListType, class T>
-DictionaryBase<IDLListType, T>::DictionaryBase(const DictionaryBase& dict)
+Foam::DictionaryBase<IDLListType, T>::DictionaryBase
+(
+    const DictionaryBase& dict
+)
 :
     IDLListType(dict)
 {
@@ -66,17 +64,20 @@ DictionaryBase<IDLListType, T>::DictionaryBase(const DictionaryBase& dict)
 
 template<class IDLListType, class T>
 template<class INew>
-DictionaryBase<IDLListType, T>::DictionaryBase(Istream& is, const INew& inewt)
+Foam::DictionaryBase<IDLListType, T>::DictionaryBase
+(
+    Istream& is,
+    const INew& iNew
+)
 :
-    IDLListType(is, inewt)
+    IDLListType(is, iNew)
 {
     addEntries();
 }
 
 
-// Istream constructor
 template<class IDLListType, class T>
-DictionaryBase<IDLListType, T>::DictionaryBase(Istream& is)
+Foam::DictionaryBase<IDLListType, T>::DictionaryBase(Istream& is)
 :
     IDLListType(is)
 {
@@ -88,25 +89,60 @@ DictionaryBase<IDLListType, T>::DictionaryBase(Istream& is)
 
 // Find and return T
 template<class IDLListType, class T>
-bool DictionaryBase<IDLListType, T>::found(const word& keyword) const
+bool Foam::DictionaryBase<IDLListType, T>::found(const word& keyword) const
 {
     return hashedTs_.found(keyword);
 }
 
 
-// Find and return T*
+// Find and return T*, return NULL if not found
 template<class IDLListType, class T>
-const T* DictionaryBase<IDLListType, T>::lookup(const word& keyword) const
+const T* Foam::DictionaryBase<IDLListType, T>::lookupPtr
+(
+    const word& keyword
+) const
+{
+    typename HashTable<T*>::const_iterator iter = hashedTs_.find(keyword);
+
+    if (iter != hashedTs_.end())
+    {
+        return *iter;
+    }
+    else
+    {
+        return NULL;
+    }
+}
+
+
+// Find and return T*, return NULL if not found
+template<class IDLListType, class T>
+T* Foam::DictionaryBase<IDLListType, T>::lookupPtr(const word& keyword)
+{
+    typename HashTable<T*>::iterator iter = hashedTs_.find(keyword);
+
+    if (iter != hashedTs_.end())
+    {
+        return *iter;
+    }
+    else
+    {
+        return NULL;
+    }
+}
+
+
+// Find and return T*, FatalError if keyword not found
+template<class IDLListType, class T>
+const T* Foam::DictionaryBase<IDLListType, T>::lookup(const word& keyword) const
 {
     typename HashTable<T*>::const_iterator iter = hashedTs_.find(keyword);
 
     if (iter == hashedTs_.end())
     {
-        // If keyword not found print error message ...
         FatalErrorIn
         (
-            "DictionaryBase<IDLListType, T>::"
+            "DictionaryBase<IDLListType, T>::lookup(const word&) const"
-            "lookup(const word& keyword) const"
         )   << keyword << " is undefined"
             << exit(FatalError);
     }
@@ -115,18 +151,17 @@ const T* DictionaryBase<IDLListType, T>::lookup(const word& keyword) const
 }
 
 
-// Find and return T*
+// Find and return T*, FatalError if keyword not found
 template<class IDLListType, class T>
-T* DictionaryBase<IDLListType, T>::lookup(const word& keyword)
+T* Foam::DictionaryBase<IDLListType, T>::lookup(const word& keyword)
 {
     typename HashTable<T*>::iterator iter = hashedTs_.find(keyword);
 
     if (iter == hashedTs_.end())
     {
-        // If keyword not found print error message ...
         FatalErrorIn
         (
-            "DictionaryBase<IDLListType, T>::lookup(const word& keyword)"
+            "DictionaryBase<IDLListType, T>::lookup(const word&)"
         )   << keyword << " is undefined"
             << exit(FatalError);
     }
@@ -137,7 +172,7 @@ T* DictionaryBase<IDLListType, T>::lookup(const word& keyword)
 
 // Return the table of contents
 template<class IDLListType, class T>
-wordList DictionaryBase<IDLListType, T>::toc() const
+Foam::wordList Foam::DictionaryBase<IDLListType, T>::toc() const
 {
     wordList keywords(this->size());
 
@@ -158,26 +193,28 @@ wordList DictionaryBase<IDLListType, T>::toc() const
 
 // Add at head of dictionary
 template<class IDLListType, class T>
-void DictionaryBase<IDLListType, T>::insert(const word& keyword, T* tPtr)
+void Foam::DictionaryBase<IDLListType, T>::insert(const word& keyword, T* tPtr)
 {
-    IDLListType::insert(tPtr);
+    // NOTE: we should probably check that HashTable::insert actually worked
     hashedTs_.insert(keyword, tPtr);
+    IDLListType::insert(tPtr);
 }
 
 
 // Add at tail of dictionary
 template<class IDLListType, class T>
-void DictionaryBase<IDLListType, T>::append(const word& keyword, T* tPtr)
+void Foam::DictionaryBase<IDLListType, T>::append(const word& keyword, T* tPtr)
 {
-    IDLListType::append(tPtr);
+    // NOTE: we should probably check that HashTable::insert actually worked
     hashedTs_.insert(keyword, tPtr);
+    IDLListType::append(tPtr);
 }
 
 
 template<class IDLListType, class T>
-T* DictionaryBase<IDLListType, T>::remove(const word& Keyword)
+T* Foam::DictionaryBase<IDLListType, T>::remove(const word& keyword)
 {
-    typename HashTable<T*>::iterator iter = hashedTs_.find(Keyword);
+    typename HashTable<T*>::iterator iter = hashedTs_.find(keyword);
 
     if (iter != hashedTs_.end())
     {
@@ -192,19 +229,29 @@ T* DictionaryBase<IDLListType, T>::remove(const word& Keyword)
 }
 
 
-//- Clear the dictionary
 template<class IDLListType, class T>
-void DictionaryBase<IDLListType, T>::clear()
+void Foam::DictionaryBase<IDLListType, T>::clear()
 {
     IDLListType::clear();
     hashedTs_.clear();
 }
 
 
+template<class IDLListType, class T>
+void Foam::DictionaryBase<IDLListType, T>::transfer
+(
+    DictionaryBase<IDLListType, T>& dict
+)
+{
+    IDLListType::transfer(dict);
+    hashedTs_.transfer(dict.hashedTs_);
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class IDLListType, class T>
-void DictionaryBase<IDLListType, T>::operator=
+void Foam::DictionaryBase<IDLListType, T>::operator=
 (
     const DictionaryBase<IDLListType, T>& dict
 )
@@ -218,25 +265,11 @@ void DictionaryBase<IDLListType, T>::operator=
     }
 
     IDLListType::operator=(dict);
-
     this->hashedTs_.clear();
-
+    this->addEntries();
-    for
-    (
-        typename IDLListType::iterator iter = this->begin();
-        iter != this->end();
-        ++iter
-    )
-    {
-        this->hashedTs_.insert((*iter).keyword(), &(*iter));
-    }
 }
 
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 #include "DictionaryBaseIO.C"

src/OpenFOAM/containers/Dictionaries/DictionaryBase/DictionaryBase.H

@@ -29,12 +29,12 @@ Description
     Base dictionary class templated on both the form of doubly-linked list
     it uses as well as the type it holds.
 
-    The double templating allows for the instantiation of forms with and
+    The double templating allows for the instantiation of forms with or
     without storage management.
 
 Note
     The IDLListType parameter should itself be a template but this confused
-    gcc 2.95.2 so it has to be instantiated for T when an intantiation of
+    gcc 2.95.2 so it has to be instantiated for T when an instantiation of
     DictionaryBase is requested
 
 See Also
@@ -67,7 +67,7 @@ Ostream& operator<<(Ostream&, const DictionaryBase<IDLListType, T>&);
 
 
 /*---------------------------------------------------------------------------*\
-                           Class DictionaryBase Declaration
+                      Class DictionaryBase Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class IDLListType, class T>
@@ -77,7 +77,7 @@ class DictionaryBase
 {
     // Private data
 
-        //- HashTable of the enries held on the DL-list for quick lookup
+        //- HashTable of the entries held on the IDLListType for quick lookup
         HashTable<T*> hashedTs_;
 
 
@@ -99,10 +99,10 @@ public:
 
         //- Construct from Istream using given Istream constructor class
         template<class INew>
-        DictionaryBase(Istream& is, const INew& inewt);
+        DictionaryBase(Istream&, const INew&);
 
-        //- Construct from Istream
+        //- Construct from Istream using default Istream constructor class
-        DictionaryBase(Istream& is);
+        DictionaryBase(Istream&);
 
 
     // Member functions
@@ -110,7 +110,13 @@ public:
         // Search and lookup
 
             //- Search DictionaryBase for given keyword
-            bool found(const word& keyword) const;
+            bool found(const word&) const;
+
+            //- Find and return an entry if present, otherwise return NULL
+            const T* lookupPtr(const word&) const;
+
+            //- Find and return an entry if present, otherwise return NULL
+            T* lookupPtr(const word&);
 
             //- Find and return entry
             const T* lookup(const word&) const;
@@ -125,17 +131,21 @@ public:
         // Editing
 
             //- Add at head of dictionary
-            void insert(const word& keyword, T*);
+            void insert(const word&, T*);
 
             //- Add at tail of dictionary
-            void append(const word& keyword, T*);
+            void append(const word&, T*);
 
-            //- Remove and return entry specified by keyword
+            //- Remove and return entry specified by keyword.
-            T* remove(const word& keyword);
+            //  Return NULL if the keyword was not found.
+            T* remove(const word&);
 
             //- Clear the dictionary
             void clear();
 
+            //- Transfer the contents of the argument into this DictionaryBase
+            //  and annull the argument.
+            void transfer(DictionaryBase<IDLListType, T>&);
 
     // Member operators
 

src/OpenFOAM/containers/Dictionaries/DictionaryBase/DictionaryBaseIO.C

@@ -30,15 +30,13 @@ Description
 #include "DictionaryBase.H"
 #include "IOstreams.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * Ostream Operator  * * * * * * * * * * * * * * //
 
 template<class IDLListType, class T>
-Ostream& operator<<(Ostream& os, const DictionaryBase<IDLListType, T>& dict)
+Foam::Ostream& Foam::operator<<
+(
+    Ostream& os,
+    const DictionaryBase<IDLListType, T>& dict)
 {
     for
     (
@@ -53,7 +51,7 @@ Ostream& operator<<(Ostream& os, const DictionaryBase<IDLListType, T>& dict)
         if (!os.good())
         {
             Info
-                << "operator<<(Ostream& os, const DictionaryBase&) : "
+                << "operator<<(Ostream&, const DictionaryBase&) : "
                 << "Can't write entry for DictionaryBase"
                 << endl;
 
@@ -67,6 +65,4 @@ Ostream& operator<<(Ostream& os, const DictionaryBase<IDLListType, T>& dict)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/Dictionaries/PtrDictionary/PtrDictionary.C

@@ -26,20 +26,15 @@ License
 
 #include "PtrDictionary.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class T>
-PtrDictionary<T>::PtrDictionary()
+Foam::PtrDictionary<T>::PtrDictionary()
 {}
 
 
 template<class T>
-PtrDictionary<T>::PtrDictionary(const PtrDictionary& dict)
+Foam::PtrDictionary<T>::PtrDictionary(const PtrDictionary& dict)
 :
     DictionaryBase<DLPtrList<T>, T>(dict)
 {}
@@ -47,14 +42,14 @@ PtrDictionary<T>::PtrDictionary(const PtrDictionary& dict)
 
 template<class T>
 template<class INew>
-PtrDictionary<T>::PtrDictionary(Istream& is, const INew& iNew)
+Foam::PtrDictionary<T>::PtrDictionary(Istream& is, const INew& iNew)
 :
     DictionaryBase<DLPtrList<T>, T>(is, iNew)
 {}
 
 
 template<class T>
-PtrDictionary<T>::PtrDictionary(Istream& is)
+Foam::PtrDictionary<T>::PtrDictionary(Istream& is)
 :
     DictionaryBase<DLPtrList<T>, T>(is)
 {}
@@ -62,6 +57,4 @@ PtrDictionary<T>::PtrDictionary(Istream& is)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/Dictionaries/PtrDictionary/PtrDictionary.H

@@ -27,8 +27,10 @@ Class
 
 Description
     Template dictionary class which does not manages the storage
-    associated with it.  It is derived from DictionaryBase instantiated on
+    associated with it.
-    a non-memory managed form of intrusive doubly-linked list of T.
+
+    It is derived from DictionaryBase instantiated on a non-memory managed
+    form of intrusive doubly-linked list of T.
 
 SourceFiles
     PtrDictionary.C
@@ -47,7 +49,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class PtrDictionary Declaration
+                        Class PtrDictionary Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class T>

src/OpenFOAM/containers/Dictionaries/UDictionary/UDictionary.C

@@ -26,22 +26,15 @@ License
 
 #include "UDictionary.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-// Null constructor
 template<class T>
-UDictionary<T>::UDictionary()
+Foam::UDictionary<T>::UDictionary()
 {}
 
 
-// Copy constructor
 template<class T>
-UDictionary<T>::UDictionary(const UDictionary& dict)
+Foam::UDictionary<T>::UDictionary(const UDictionary& dict)
 :
     DictionaryBase<UIDLList<T>, T>(dict)
 {}
@@ -49,6 +42,4 @@ UDictionary<T>::UDictionary(const UDictionary& dict)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/Dictionaries/UDictionary/UDictionary.H

@@ -49,7 +49,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class UDictionary Declaration
+                         Class UDictionary Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class T>

src/OpenFOAM/containers/Dictionaries/UPtrDictionary/UPtrDictionary.C

@@ -26,22 +26,15 @@ License
 
 #include "UPtrDictionary.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-// Null constructor
 template<class T>
-UPtrDictionary<T>::UPtrDictionary()
+Foam::UPtrDictionary<T>::UPtrDictionary()
 {}
 
 
-// Copy constructor
 template<class T>
-UPtrDictionary<T>::UPtrDictionary(const UPtrDictionary& dict)
+Foam::UPtrDictionary<T>::UPtrDictionary(const UPtrDictionary& dict)
 :
     DictionaryBase<DLList<T*>, T>(dict)
 {}
@@ -49,6 +42,4 @@ UPtrDictionary<T>::UPtrDictionary(const UPtrDictionary& dict)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/Dictionaries/UPtrDictionary/UPtrDictionary.H

@@ -27,8 +27,10 @@ Class
 
 Description
     Template dictionary class which does not manages the storage
-    associated with it.  It is derived from DictionaryBase instantiated on
+    associated with it.
-    a non-memory managed form of intrusive doubly-linked list of \<T\>.
+
+    It is derived from DictionaryBase instantiated on a non-memory managed
+    form of intrusive doubly-linked list of \<T\>.
 
 SourceFiles
     UPtrDictionary.C
@@ -47,7 +49,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class UPtrDictionary Declaration
+                       Class UPtrDictionary Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class T>

src/OpenFOAM/containers/HashTables/HashTable/HashTable.C

@@ -456,6 +456,14 @@ void HashTable<T, Key, Hash>::clear()
 }
 
 
+template<class T, class Key, class Hash>
+void HashTable<T, Key, Hash>::clearStorage()
+{
+    clear();
+    resize(0);
+}
+
+
 template<class T, class Key, class Hash>
 void HashTable<T, Key, Hash>::transfer(HashTable<T, Key, Hash>& ht)
 {

src/OpenFOAM/containers/HashTables/HashTable/HashTable.H

@@ -54,6 +54,7 @@ template<class T>
 class List;
 
 template<class T, class Key, class Hash> class HashTable;
+template<class T, class Key, class Hash> class HashPtrTable;
 
 template<class T, class Key, class Hash> Istream& operator>>
 (
@@ -102,7 +103,7 @@ class HashTable
                 //- Construct given key, next pointer and object
                 inline hashedEntry
                 (
-                    const Key& key,
+                    const Key&,
                     hashedEntry* next,
                     const T& newEntry
                 );
@@ -127,7 +128,7 @@ class HashTable
     // Private Member Functions
 
         //- Assign a new hashedEntry to a possibly already existing key
-        bool set(const Key& key, const T& newElmt, bool protect);
+        bool set(const Key&, const T& newElmt, bool protect);
 
 public:
 
@@ -173,15 +174,15 @@ public:
             inline label size() const;
 
             //- Return true if hashedEntry is found in table
-            bool found(const Key& key) const;
+            bool found(const Key&) const;
 
             //- Find and return an iterator set at the hashedEntry
             //  If not found iterator = end()
-            iterator find(const Key& key);
+            iterator find(const Key&);
 
             //- Find and return an const_iterator set at the hashedEntry
             //  If not found iterator = end()
-            const_iterator find(const Key& key) const;
+            const_iterator find(const Key&) const;
 
             //- Return the table of contents
             List<Key> toc() const;
@@ -190,16 +191,16 @@ public:
         // Edit
 
             //- Insert a new hashedEntry
-            inline bool insert(const Key& key, const T& newElmt);
+            inline bool insert(const Key&, const T& newElmt);
 
             //- Assign a new hashedEntry, overwriting existing entries
-            inline bool set(const Key& key, const T& newElmt);
+            inline bool set(const Key&, const T& newElmt);
 
             //- Erase an hashedEntry specified by given iterator
-            bool erase(const iterator& it);
+            bool erase(const iterator&);
 
             //- Erase an hashedEntry specified by given key if in table
-            bool erase(const Key& key);
+            bool erase(const Key&);
 
             //- Resize the hash table for efficiency
             void resize(const label newSize);
@@ -207,6 +208,10 @@ public:
             //- Clear all entries from table
             void clear();
 
+            //- Clear the table entries and the table itself.
+            //  Equivalent to clear() followed by resize(0)
+            void clearStorage();
+
             //- Transfer the contents of the argument table into this table
             //  and annull the argument table.
             void transfer(HashTable<T, Key, Hash>&);
@@ -215,14 +220,14 @@ public:
     // Member Operators
 
         //- Find and return an hashedEntry
-        inline T& operator[](const Key& key);
+        inline T& operator[](const Key&);
 
         //- Find and return an hashedEntry
-        inline const T& operator[](const Key& key) const;
+        inline const T& operator[](const Key&) const;
 
         //- Find and return an hashedEntry and
         //  if it is not present create it null.
-        inline T& operator()(const Key& key);
+        inline T& operator()(const Key&);
 
         //- Assignment
         void operator=(const HashTable<T, Key, Hash>&);
@@ -290,13 +295,13 @@ public:
 
             // Member operators
 
-                inline void operator=(const iterator& iter);
+                inline void operator=(const iterator&);
 
-                inline bool operator==(const iterator& iter) const;
+                inline bool operator==(const iterator&) const;
-                inline bool operator!=(const iterator& iter) const;
+                inline bool operator!=(const iterator&) const;
 
-                inline bool operator==(const const_iterator& iter) const;
+                inline bool operator==(const const_iterator&) const;
-                inline bool operator!=(const const_iterator& iter) const;
+                inline bool operator!=(const const_iterator&) const;
 
                 inline T& operator*();
                 inline T& operator()();
@@ -352,13 +357,13 @@ public:
 
             // Member operators
 
-                inline void operator=(const const_iterator& iter);
+                inline void operator=(const const_iterator&);
 
-                inline bool operator==(const const_iterator& iter) const;
+                inline bool operator==(const const_iterator&) const;
-                inline bool operator!=(const const_iterator& iter) const;
+                inline bool operator!=(const const_iterator&) const;
 
-                inline bool operator==(const iterator& iter) const;
+                inline bool operator==(const iterator&) const;
-                inline bool operator!=(const iterator& iter) const;
+                inline bool operator!=(const iterator&) const;
 
                 inline const T& operator*();
                 inline const T& operator()();

src/OpenFOAM/containers/LinkedLists/accessTypes/ILList/ILList.C

@@ -26,22 +26,17 @@ License
 
 #include "ILList.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-ILList<LListBase, T>::ILList(const ILList<LListBase, T>& slpl)
+Foam::ILList<LListBase, T>::ILList(const ILList<LListBase, T>& lst)
 :
     UILList<LListBase, T>()
 {
     for
     (
-        typename UILList<LListBase, T>::const_iterator iter = slpl.begin();
+        typename UILList<LListBase, T>::const_iterator iter = lst.begin();
-        iter != slpl.end();
+        iter != lst.end();
         ++iter
     )
     {
@@ -53,9 +48,9 @@ ILList<LListBase, T>::ILList(const ILList<LListBase, T>& slpl)
 #ifndef __INTEL_COMPILER
 template<class LListBase, class T>
 template<class CloneArg>
-ILList<LListBase, T>::ILList
+Foam::ILList<LListBase, T>::ILList
 (
-    const ILList<LListBase, T>& slpl,
+    const ILList<LListBase, T>& lst,
     const CloneArg& cloneArg
 )
 :
@@ -63,8 +58,8 @@ ILList<LListBase, T>::ILList
 {
     for
     (
-        typename UILList<LListBase, T>::const_iterator iter = slpl.begin();
+        typename UILList<LListBase, T>::const_iterator iter = lst.begin();
-        iter != slpl.end();
+        iter != lst.end();
         ++iter
     )
     {
@@ -77,7 +72,7 @@ ILList<LListBase, T>::ILList
 // * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-ILList<LListBase, T>::~ILList()
+Foam::ILList<LListBase, T>::~ILList()
 {
     this->clear();
 }
@@ -85,9 +80,8 @@ ILList<LListBase, T>::~ILList()
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-//- Return and remove head
 template<class LListBase, class T>
-bool ILList<LListBase, T>::eraseHead()
+bool Foam::ILList<LListBase, T>::eraseHead()
 {
     T* tPtr;
     if ((tPtr = this->removeHead()))
@@ -101,9 +95,8 @@ bool ILList<LListBase, T>::eraseHead()
     }
 }
 
-//- Return and remove element
 template<class LListBase, class T>
-bool ILList<LListBase, T>::erase(T* p)
+bool Foam::ILList<LListBase, T>::erase(T* p)
 {
     T* tPtr;
     if ((tPtr = remove(p)))
@@ -119,7 +112,7 @@ bool ILList<LListBase, T>::erase(T* p)
 
 
 template<class LListBase, class T>
-void ILList<LListBase, T>::clear()
+void Foam::ILList<LListBase, T>::clear()
 {
     label oldSize = this->size();
     for (label i=0; i<oldSize; i++)
@@ -131,17 +124,25 @@ void ILList<LListBase, T>::clear()
 }
 
 
+template<class LListBase, class T>
+void Foam::ILList<LListBase, T>::transfer(ILList<LListBase, T>& lst)
+{
+    clear();
+    LListBase::transfer(lst);
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-void ILList<LListBase, T>::operator=(const ILList<LListBase, T>& slpl)
+void Foam::ILList<LListBase, T>::operator=(const ILList<LListBase, T>& lst)
 {
     this->clear();
 
     for
     (
-        typename UILList<LListBase, T>::const_iterator iter = slpl.begin();
+        typename UILList<LListBase, T>::const_iterator iter = lst.begin();
-        iter != slpl.end();
+        iter != lst.end();
         ++iter
     )
     {
@@ -149,11 +150,6 @@ void ILList<LListBase, T>::operator=(const ILList<LListBase, T>& slpl)
     }
 }
 
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
 
 #include "ILListIO.C"

src/OpenFOAM/containers/LinkedLists/accessTypes/ILList/ILList.H

@@ -71,7 +71,7 @@ class ILList
 
         //- Read from Istream using given Istream constructor class
         template<class INew>
-        void read(Istream&, const INew& inewt);
+        void read(Istream&, const INew&);
 
 
 public:
@@ -96,7 +96,7 @@ public:
 
         //- Copy constructor with additional argument for clone
         template<class CloneArg>
-        ILList(const ILList<LListBase, T>& slpl, const CloneArg& cloneArg)
+        ILList(const ILList<LListBase, T>& lst, const CloneArg& cloneArg)
         #ifdef __INTEL_COMPILER
         :
             UILList<LListBase, T>()
@@ -104,8 +104,8 @@ public:
             for
             (
                 typename UILList<LListBase, T>::const_iterator iter =
-                    slpl.begin();
+                    lst.begin();
-                iter != slpl.end();
+                iter != lst.end();
                 ++iter
             )
             {
@@ -118,7 +118,7 @@ public:
 
         //- Construct from Istream using given Istream constructor class
         template<class INew>
-        ILList(Istream&, const INew& inewt);
+        ILList(Istream&, const INew&);
 
 
     // Destructor
@@ -139,6 +139,10 @@ public:
             //- Clear the contents of the list
             void clear();
 
+            //- Transfer the contents of the argument into this List
+            //  and annull the argument list.
+            void transfer(ILList<LListBase, T>&);
+
 
     // Member operators
 

src/OpenFOAM/containers/LinkedLists/accessTypes/ILList/ILListIO.C

@@ -30,24 +30,19 @@ Description
 #include "Istream.H"
 #include "INew.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
 template<class INew>
-void ILList<LListBase, T>::read(Istream& is, const INew& inewt)
+void Foam::ILList<LListBase, T>::read(Istream& is, const INew& iNew)
 {
-    is.fatalCheck("operator>>(Istream& is, ILList<LListBase, T>& L)");
+    is.fatalCheck("operator>>(Istream&, ILList<LListBase, T>&)");
 
     token firstToken(is);
 
     is.fatalCheck
     (
-        "operator>>(Istream& is, ILList<LListBase, T>& L) : reading first token"
+        "operator>>(Istream&, ILList<LListBase, T>&) : reading first token"
     );
 
     if (firstToken.isLabel())
@@ -63,26 +58,26 @@ void ILList<LListBase, T>::read(Istream& is, const INew& inewt)
             {
                 for (label i=0; i<s; i++)
                 {
-                    append(inewt(is).ptr());
+                    append(iNew(is).ptr());
-                
+
                     is.fatalCheck
                     (
-                        "operator>>(Istream& is, ILList<LListBase, T>& L) : "
+                        "operator>>(Istream&, ILList<LListBase, T>&) : "
                         "reading entry"
                     );
                 }
             }
             else
             {
-                T* tPtr = inewt(is).ptr();
+                T* tPtr = iNew(is).ptr();
                 append(tPtr);
 
                 is.fatalCheck
                 (
-                    "operator>>(Istream& is, ILList<LListBase, T>& L) : "
+                    "operator>>(Istream&, ILList<LListBase, T>&) : "
                     "reading entry"
                 );
-                
+
                 for (label i=1; i<s; i++)
                 {
                     append(new T(*tPtr));
@@ -99,14 +94,14 @@ void ILList<LListBase, T>::read(Istream& is, const INew& inewt)
         {
             FatalIOErrorIn
             (
-                "operator>>(Istream& is, ILList<LListBase, T>& L)",
+                "operator>>(Istream&, ILList<LListBase, T>&)",
                 is
             )   << "incorrect first token, '(', found " << firstToken.info()
                 << exit(FatalIOError);
         }
 
         token lastToken(is);
-        is.fatalCheck("operator>>(Istream& is, ILList<LListBase, T>& L)");
+        is.fatalCheck("operator>>(Istream&, ILList<LListBase, T>&)");
 
         while
         (
@@ -117,36 +112,34 @@ void ILList<LListBase, T>::read(Istream& is, const INew& inewt)
         )
         {
             is.putBack(lastToken);
-            append(inewt(is).ptr());
+            append(iNew(is).ptr());
 
             is >> lastToken;
-            is.fatalCheck("operator>>(Istream& is, ILList<LListBase, T>& L)");
+            is.fatalCheck("operator>>(Istream&, ILList<LListBase, T>&)");
         }
     }
     else
     {
-        FatalIOErrorIn("operator>>(Istream& is, ILList<LListBase, T>& L)", is)
+        FatalIOErrorIn("operator>>(Istream&, ILList<LListBase, T>&)", is)
             << "incorrect first token, expected <int> or '(', found "
             << firstToken.info()
             << exit(FatalIOError);
     }
 
-    is.fatalCheck("operator>>(Istream& is, ILList<LListBase, T>& L)");
+    is.fatalCheck("operator>>(Istream&, ILList<LListBase, T>&)");
 }
 
 
-//- Construct from Istream using given Istream constructor class
 template<class LListBase, class T>
 template<class INew>
-ILList<LListBase, T>::ILList(Istream& is, const INew& inewt)
+Foam::ILList<LListBase, T>::ILList(Istream& is, const INew& iNew)
 {
-    read(is, inewt);
+    read(is, iNew);
 }
 
 
-// Construct from Istream
 template<class LListBase, class T>
-ILList<LListBase, T>::ILList(Istream& is)
+Foam::ILList<LListBase, T>::ILList(Istream& is)
 {
     read(is, INew<T>());
 }
@@ -155,7 +148,7 @@ ILList<LListBase, T>::ILList(Istream& is)
 // * * * * * * * * * * * * * * * Istream Operator  * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-Istream& operator>>(Istream& is, ILList<LListBase, T>& L)
+Foam::Istream& Foam::operator>>(Istream& is, ILList<LListBase, T>& L)
 {
     L.clear();
     L.read(is, INew<T>());
@@ -166,6 +159,4 @@ Istream& operator>>(Istream& is, ILList<LListBase, T>& L)
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/containers/LinkedLists/accessTypes/LList/LList.C

@@ -27,22 +27,16 @@ Description
 \*---------------------------------------------------------------------------*/
 
 #include "error.H"
-
 #include "LList.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-LList<LListBase, T>::LList(const LList<LListBase, T>& slpl)
+Foam::LList<LListBase, T>::LList(const LList<LListBase, T>& lst)
 :
     LListBase()
 {
-    for (const_iterator iter = slpl.begin(); iter != slpl.end(); ++iter)
+    for (const_iterator iter = lst.begin(); iter != lst.end(); ++iter)
     {
         append(iter());
     }
@@ -50,7 +44,7 @@ LList<LListBase, T>::LList(const LList<LListBase, T>& slpl)
 
 
 template<class LListBase, class T>
-LList<LListBase, T>::~LList()
+Foam::LList<LListBase, T>::~LList()
 {
     this->clear();
 }
@@ -59,7 +53,7 @@ LList<LListBase, T>::~LList()
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-void LList<LListBase, T>::clear()
+void Foam::LList<LListBase, T>::clear()
 {
     label oldSize = this->size();
     for (label i=0; i<oldSize; i++)
@@ -71,24 +65,28 @@ void LList<LListBase, T>::clear()
 }
 
 
+template<class LListBase, class T>
+void Foam::LList<LListBase, T>::transfer(LList<LListBase, T>& lst)
+{
+    clear();
+    LListBase::transfer(lst);
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class LListBase, class T>
-void LList<LListBase, T>::operator=(const LList<LListBase, T>& slpl)
+void Foam::LList<LListBase, T>::operator=(const LList<LListBase, T>& lst)
 {
     this->clear();
 
-    for (const_iterator iter = slpl.begin(); iter != slpl.end(); ++iter)
+    for (const_iterator iter = lst.begin(); iter != lst.end(); ++iter)
     {
         append(iter());
     }
 }
 
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
 
 #include "LListIO.C"