Merge branch 'master' of /home/noisy3/OpenFOAM/OpenFOAM-dev

applications/solvers/heatTransfer/buoyantBoussinesqFoam/Make/files

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

applications/solvers/heatTransfer/buoyantBoussinesqFoam/Make/options

@@ -0,0 +1,12 @@
+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/turbulenceModels \
+    -I$(LIB_SRC)/turbulenceModels/incompressible/RAS/lnInclude \
+    -I$(LIB_SRC)/transportModels \
+    -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -lmeshTools \
+    -lincompressibleRASModels \
+    -lincompressibleTransportModels

applications/solvers/heatTransfer/buoyantBoussinesqFoam/TEqn.H

@@ -0,0 +1,18 @@
+{
+    volScalarField kappaEff
+    (
+        "kappaEff",
+        turbulence->nu() + turbulence->nut()/Prt
+    );
+
+    fvScalarMatrix TEqn
+    (
+        fvm::ddt(T)
+      + fvm::div(phi, T)
+      - fvm::laplacian(kappaEff, T)
+    );
+
+    TEqn.relax();
+
+    TEqn.solve();
+}

applications/solvers/heatTransfer/buoyantBoussinesqFoam/UEqn.H

@@ -0,0 +1,23 @@
+    // Solve the momentum equation
+
+    tmp<fvVectorMatrix> UEqn
+    (
+        fvm::ddt(U)
+      + fvm::div(phi, U)
+      + turbulence->divDevReff(U)
+    );
+
+    UEqn().relax();
+
+    solve
+    (
+        UEqn()
+      ==
+       -fvc::reconstruct
+        (
+            (
+                fvc::snGrad(pd)
+              - betaghf*fvc::snGrad(T)
+            ) * mesh.magSf()
+        )
+    );

applications/solvers/heatTransfer/buoyantBoussinesqFoam/buoyantBoussinesqFoam.C

@@ -0,0 +1,108 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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
+    buoyantBoussinesqSimpleFoam
+
+Description
+    Steady-state solver for buoyant, turbulent flow of incompressible fluids
+
+    Uses the Boussinesq approximation:
+    \f[
+        rho_{eff} = 1 - beta(T - T_{ref})
+    \f]
+
+    where:
+        \f$ rho_{eff} \f$ = the effective (driving) density
+        beta = thermal expansion coefficient [1/K]
+        T = temperature [K]
+        \f$ T_{ref} \f$ = reference temperature [K]
+
+    Valid when:
+    \f[
+        rho_{eff} << 1
+    \f]
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "singlePhaseTransportModel.H"
+#include "RASModel.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+#   include "readEnvironmentalProperties.H"
+#   include "createFields.H"
+#   include "initContinuityErrs.H"
+#   include "readTimeControls.H"
+#   include "CourantNo.H"
+#   include "setInitialDeltaT.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+    Info<< "\nStarting time loop\n" << endl;
+
+    for (runTime++; !runTime.end(); runTime++)
+    {
+        Info<< "Time = " << runTime.timeName() << nl << endl;
+
+#       include "readTimeControls.H"
+#       include "readPISOControls.H"
+#       include "CourantNo.H"
+#       include "setDeltaT.H"
+
+#       include "UEqn.H"
+
+        // --- PISO loop
+        for (int corr=0; corr<nCorr; corr++)
+        {
+#           include "TEqn.H"
+#           include "pdEqn.H"
+        }
+
+        turbulence->correct();
+
+        if (runTime.write())
+        {
+#           include "writeAdditionalFields.H"
+        }
+
+        Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info<< "End\n" << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/solvers/heatTransfer/buoyantBoussinesqFoam/createFields.H

@@ -0,0 +1,67 @@
+    Info<< "Reading thermophysical properties\n" << endl;
+
+    Info<< "Reading field T\n" << endl;
+    volScalarField T
+    (
+        IOobject
+        (
+            "T",
+            runTime.timeName(),
+            mesh,
+            IOobject::MUST_READ,
+            IOobject::AUTO_WRITE
+        ),
+        mesh
+    );
+
+    // kinematic pd
+    Info<< "Reading field pd\n" << endl;
+    volScalarField pd
+    (
+        IOobject
+        (
+            "pd",
+            runTime.timeName(),
+            mesh,
+            IOobject::MUST_READ,
+            IOobject::AUTO_WRITE
+        ),
+        mesh
+    );
+
+    Info<< "Reading field U\n" << endl;
+    volVectorField U
+    (
+        IOobject
+        (
+            "U",
+            runTime.timeName(),
+            mesh,
+            IOobject::MUST_READ,
+            IOobject::AUTO_WRITE
+        ),
+        mesh
+    );
+
+#   include "createPhi.H"
+
+#   include "readTransportProperties.H"
+
+    Info<< "Creating turbulence model\n" << endl;
+    autoPtr<incompressible::RASModel> turbulence
+    (
+        incompressible::RASModel::New(U, phi, laminarTransport)
+    );
+
+    Info<< "Calculating field beta*(g.h)\n" << endl;
+    surfaceScalarField betaghf("betagh", beta*(g & mesh.Cf()));
+
+    label pdRefCell = 0;
+    scalar pdRefValue = 0.0;
+    setRefCell
+    (
+        pd,
+        mesh.solutionDict().subDict("SIMPLE"),
+        pdRefCell,
+        pdRefValue
+    );

applications/solvers/heatTransfer/buoyantBoussinesqFoam/pdEqn.H

@@ -0,0 +1,42 @@
+{
+    volScalarField rUA("rUA", 1.0/UEqn().A());
+    surfaceScalarField rUAf("(1|A(U))", fvc::interpolate(rUA));
+
+    U = rUA*UEqn().H();
+    UEqn.clear();
+
+    surfaceScalarField phiU
+    (
+        (fvc::interpolate(U) & mesh.Sf())
+      + fvc::ddtPhiCorr(rUA, U, phi)
+    );
+
+    phi = phiU + betaghf*fvc::snGrad(T)*rUAf*mesh.magSf();
+
+    for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
+    {
+        fvScalarMatrix pdEqn
+        (
+            fvm::laplacian(rUAf, pd) == fvc::div(phi)
+        );
+
+        if (corr == nCorr-1 && nonOrth == nNonOrthCorr)
+        {
+            pdEqn.solve(mesh.solver(pd.name() + "Final"));
+        }
+        else
+        {
+            pdEqn.solve(mesh.solver(pd.name()));
+        }
+
+        if (nonOrth == nNonOrthCorr)
+        {
+            phi += pdEqn.flux();
+        }
+    }
+
+    U -= rUA*fvc::reconstruct((phi - phiU)/rUAf);
+    U.correctBoundaryConditions();
+
+    #include "continuityErrs.H"
+}

applications/solvers/heatTransfer/buoyantBoussinesqFoam/readTransportProperties.H

@@ -0,0 +1,13 @@
+    singlePhaseTransportModel laminarTransport(U, phi);
+
+    // thermal expansion coefficient [1/K]
+    dimensionedScalar beta(laminarTransport.lookup("beta"));
+
+    // reference temperature [K]
+    dimensionedScalar TRef(laminarTransport.lookup("TRef"));
+
+    // reference kinematic pressure [m2/s2]
+    dimensionedScalar pRef(laminarTransport.lookup("pRef"));
+
+    // turbulent Prandtl number
+    dimensionedScalar Prt(laminarTransport.lookup("Prt"));

applications/solvers/heatTransfer/buoyantBoussinesqFoam/writeAdditionalFields.H

@@ -0,0 +1,29 @@
+{
+    volScalarField rhoEff
+    (
+        IOobject
+        (
+            "rhoEff",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::AUTO_WRITE
+        ),
+        1.0 - beta*(T - TRef)
+    );
+    rhoEff.write();
+
+    volScalarField p
+    (
+        IOobject
+        (
+            "p",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::AUTO_WRITE
+        ),
+        pd + rhoEff*(g & mesh.C()) + pRef
+    );
+    p.write();
+}

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/buoyantSimpleRadiationFoam.C

@@ -47,6 +47,7 @@ int main(int argc, char *argv[])
 #   include "createMesh.H"
 #   include "readEnvironmentalProperties.H"
 #   include "createFields.H"
+#   include "createRadiationModel.H"
 #   include "initContinuityErrs.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/convergenceCheck.H

@@ -1,9 +0,0 @@
-// check convergence
-
-if (maxResidual < convergenceCriterion)
-{
-    Info<< "reached convergence criterion: " << convergenceCriterion << endl;
-    runTime.writeAndEnd();
-    Info<< "latestTime = " << runTime.timeName() << endl;
-}
-

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/createFields.H

@@ -1,97 +0,0 @@
-    Info<< "Reading thermophysical properties\n" << endl;
-
-    autoPtr<basicThermo> thermo
-    (
-        basicThermo::New(mesh)
-    );
-
-    volScalarField rho
-    (
-        IOobject
-        (
-            "rho",
-            runTime.timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::NO_WRITE
-        ),
-        thermo->rho()
-    );
-
-    volScalarField& p = thermo->p();
-    volScalarField& h = thermo->h();
-    const volScalarField& T = thermo->T();
-
-
-    Info<< "Reading field U\n" << endl;
-    volVectorField U
-    (
-        IOobject
-        (
-            "U",
-            runTime.timeName(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::AUTO_WRITE
-        ),
-        mesh
-    );
-
-#   include "compressibleCreatePhi.H"
-
-
-    Info<< "Creating turbulence model\n" << endl;
-    autoPtr<compressible::RASModel> turbulence
-    (
-        compressible::RASModel::New
-        (
-            rho,
-            U,
-            phi,
-            thermo()
-        )
-    );
-
-    Info<< "Calculating field g.h\n" << endl;
-    volScalarField gh("gh", g & mesh.C());
-    surfaceScalarField ghf("gh", g & mesh.Cf());
-
-    dimensionedScalar pRef("pRef", p.dimensions(), thermo->lookup("pRef"));
-
-    Info<< "Creating field pd\n" << endl;
-    volScalarField pd
-    (
-        IOobject
-        (
-            "pd",
-            runTime.timeName(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::AUTO_WRITE
-        ),
-        mesh
-    );
-
-    p = pd + rho*gh + pRef;
-    thermo->correct();
-
-
-    label pdRefCell = 0;
-    scalar pdRefValue = 0.0;
-    setRefCell
-    (
-        pd,
-        mesh.solutionDict().subDict("SIMPLE"),
-        pdRefCell,
-        pdRefValue
-    );
-
-
-    Info<< "Creating radiation model\n" << endl;
-    autoPtr<radiation::radiationModel> radiation
-    (
-        radiation::radiationModel::New(T)
-    );
-
-
-    dimensionedScalar initialMass = fvc::domainIntegrate(rho);

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/createRadiationModel.H

@@ -0,0 +1,5 @@
+    Info<< "Creating radiation model\n" << endl;
+    autoPtr<radiation::radiationModel> radiation
+    (
+        radiation::radiationModel::New(thermo->T())
+    );

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/initConvergenceCheck.H

@@ -1,7 +0,0 @@
-// initialize values for convergence checks
-
-    scalar eqnResidual = 1, maxResidual = 0;
-    scalar convergenceCriterion = 0;
-
-    simple.readIfPresent("convergence", convergenceCriterion);
-

applications/solvers/heatTransfer/chtMultiRegionFoam/fluid/compressibleCourantNo.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

applications/solvers/heatTransfer/chtMultiRegionFoam/fluid/compressibleCourantNo.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

applications/solvers/heatTransfer/chtMultiRegionFoam/fluid/hEqn.H

@@ -12,6 +12,6 @@
 
     thermo.correct();
 
-    Info<< "Min/max T:" << min(thermo.T()) << ' ' << max(thermo.T())
+    Info<< "Min/max T:" << min(thermo.T()).value() << ' '
-        << endl;
+        << max(thermo.T()).value() << endl;
 }

applications/test/PackedList/PackedListTest.C

@@ -52,27 +52,47 @@ int main(int argc, char *argv[])
     list1 = -1;
     list1.print(Info);
 
+    Info<< "\ntest zero\n";
+    list1 = 0;
+    list1.print(Info);
+
+    Info<< "\ntest set() with default argument (max_value)\n";
+    list1.set(3);
+    list1.print(Info);
+
     Info<< "\ntest assign between references\n";
     list1[2] = 3;
     list1[4] = list1[2];
     list1.print(Info);
 
     Info<< "\ntest assign between references, with chaining\n";
-    list1[4] = list1[2] = 1;
+    list1[0] = list1[4] = 1;
+    list1.print(Info);
+
+    Info<< "\ntest assign between references, with chaining and auto-vivify\n";
+    list1[1] = list1[8] = list1[10] = list1[14] = 2;
     list1.print(Info);
 
     {
         const PackedList<3>& constLst = list1;
         Info<< "\ntest operator[] const with out-of-range index\n";
         constLst.print(Info);
-        if (!constLst[20])
+        if (constLst[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
         {
             Info<< "[20] is false (expected) list size should be unchanged (const)\n";
         }
         constLst.print(Info);
 
         Info<< "\ntest operator[] non-const with out-of-range index\n";
-        if (!list1[20])
+        if (list1[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
         {
             Info<< "[20] is false (expected) but list was resized?? (non-const)\n";
         }
@@ -91,6 +111,14 @@ int main(int argc, char *argv[])
     list1.resize(8, list1.max_value());
     list1.print(Info);
 
+    Info<< "\ntest flip() function\n";
+    list1.flip();
+    list1.print(Info);
+
+    Info<< "\nre-flip()\n";
+    list1.flip();
+    list1.print(Info);
+
     Info<< "\ntest set() function\n";
     list1.set(1, 5);
     list1.print(Info);
@@ -188,15 +216,23 @@ int main(int argc, char *argv[])
     {
         Info<< "\ntest assignment of iterator\n";
         list1.print(Info);
-        PackedList<3>::iterator cit = list1[25];
+        Info<< "cend()\n";
-        cit.print(Info);
         list1.end().print(Info);
+        PackedList<3>::iterator cit = list1[100];
+        Info<< "out-of-range: ";
+        cit.print(Info);
+        cit = list1[15];
+        Info<< "in-range: ";
+        cit.print(Info);
+        Info<< "out-of-range: ";
+        cit = list1[1000];
+        cit.print(Info);
     }
 
 
     for
     (
-        PackedList<3>::iterator cit = list1[5];
+        PackedList<3>::iterator cit = list1[30];
         cit != list1.end();
         ++cit
     )
@@ -204,14 +240,19 @@ int main(int argc, char *argv[])
         cit.print(Info);
     }
 
-//     Info<< "\ntest operator[] auto-vivify\n";
+    Info<< "\ntest operator[] auto-vivify\n";
-//     const unsigned int val = list1[45];
+    Info<< "size:" << list1.size() << "\n";
-//
+
-//     Info<< "list[45]:" << val << "\n";
+    const unsigned int val = list1[45];
-//     list1[45] = list1.max_value();
+
-//     Info<< "list[45]:" << list1[45] << "\n";
+    Info<< "list[45]:" << val << "\n";
-//     list1[49] = list1.max_value();
+    Info<< "size after read:" << list1.size() << "\n";
-//     list1.print(Info);
+
+    list1[45] = list1.max_value();
+    Info<< "size after write:" << list1.size() << "\n";
+    Info<< "list[45]:" << list1[45] << "\n";
+    list1[49] = list1[100];
+    list1.print(Info);
 
 
     Info<< "\ntest copy constructor + append\n";
@@ -235,6 +276,23 @@ int main(int argc, char *argv[])
     Info<< "removed final value: " << list3.remove() << endl;
     list3.print(Info);
 
+
+    List<bool> list4(4, true);
+    {
+        const List<bool>& constLst = list4;
+        Info<< "\ntest operator[] const with out-of-range index\n";
+        Info<< constLst << endl;
+        if (constLst[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
+        {
+            Info<< "[20] is false (expected) list size should be unchanged (const)\n";
+        }
+        Info<< constLst << endl;
+    }
+
     Info<< "\n\nDone.\n";
 
     return 0;

applications/test/fileName/fileNameTest.C

@@ -32,6 +32,7 @@ Description
 
 #include "fileName.H"
 #include "SubList.H"
+#include "IOobject.H"
 #include "IOstreams.H"
 #include "OSspecific.H"
 
@@ -61,7 +62,8 @@ int main()
         << endl;
 
     // try with different combination
-    for (label start = 0; start < wrdList.size(); ++start)
+    // The final one should emit warnings
+    for (label start = 0; start <= wrdList.size(); ++start)
     {
         fileName instance, local;
         word name;
@@ -69,26 +71,28 @@ int main()
         fileName path(SubList<word>(wrdList, wrdList.size()-start, start));
         fileName path2 = "." / path;
 
-        path.IOobjectComponents
+        IOobject::fileNameComponents
         (
+            path,
             instance,
             local,
             name
         );
 
-        Info<< "IOobjectComponents for " << path << nl
+        Info<< "IOobject::fileNameComponents for " << path << nl
             << "  instance = " << instance << nl
             << "  local    = " << local << nl
             << "  name     = " << name << endl;
 
-        path2.IOobjectComponents
+        IOobject::fileNameComponents
         (
+            path2,
             instance,
             local,
             name
         );
 
-        Info<< "IOobjectComponents for " << path2 << nl
+        Info<< "IOobject::fileNameComponents for " << path2 << nl
             << "  instance = " << instance << nl
             << "  local    = " << local << nl
             << "  name     = " << name << endl;

applications/test/primitivePatch/testPrimitivePatch.C

@@ -69,7 +69,7 @@ void checkFaceEdges
 
         forAll(f, fp)
         {
-            label fp1 = (fp + 1) % f.size();
+            label fp1 = f.fcIndex(fp);
 
             if (edges[myEdges[fp]] != edge(f[fp], f[fp1]))
             {

applications/test/sha1/Make/files

@@ -0,0 +1,3 @@
+testSHA1.C
+
+EXE = $(FOAM_USER_APPBIN)/testSHA1

applications/test/sha1/testSHA1.C

@@ -0,0 +1,135 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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
+    testSHA1
+
+Description
+
+
+\*---------------------------------------------------------------------------*/
+
+#include "OSHA1stream.H"
+#include "IStringStream.H"
+#include "dictionary.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+int main(int argc, char * argv[])
+{
+    SHA1 sha;
+    SHA1Digest shaDig;
+
+    std::string str("The quick brown fox jumps over the lazy dog");
+    Info<< shaDig << nl;
+    Info<< SHA1("The quick brown fox jumps over the lazy dog") << nl;
+
+    sha.append("The quick brown fox jumps over the lazy dog");
+    Info<< sha << nl;
+
+    sha.clear();
+    sha.append("The quick brown fox jumps over the lazy dog");
+    shaDig = sha;
+
+    sha.append("\n");
+    Info<< sha << nl;
+    Info<< shaDig << nl;
+
+    if (sha == shaDig)
+    {
+        Info<<"SHA1 digests are identical\n";
+    }
+    else
+    {
+        Info<<"SHA1 digests are different\n";
+    }
+    Info<<"lhs:" << sha << " rhs:" << shaDig << endl;
+
+    // start over:
+    sha.clear();
+    sha.append(str);
+
+    SHA1Digest shaDig_A = sha;
+
+    SHA1 sha_A = sha;
+
+    sha.append("\n");
+
+    Info<< "digest1: " << sha_A << nl;
+    Info<< "digest2: " << sha << nl;
+
+    // start over:
+    sha.clear();
+    sha.append("\"");
+    sha.append(str);
+    sha.append("\"");
+
+    Info<< "digest3: " << sha << nl;
+
+    // try the output buffer interface
+    {
+        OSHA1stream os;
+
+        os << str;
+        Info<< os.digest() << endl;
+
+        os << str;
+        Info<< os.digest() << endl;
+
+        os.rewind();
+        os << "The quick brown fox jumps over the lazy dog";
+        Info<< os.digest() << endl;
+
+    }
+
+    {
+        dictionary dict
+        (
+            IStringStream
+            (
+                "parent { Default_Boundary_Region { type zeroGradient; } }"
+                "inlet_1 { value inlet_1; }"
+                "inlet_2 { value inlet_2; }"
+                "inlet_3 { value inlet_3; }"
+                "\"inlet_.*\" { value XXX; }"
+            ) ()
+        );
+
+        Info<< "dict:" << endl;
+        dict.write(Info, false);
+
+        dictionary dict2(dict);
+
+        OSHA1stream os;
+        dict.write(os, false);
+        Info<< os.digest() << endl;
+
+        Info<< dict2.digest() << endl;
+    }
+
+
+    return 0;
+}

applications/utilities/mesh/advanced/collapseEdges/collapseEdges.C

@@ -74,20 +74,17 @@ labelList getSortedEdges
         const edge& e = edges[edgeI];
 
         label fp = findIndex(f, e[0]);
-
+        label fp1 = f.fcIndex(fp);
-        label fp1 = (fp+1) % f.size();
 
         if (f[fp1] == e[1])
         {
-            // Edgei in fp-fp1 order
+            // EdgeI between fp -> fp1
             faceEdges[fp] = edgeI;
         }
         else
         {
-            // Edgei between fp-1 and fp
+            // EdgeI between fp-1 -> fp
-            label fpMin1 = (fp == 0 ? f.size()-1 : fp-1);
+            faceEdges[f.rcIndex(fp)] = edgeI;
-
-            faceEdges[fpMin1] = edgeI;
         }
     }
 

applications/utilities/mesh/advanced/modifyMesh/cellSplitter.C

@@ -211,7 +211,7 @@ void Foam::cellSplitter::setRefinement
 
         // Add other pyramids
         for (label i = 1; i < cFaces.size(); i++)
-        {    
+        {
             label addedCellI =
                 meshMod.setAction
                 (
@@ -277,7 +277,7 @@ void Foam::cellSplitter::setRefinement
 
                 label index = findIndex(f0, e[0]);
 
-                bool edgeInFaceOrder = (f0[(index+1) % f0.size()] == e[1]);
+                bool edgeInFaceOrder = (f0[f0.fcIndex(index)] == e[1]);
 
                 // Check if cellI is the face owner
 
@@ -323,7 +323,7 @@ void Foam::cellSplitter::setRefinement
 
                 label index = findIndex(f1, e[0]);
 
-                bool edgeInFaceOrder = (f1[(index+1) % f1.size()] == e[1]);
+                bool edgeInFaceOrder = (f1[f1.fcIndex(index)] == e[1]);
 
                 // Check if cellI is the face owner
 
@@ -362,7 +362,7 @@ void Foam::cellSplitter::setRefinement
             }
         }
     }
-            
+
 
     //
     // Update all existing faces for split owner or neighbour.
@@ -441,7 +441,7 @@ void Foam::cellSplitter::setRefinement
 
                 label patchID, zoneID, zoneFlip;
                 getFaceInfo(faceI, patchID, zoneID, zoneFlip);
-                
+
                 meshMod.setAction
                 (
                     polyModifyFace
@@ -458,7 +458,7 @@ void Foam::cellSplitter::setRefinement
                     )
                 );
             }
-    
+
             faceUpToDate[faceI] = true;
         }
     }

applications/utilities/mesh/conversion/Optional/ccm26ToFoam/ccm26ToFoam.C

@@ -615,7 +615,7 @@ int main(int argc, char *argv[])
     {
         fileName ccmFile(args.additionalArgs()[0]);
 
-        if (!exists(ccmFile))
+        if (!isFile(ccmFile))
         {
             FatalErrorIn(args.executable())
                 << "Cannot read file " << ccmFile

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

@@ -129,14 +129,14 @@ int main(int argc, char *argv[])
         Info<< "Reading .face file for boundary information" << nl << endl;
     }
 
-    if (!exists(nodeFile) || !exists(eleFile))
+    if (!isFile(nodeFile) || !isFile(eleFile))
     {
         FatalErrorIn(args.executable())
             << "Cannot read " << nodeFile << " or " << eleFile
             << exit(FatalError);
     }
 
-    if (readFaceFile && !exists(faceFile))
+    if (readFaceFile && !isFile(faceFile))
     {
         FatalErrorIn(args.executable())
             << "Cannot read " << faceFile << endl

applications/utilities/mesh/generation/blockMesh/blockMeshApp.C

@@ -108,7 +108,11 @@ int main(int argc, char *argv[])
         (
             new IOobject
             (
-                ( dictPath.isDir() ? dictPath/dictName : dictPath ),
+                (
+                    isDir(dictPath)
+                  ? dictPath/dictName 
+                  : dictPath
+                ),
                 runTime,
                 IOobject::MUST_READ,
                 IOobject::NO_WRITE,

applications/utilities/mesh/manipulation/cellSet/cellSetDict

@@ -79,6 +79,22 @@ topoSetSources
        k        (10 10 10);
     }
 
+    // Cells with centre within cylinder
+    cylinderToCell
+    {
+       p1       (0.2 0.2 -10); // start point on cylinder axis
+       p2       (0.2 0.2 0);   // end point on cylinder axis
+       radius   5.0;
+    }
+
+
+    // Cells with centre within sphere
+    sphereToCell
+    {
+       centre   (0.2 0.2 -10);
+       radius   5.0;
+    }
+
     // Cells in cell zone
     zoneToCell
     {

applications/utilities/mesh/manipulation/setSet/setSet.C

@@ -746,7 +746,8 @@ int main(int argc, char *argv[])
 
         Pout<< "Reading commands from file " << batchFile << endl;
 
-        if (!exists(batchFile))
+        // we also cannot handle .gz files
+        if (!isFile(batchFile, false))
         {
             FatalErrorIn(args.executable())
                 << "Cannot open file " << batchFile << exit(FatalError);

applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C

@@ -627,7 +627,7 @@ autoPtr<mapPolyMesh> createRegionMesh
         Info<< "Testing:" << io.objectPath() << endl;
 
         if (!io.headerOk())
-        //if (!exists(io.objectPath()))
+        // if (!exists(io.objectPath()))
         {
             Info<< "Writing dummy " << regionName/io.name() << endl;
             dictionary dummyDict;

applications/utilities/miscellaneous/patchSummary/patchSummary.C

@@ -63,7 +63,6 @@ int main(int argc, char *argv[])
         Info<< "Time = " << runTime.timeName() << nl << endl;
 
         const IOobjectList fieldObjs(mesh, runTime.timeName());
-
         const wordList objNames = fieldObjs.names();
 
         PtrList<volScalarField> vsf(objNames.size());
@@ -99,7 +98,7 @@ int main(int argc, char *argv[])
         const polyBoundaryMesh& bm = mesh.boundaryMesh();
         forAll(bm, patchI)
         {
-            Info<< "Patch: " << bm[patchI].name() << nl;
+            Info<< bm[patchI].type() << ": " << bm[patchI].name() << nl;
             outputFieldList<scalar>(vsf, patchI);
             outputFieldList<vector>(vvf, patchI);
             outputFieldList<sphericalTensor>(vsptf, patchI);

applications/utilities/parallelProcessing/decomposePar/decomposePar.C

@@ -105,7 +105,7 @@ int main(int argc, char *argv[])
 
     // determine the existing processor count directly
     label nProcs = 0;
-    while (dir(runTime.path()/(word("processor") + name(nProcs))))
+    while (isDir(runTime.path()/(word("processor") + name(nProcs))))
     {
         ++nProcs;
     }
@@ -480,7 +480,7 @@ int main(int argc, char *argv[])
     // Any uniform data to copy/link?
     fileName uniformDir("uniform");
 
-    if (dir(runTime.timePath()/uniformDir))
+    if (isDir(runTime.timePath()/uniformDir))
     {
         Info<< "Detected additional non-decomposed files in "
             << runTime.timePath()/uniformDir

applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C

@@ -63,7 +63,7 @@ int main(int argc, char *argv[])
 
     // determine the processor count directly
     label nProcs = 0;
-    while (dir(args.path()/(word("processor") + name(nProcs))))
+    while (isDir(args.path()/(word("processor") + name(nProcs))))
     {
         ++nProcs;
     }
@@ -383,7 +383,7 @@ int main(int argc, char *argv[])
         // the master processor.
 
         fileName uniformDir0 = databases[0].timePath()/"uniform";
-        if (dir(uniformDir0))
+        if (isDir(uniformDir0))
         {
             cp(uniformDir0, runTime.timePath());
         }

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -355,7 +355,7 @@ int main(int argc, char *argv[])
 
     while
     (
-        exists
+        isDir
         (
             args.rootPath()
           / args.caseName()

applications/utilities/parallelProcessing/redistributeMeshPar/redistributeMeshPar.C

@@ -503,7 +503,7 @@ int main(int argc, char *argv[])
 #   include "setRootCase.H"
 
     // Create processor directory if non-existing
-    if (!Pstream::master() && !dir(args.path()))
+    if (!Pstream::master() && !isDir(args.path()))
     {
         Pout<< "Creating case directory " << args.path() << endl;
         mkDir(args.path());
@@ -525,7 +525,7 @@ int main(int argc, char *argv[])
     const fileName meshDir = runTime.path()/masterInstDir/polyMesh::meshSubDir;
 
     boolList haveMesh(Pstream::nProcs(), false);
-    haveMesh[Pstream::myProcNo()] = dir(meshDir);
+    haveMesh[Pstream::myProcNo()] = isDir(meshDir);
     Pstream::gatherList(haveMesh);
     Pstream::scatterList(haveMesh);
     Info<< "Per processor mesh availability : " << haveMesh << endl;

applications/utilities/postProcessing/dataConversion/foamToEnsight/foamToEnsight.C

@@ -131,7 +131,7 @@ int main(int argc, char *argv[])
 
     if (Pstream::master())
     {
-        if (dir(postProcPath))
+        if (isDir(postProcPath))
         {
             rmDir(postProcPath);
         }

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

@@ -136,7 +136,7 @@ int main(int argc, char *argv[])
     // Ensight and Ensight/data directories must exist
     // do not remove old data - we might wish to convert new results
     // or a particular time interval
-    if (dir(ensightDir))
+    if (isDir(ensightDir))
     {
         Info<<"Warning: reusing existing directory" << nl
             << "    " << ensightDir << endl;
@@ -324,7 +324,7 @@ int main(int argc, char *argv[])
         {
             const word& cloudName = cloudIter.key();
 
-            if (!dir(runTime.timePath()/regionPrefix/"lagrangian"/cloudName))
+            if (!isDir(runTime.timePath()/regionPrefix/"lagrangian"/cloudName))
             {
                 continue;
             }

applications/utilities/postProcessing/dataConversion/foamToFieldview9/foamToFieldview9.C

@@ -260,7 +260,7 @@ int main(int argc, char *argv[])
     // make a directory called FieldView in the case
     fileName fvPath(runTime.path()/"Fieldview");
 
-    if (dir(fvPath))
+    if (isDir(fvPath))
     {
         rmDir(fvPath);
     }
@@ -346,7 +346,7 @@ int main(int argc, char *argv[])
 
         // Output the magic number.
         writeInt(fvFile, FV_MAGIC);
-        
+
         // Output file header and version number.
         writeStr80(fvFile, "FIELDVIEW");
 
@@ -417,7 +417,7 @@ int main(int argc, char *argv[])
         {
             if (volFieldPtrs[fieldI] == NULL)
             {
-                Info<< "    dummy field for "   
+                Info<< "    dummy field for "
                     << volFieldNames[fieldI].c_str() << endl;
             }
 

applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.C

@@ -333,7 +333,7 @@ int main(int argc, char *argv[])
         regionPrefix = regionName;
     }
 
-    if (dir(fvPath))
+    if (isDir(fvPath))
     {
         if
         (

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3Foam.C

@@ -228,7 +228,7 @@ Foam::vtkPV3Foam::vtkPV3Foam
     // avoid argList and get rootPath/caseName directly from the file
     fileName fullCasePath(fileName(FileName).path());
 
-    if (!dir(fullCasePath))
+    if (!isDir(fullCasePath))
     {
         return;
     }
@@ -518,7 +518,7 @@ double* Foam::vtkPV3Foam::findTimes(int& nTimeSteps)
 
             if
             (
-                file(runTime.path()/timeName/meshDir_/"points")
+                isFile(runTime.path()/timeName/meshDir_/"points")
              && IOobject("points", timeName, meshDir_, runTime).headerOk()
             )
             {

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3Foam.H

@@ -156,7 +156,7 @@ class vtkPV3Foam
 
             bool empty() const
             {
-                return (size_ == 0);
+                return !size_;
             }
 
             void reset()

applications/utilities/postProcessing/graphics/PVFoamReader/vtkFoam/vtkFoam.C

@@ -194,7 +194,7 @@ void Foam::vtkFoam::updateSelectedRegions()
     // Read the selected patches and add to the region list
     for (int i=0; i<nRegions; i++)
     {
-        selectedRegions_[i] = 
+        selectedRegions_[i] =
             reader_->GetRegionSelection()->GetArraySetting(i);
     }
 }
@@ -282,7 +282,7 @@ void Foam::vtkFoam::convertMesh()
             else
             {
                 // A patch already existent in the list and which
-                // continues to exist found 
+                // continues to exist found
                 regioni++;
             }
         }
@@ -391,7 +391,7 @@ Foam::vtkFoam::vtkFoam(const char* const FileName, vtkFoamReader* reader)
 {
     fileName fullCasePath(fileName(FileName).path());
 
-    if (!dir(fullCasePath))
+    if (!isDir(fullCasePath))
     {
         return;
     }
@@ -572,7 +572,7 @@ void Foam::vtkFoam::Update()
         {
             Info<< "Reading Mesh" << endl;
         }
-        meshPtr_ = 
+        meshPtr_ =
             new fvMesh
             (
                 IOobject

applications/utilities/postProcessing/graphics/ensightFoamReader/USERD_set_filenames.H

@@ -47,7 +47,7 @@ int USERD_set_filenames
     }
     caseDir = tmp;
 
-    if (!dir(rootDir/caseDir))
+    if (!isDir(rootDir/caseDir))
     {
        Info<< rootDir/caseDir << " is not a valid directory."
            << endl;
@@ -144,7 +144,7 @@ int USERD_set_filenames
         }
         isTensor[n] = isitTensor;
     }
-    
+
     bool lagrangianNamesFound = false;
     label n = 0;
     while (!lagrangianNamesFound && n < Num_time_steps)
@@ -176,7 +176,7 @@ int USERD_set_filenames
         Info << "[Found lagrangian]" << endl;
 
         delete sprayPtr;
-        
+
         sprayPtr = new Cloud<passiveParticle>(*meshPtr);
 
         IOobjectList objects(*meshPtr, runTime.timeName(), "lagrangian");

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

@@ -132,8 +132,8 @@ static void errorMsg(const string& msg)
 // Simple check if directory is valid case directory.
 static bool validCase(const fileName& rootAndCase)
 {
-    //if (dir(rootAndCase/"system") && dir(rootAndCase/"constant"))
+    //if (isDir(rootAndCase/"system") && isDir(rootAndCase/"constant"))
-    if (dir(rootAndCase/"constant"))
+    if (isDir(rootAndCase/"constant"))
     {
         return true;
     }
@@ -528,7 +528,7 @@ void user_query_file_function
 
             return;
         }
-        
+
     }
 
     fileName rootDir(rootAndCase.path());

applications/utilities/postProcessing/velocityField/Mach/Mach.C

@@ -63,7 +63,7 @@ void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
 
         volVectorField U(Uheader, mesh);
 
-        if (file(runTime.constantPath()/"thermophysicalProperties"))
+        if (isFile(runTime.constantPath()/"thermophysicalProperties"))
         {
             // thermophysical Mach
             autoPtr<basicThermo> thermo

applications/utilities/surface/surfaceCoordinateSystemTransform/Make/files

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

applications/utilities/surface/surfaceMeshConvert/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(LIB_SRC)/triSurface/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/surfMesh/lnInclude
 
-EXE_LIBS = -lsurfMesh
+EXE_LIBS = -lmeshTools -lsurfMesh

applications/utilities/surface/surfaceMeshConvert/surfaceMeshConvert.C

@@ -26,25 +26,30 @@ Application
     surfaceMeshConvert
 
 Description
-    Converts from one surface mesh format to another
+
+    Convert between surface formats with optional scaling or
+    transformations (rotate/translate) on a coordinateSystem.
 
 Usage
     - surfaceMeshConvert inputFile outputFile [OPTION]
 
     @param -clean \n
-    Perform some surface checking/cleanup on the input surface
+    Perform some surface checking/cleanup on the input surface.
 
-    @param -orient \n
+    @param -scaleIn \<scale\> \n
-    Check face orientation on the input surface
+    Specify a scaling factor when reading files.
 
-    @param -scale \<scale\> \n
+    @param -scaleOut \<scale\> \n
-    Specify a scaling factor for writing the files
+    Specify a scaling factor when writing files.
 
-    @param -triSurface \n
+    @param -dict \<dictionary\> \n
-    Use triSurface library for input/output
+    Specify an alternative dictionary for constant/coordinateSystems.
 
-    @param -keyed \n
+    @param -from \<coordinateSystem\> \n
-    Use keyedSurface for input/output
+    Specify a coordinate System when reading files.
+
+    @param -to \<coordinateSystem\> \n
+    Specify a coordinate System when writing files.
 
 Note
     The filename extensions are used to determine the file format type.
@@ -54,12 +59,9 @@ Note
 #include "argList.H"
 #include "timeSelector.H"
 #include "Time.H"
-#include "polyMesh.H"
-#include "triSurface.H"
-#include "PackedBoolList.H"
 
 #include "MeshedSurfaces.H"
-#include "UnsortedMeshedSurfaces.H"
+#include "coordinateSystems.H"
 
 using namespace Foam;
 
@@ -71,24 +73,21 @@ int main(int argc, char *argv[])
     argList::noParallel();
     argList::validArgs.append("inputFile");
     argList::validArgs.append("outputFile");
-    argList::validOptions.insert("clean", "");
+    argList::validOptions.insert("clean",  "scale");
-    argList::validOptions.insert("orient", "");
+    argList::validOptions.insert("scaleIn",  "scale");
-    argList::validOptions.insert("scale", "scale");
+    argList::validOptions.insert("scaleOut", "scale");
-    argList::validOptions.insert("triSurface", "");
+    argList::validOptions.insert("dict", "coordinateSystemsDict");
-    argList::validOptions.insert("unsorted", "");
+    argList::validOptions.insert("from", "sourceCoordinateSystem");
-    argList::validOptions.insert("triFace", "");
+    argList::validOptions.insert("to",   "targetCoordinateSystem");
-#   include "setRootCase.H"
-    const stringList& params = args.additionalArgs();
 
-    scalar scaleFactor = 0;
+    argList args(argc, argv);
-    if (args.options().found("scale"))
+    Time runTime(args.rootPath(), args.caseName());
-    {
+    const stringList& params = args.additionalArgs();
-        IStringStream(args.options()["scale"])() >> scaleFactor;
-    }
 
     fileName importName(params[0]);
     fileName exportName(params[1]);
 
+    // disable inplace editing
     if (importName == exportName)
     {
         FatalErrorIn(args.executable())
@@ -96,165 +95,161 @@ int main(int argc, char *argv[])
             << exit(FatalError);
     }
 
+    // check that reading/writing is supported
     if
     (
-        !meshedSurface::canRead(importName, true)
+        !MeshedSurface<face>::canRead(importName, true)
-     || !meshedSurface::canWriteType(exportName.ext(), true)
+     || !MeshedSurface<face>::canWriteType(exportName.ext(), true)
     )
     {
         return 1;
     }
 
-    if (args.options().found("triSurface"))
+
+    // get the coordinate transformations
+    autoPtr<coordinateSystem> fromCsys;
+    autoPtr<coordinateSystem> toCsys;
+
+    if (args.options().found("from") || args.options().found("to"))
     {
-        triSurface surf(importName);
+        autoPtr<IOobject> csDictIoPtr;
 
-        Info<< "Read surface:" << endl;
+        if (args.options().found("dict"))
-        surf.writeStats(Info);
-        Info<< endl;
-
-        if (args.options().found("orient"))
         {
-            Info<< "Checking surface orientation" << endl;
+            fileName dictPath(args.options()["dict"]);
-            PatchTools::checkOrientation(surf, true);
-            Info<< endl;
-        }
 
-        if (args.options().found("clean"))
+            csDictIoPtr.set
-        {
+            (
-            Info<< "Cleaning up surface" << endl;
+                new IOobject
-            surf.cleanup(true);
+                (
-            surf.writeStats(Info);
+                    (
-            Info<< endl;
+                        isDir(dictPath)
-        }
+                      ? dictPath/coordinateSystems::typeName
-
+                      : dictPath
-        Info<< "writing " << exportName;
+                    ),
-        if (scaleFactor <= 0)
+                    runTime,
-        {
+                    IOobject::MUST_READ,
-            Info<< " without scaling" << endl;
+                    IOobject::NO_WRITE,
+                    false
+                )
+            );
         }
         else
         {
-            Info<< " with scaling " << scaleFactor << endl;
+            csDictIoPtr.set
-            surf.scalePoints(scaleFactor);
+            (
-            surf.writeStats(Info);
+                new IOobject
-            Info<< endl;
+                (
+                    coordinateSystems::typeName,
+                    runTime.constant(),
+                    runTime,
+                    IOobject::MUST_READ,
+                    IOobject::NO_WRITE,
+                    false
+                )
+            );
         }
 
-        // write sorted by region
+
-        surf.write(exportName, true);
+        if (!csDictIoPtr->headerOk())
+        {
+            FatalErrorIn(args.executable())
+                << "Cannot open coordinateSystems file\n    "
+                << csDictIoPtr->objectPath() << nl
+                << exit(FatalError);
+        }
+
+        coordinateSystems csLst(csDictIoPtr());
+
+        if (args.options().found("from"))
+        {
+            const word csName(args.options()["from"]);
+
+            label csId = csLst.find(csName);
+            if (csId < 0)
+            {
+                FatalErrorIn(args.executable())
+                    << "Cannot find -from " << csName << nl
+                    << "available coordinateSystems: " << csLst.toc() << nl
+                    << exit(FatalError);
+            }
+
+            fromCsys.reset(new coordinateSystem(csLst[csId]));
+        }
+
+        if (args.options().found("to"))
+        {
+            const word csName(args.options()["to"]);
+
+            label csId = csLst.find(csName);
+            if (csId < 0)
+            {
+                FatalErrorIn(args.executable())
+                    << "Cannot find -to " << csName << nl
+                    << "available coordinateSystems: " << csLst.toc() << nl
+                    << exit(FatalError);
+            }
+
+            toCsys.reset(new coordinateSystem(csLst[csId]));
+        }
+
+
+        // maybe fix this later
+        if (fromCsys.valid() && toCsys.valid())
+        {
+            FatalErrorIn(args.executable())
+                << "Only allowed  '-from' or '-to' option at the moment."
+                << exit(FatalError);
+        }
     }
-    else if (args.options().found("unsorted"))
+
+    scalar scaleIn = 0;
+    scalar scaleOut = 0;
+    if (args.options().found("scaleIn"))
     {
-        UnsortedMeshedSurface<face> surf(importName);
+        IStringStream(args.options()["scaleIn"])() >> scaleIn;
-
-        Info<< "Read surface:" << endl;
-        surf.writeStats(Info);
-        Info<< endl;
-
-        if (args.options().found("orient"))
-        {
-            Info<< "Checking surface orientation" << endl;
-            PatchTools::checkOrientation(surf, true);
-            Info<< endl;
-        }
-
-        if (args.options().found("clean"))
-        {
-            Info<< "Cleaning up surface" << endl;
-            surf.cleanup(true);
-            surf.writeStats(Info);
-            Info<< endl;
-        }
-
-        Info<< "writing " << exportName;
-        if (scaleFactor <= 0)
-        {
-            Info<< " without scaling" << endl;
-        }
-        else
-        {
-            Info<< " with scaling " << scaleFactor << endl;
-            surf.scalePoints(scaleFactor);
-            surf.writeStats(Info);
-            Info<< endl;
-        }
-        surf.write(exportName);
     }
-#if 1
+    if (args.options().found("scaleOut"))
-    else if (args.options().found("triFace"))
     {
-        MeshedSurface<triFace> surf(importName);
+        IStringStream(args.options()["scaleOut"])() >> scaleOut;
-
-        Info<< "Read surface:" << endl;
-        surf.writeStats(Info);
-        Info<< endl;
-
-        if (args.options().found("orient"))
-        {
-            Info<< "Checking surface orientation" << endl;
-            PatchTools::checkOrientation(surf, true);
-            Info<< endl;
-        }
-
-        if (args.options().found("clean"))
-        {
-            Info<< "Cleaning up surface" << endl;
-            surf.cleanup(true);
-            surf.writeStats(Info);
-            Info<< endl;
-        }
-
-        Info<< "writing " << exportName;
-        if (scaleFactor <= 0)
-        {
-            Info<< " without scaling" << endl;
-        }
-        else
-        {
-            Info<< " with scaling " << scaleFactor << endl;
-            surf.scalePoints(scaleFactor);
-            surf.writeStats(Info);
-            Info<< endl;
-        }
-        surf.write(exportName);
     }
-#endif
+
-    else
+
     {
         MeshedSurface<face> surf(importName);
 
-        Info<< "Read surface:" << endl;
-        surf.writeStats(Info);
-        Info<< endl;
-
-        if (args.options().found("orient"))
-        {
-            Info<< "Checking surface orientation" << endl;
-            PatchTools::checkOrientation(surf, true);
-            Info<< endl;
-        }
-
         if (args.options().found("clean"))
         {
-            Info<< "Cleaning up surface" << endl;
             surf.cleanup(true);
-            surf.writeStats(Info);
+        }
-            Info<< endl;
+
+        if (scaleIn > 0)
+        {
+            Info<< " -scaleIn " << scaleIn << endl;
+            surf.scalePoints(scaleIn);
+        }
+
+        if (fromCsys.valid())
+        {
+            Info<< " -from " << fromCsys().name() << endl;
+            tmp<pointField> tpf = fromCsys().localPosition(surf.points());
+            surf.movePoints(tpf());
+        }
+
+        if (toCsys.valid())
+        {
+            Info<< " -to " << toCsys().name() << endl;
+            tmp<pointField> tpf = toCsys().globalPosition(surf.points());
+            surf.movePoints(tpf());
+        }
+
+        if (scaleOut > 0)
+        {
+            Info<< " -scaleOut " << scaleOut << endl;
+            surf.scalePoints(scaleOut);
         }
 
         Info<< "writing " << exportName;
-        if (scaleFactor <= 0)
-        {
-            Info<< " without scaling" << endl;
-        }
-        else
-        {
-            Info<< " with scaling " << scaleFactor << endl;
-            surf.scalePoints(scaleFactor);
-            surf.writeStats(Info);
-            Info<< endl;
-        }
         surf.write(exportName);
     }
 

applications/utilities/surface/surfaceMeshConvertTesting/Make/files

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

applications/utilities/surface/surfaceMeshConvertTesting/Make/options

@@ -0,0 +1,5 @@
+EXE_INC = \
+    -I$(LIB_SRC)/triSurface/lnInclude \
+    -I$(LIB_SRC)/surfMesh/lnInclude
+
+EXE_LIBS = -ltriSurface -lsurfMesh

applications/utilities/surface/surfaceMeshConvertTesting/surfaceMeshConvertTesting.C

@@ -0,0 +1,348 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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
+    surfaceMeshConvertTesting
+
+Description
+    Converts from one surface mesh format to another, but primarily
+    used for testing functionality.
+
+Usage
+    - surfaceMeshConvertTesting inputFile outputFile [OPTION]
+
+    @param -clean \n
+    Perform some surface checking/cleanup on the input surface
+
+    @param -orient \n
+    Check face orientation on the input surface
+
+    @param -scale \<scale\> \n
+    Specify a scaling factor for writing the files
+
+    @param -triSurface \n
+    Use triSurface library for input/output
+
+    @param -keyed \n
+    Use keyedSurface for input/output
+
+Note
+    The filename extensions are used to determine the file format type.
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "timeSelector.H"
+#include "Time.H"
+#include "polyMesh.H"
+#include "triSurface.H"
+#include "surfMesh.H"
+#include "surfFields.H"
+#include "surfPointFields.H"
+#include "PackedBoolList.H"
+
+#include "MeshedSurfaces.H"
+#include "UnsortedMeshedSurfaces.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::noParallel();
+    argList::validArgs.append("inputFile");
+    argList::validArgs.append("outputFile");
+    argList::validOptions.insert("clean", "");
+    argList::validOptions.insert("orient", "");
+    argList::validOptions.insert("surfMesh", "");
+    argList::validOptions.insert("scale", "scale");
+    argList::validOptions.insert("triSurface", "");
+    argList::validOptions.insert("unsorted", "");
+    argList::validOptions.insert("triFace", "");
+#   include "setRootCase.H"
+    const stringList& params = args.additionalArgs();
+
+    scalar scaleFactor = 0;
+    if (args.options().found("scale"))
+    {
+        IStringStream(args.options()["scale"])() >> scaleFactor;
+    }
+
+    fileName importName(params[0]);
+    fileName exportName(params[1]);
+
+    if (importName == exportName)
+    {
+        FatalErrorIn(args.executable())
+            << "Output file " << exportName << " would overwrite input file."
+            << exit(FatalError);
+    }
+
+    if
+    (
+        !MeshedSurface<face>::canRead(importName, true)
+     || !MeshedSurface<face>::canWriteType(exportName.ext(), true)
+    )
+    {
+        return 1;
+    }
+
+    if (args.options().found("triSurface"))
+    {
+        triSurface surf(importName);
+
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
+        if (args.options().found("orient"))
+        {
+            Info<< "Checking surface orientation" << endl;
+            PatchTools::checkOrientation(surf, true);
+            Info<< endl;
+        }
+
+        if (args.options().found("clean"))
+        {
+            Info<< "Cleaning up surface" << endl;
+            surf.cleanup(true);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+
+        Info<< "writing " << exportName;
+        if (scaleFactor <= 0)
+        {
+            Info<< " without scaling" << endl;
+        }
+        else
+        {
+            Info<< " with scaling " << scaleFactor << endl;
+            surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+
+        // write sorted by region
+        surf.write(exportName, true);
+    }
+    else if (args.options().found("unsorted"))
+    {
+        UnsortedMeshedSurface<face> surf(importName);
+
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
+        if (args.options().found("orient"))
+        {
+            Info<< "Checking surface orientation" << endl;
+            PatchTools::checkOrientation(surf, true);
+            Info<< endl;
+        }
+
+        if (args.options().found("clean"))
+        {
+            Info<< "Cleaning up surface" << endl;
+            surf.cleanup(true);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+
+        Info<< "writing " << exportName;
+        if (scaleFactor <= 0)
+        {
+            Info<< " without scaling" << endl;
+        }
+        else
+        {
+            Info<< " with scaling " << scaleFactor << endl;
+            surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+        surf.write(exportName);
+    }
+#if 1
+    else if (args.options().found("triFace"))
+    {
+        MeshedSurface<triFace> surf(importName);
+
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
+        if (args.options().found("orient"))
+        {
+            Info<< "Checking surface orientation" << endl;
+            PatchTools::checkOrientation(surf, true);
+            Info<< endl;
+        }
+
+        if (args.options().found("clean"))
+        {
+            Info<< "Cleaning up surface" << endl;
+            surf.cleanup(true);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+
+        Info<< "writing " << exportName;
+        if (scaleFactor <= 0)
+        {
+            Info<< " without scaling" << endl;
+        }
+        else
+        {
+            Info<< " with scaling " << scaleFactor << endl;
+            surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+        surf.write(exportName);
+    }
+#endif
+    else
+    {
+        MeshedSurface<face> surf(importName);
+
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
+        if (args.options().found("orient"))
+        {
+            Info<< "Checking surface orientation" << endl;
+            PatchTools::checkOrientation(surf, true);
+            Info<< endl;
+        }
+
+        if (args.options().found("clean"))
+        {
+            Info<< "Cleaning up surface" << endl;
+            surf.cleanup(true);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+
+
+        Info<< "writing " << exportName;
+        if (scaleFactor <= 0)
+        {
+            Info<< " without scaling" << endl;
+        }
+        else
+        {
+            Info<< " with scaling " << scaleFactor << endl;
+            surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
+        }
+        surf.write(exportName);
+
+        if (args.options().found("surfMesh"))
+        {
+            Foam::Time runTime
+            (
+                args.rootPath(),
+                args.caseName()
+            );
+
+            surfMesh surfOut
+            (
+                IOobject
+                (
+                    "mySurf",
+                    runTime.instance(),
+                    runTime
+                ),
+                surf.xfer()
+            );
+
+            Info<< "writing surfMesh as well: " << surfOut.objectPath() << endl;
+            surfOut.write();
+
+            surfLabelField zoneIds
+            (
+                IOobject
+                (
+                    "zoneIds",
+                    surfOut.instance(),
+                    surfOut,
+                    IOobject::NO_READ,
+                    IOobject::NO_WRITE
+                ),
+                surfOut,
+                dimless
+            );
+
+            const surfZoneList& zones = surfOut.surfZones();
+            forAll(zones, zoneI)
+            {
+                SubList<label>
+                (
+                    zoneIds,
+                    zones[zoneI].size(),
+                    zones[zoneI].start()
+                ) = zoneI;
+            }
+
+            Info<< "write zoneIds (for testing only): "
+                << zoneIds.objectPath() << endl;
+            zoneIds.write();
+
+            surfPointLabelField pointIds
+            (
+                IOobject
+                (
+                    "pointIds",
+                    surfOut.instance(),
+                    "pointFields",
+                    surfOut,
+                    IOobject::NO_READ,
+                    IOobject::NO_WRITE
+                ),
+                surfOut,
+                dimless
+            );
+
+            forAll(pointIds, i)
+            {
+                pointIds[i] = i;
+            }
+
+            Info<< "write pointIds (for testing only): "
+                << pointIds.objectPath() << endl;
+            pointIds.write();
+        }
+    }
+
+    Info<< "\nEnd\n" << endl;
+
+    return 0;
+}
+
+// ************************************************************************* //

applications/utilities/surface/surfaceMeshExport/Make/files

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

applications/utilities/surface/surfaceMeshExport/surfaceMeshExport.C

@@ -23,27 +23,36 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    surfaceMeshCoordinateSystemTransform
+    surfaceMeshExport
 
 Description
-
+    Export from surfMesh to various third-party surface formats with
-    Transform (scale/rotate/translate) a surface based on
+    optional scaling or transformations (rotate/translate) on a
-    a coordinateSystem.
+    coordinateSystem.
 
 Usage
-    - surfaceMeshCoordinateSystemTransform inputFile outputFile [OPTION]
+    - surfaceMeshExport outputFile [OPTION]
 
     @param -clean \n
-    Perform some surface checking/cleanup on the input surface
+    Perform some surface checking/cleanup on the input surface.
 
-    @param -scale \<scale\> \n
+    @param -name \<name\> \n
-    Specify a scaling factor for writing the files
+    Specify an alternative surface name when writing.
 
-    @param -triSurface \n
+    @param -scaleIn \<scale\> \n
-    Use triSurface library for input/output
+    Specify a scaling factor when reading files.
+
+    @param -scaleOut \<scale\> \n
+    Specify a scaling factor when writing files.
 
     @param -dict \<dictionary\> \n
-    Specify an alternative dictionary for coordinateSystems.
+    Specify an alternative dictionary for constant/coordinateSystems.
+
+    @param -from \<coordinateSystem\> \n
+    Specify a coordinate System when reading files.
+
+    @param -to \<coordinateSystem\> \n
+    Specify a coordinate System when writing files.
 
 Note
     The filename extensions are used to determine the file format type.
@@ -55,7 +64,6 @@ Note
 #include "Time.H"
 
 #include "MeshedSurfaces.H"
-#include "UnsortedMeshedSurfaces.H"
 #include "coordinateSystems.H"
 
 using namespace Foam;
@@ -66,36 +74,55 @@ using namespace Foam;
 int main(int argc, char *argv[])
 {
     argList::noParallel();
-    argList::validArgs.append("inputFile");
     argList::validArgs.append("outputFile");
-    argList::validOptions.insert("scale", "scale");
+    argList::validOptions.insert("name",  "name");
-    argList::validOptions.insert("unsorted", "");
+    argList::validOptions.insert("clean",  "scale");
+    argList::validOptions.insert("scaleIn",  "scale");
+    argList::validOptions.insert("scaleOut", "scale");
+    argList::validOptions.insert("dict", "coordinateSystemsDict");
     argList::validOptions.insert("from", "sourceCoordinateSystem");
-    argList::validOptions.insert("to", "targetCoordinateSystem");
+    argList::validOptions.insert("to",   "targetCoordinateSystem");
-    argList::validOptions.insert("dict", "dictionary");
 
     argList args(argc, argv);
     Time runTime(args.rootPath(), args.caseName());
     const stringList& params = args.additionalArgs();
 
-    const word dictName("coordinateSystems");
+    fileName exportName(params[0]);
+    word importName("default");
 
+    // check that writing is supported
+    if (!MeshedSurface<face>::canWriteType(exportName.ext(), true))
+    {
+        return 1;
+    }
+
+    if (args.options().found("name"))
+    {
+        importName = args.options()["name"];
+    }
+
+
+    // get the coordinate transformations
     autoPtr<coordinateSystem> fromCsys;
     autoPtr<coordinateSystem> toCsys;
 
     if (args.options().found("from") || args.options().found("to"))
     {
-        autoPtr<IOobject> csDictIoPtr;
+        autoPtr<IOobject> ioPtr;
 
         if (args.options().found("dict"))
         {
             fileName dictPath(args.options()["dict"]);
 
-            csDictIoPtr.set
+            ioPtr.set
             (
                 new IOobject
                 (
-                    ( dictPath.isDir() ? dictPath/dictName : dictPath ),
+                    (
+                        isDir(dictPath)
+                      ? dictPath/coordinateSystems::typeName
+                      : dictPath
+                    ),
                     runTime,
                     IOobject::MUST_READ,
                     IOobject::NO_WRITE,
@@ -105,11 +132,11 @@ int main(int argc, char *argv[])
         }
         else
         {
-            csDictIoPtr.set
+            ioPtr.set
             (
                 new IOobject
                 (
-                    dictName,
+                    coordinateSystems::typeName,
                     runTime.constant(),
                     runTime,
                     IOobject::MUST_READ,
@@ -120,15 +147,15 @@ int main(int argc, char *argv[])
         }
 
 
-        if (!csDictIoPtr->headerOk())
+        if (!ioPtr->headerOk())
         {
             FatalErrorIn(args.executable())
                 << "Cannot open coordinateSystems file\n    "
-                << csDictIoPtr->objectPath() << nl
+                << ioPtr->objectPath() << nl
                 << exit(FatalError);
         }
 
-        coordinateSystems csLst(csDictIoPtr());
+        coordinateSystems csLst(ioPtr());
 
         if (args.options().found("from"))
         {
@@ -167,70 +194,81 @@ int main(int argc, char *argv[])
         if (fromCsys.valid() && toCsys.valid())
         {
             FatalErrorIn(args.executable())
-                << "Only allowed  -from  or  -to  option at the moment."
+                << "Only allowed  '-from' or '-to' option at the moment."
                 << exit(FatalError);
         }
     }
 
-    scalar scaleFactor = 0;
-    if (args.options().found("scale"))
-    {
-        IStringStream(args.options()["scale"])() >> scaleFactor;
-    }
 
-    fileName importName(params[0]);
+    surfMesh smesh
-    fileName exportName(params[1]);
-
-    if (importName == exportName)
-    {
-        FatalErrorIn(args.executable())
-            << "Output file " << exportName << " would overwrite input file."
-            << exit(FatalError);
-    }
-
-    if
     (
-        !meshedSurface::canRead(importName, true)
+        IOobject
-     || !meshedSurface::canWriteType(exportName.ext(), true)
+        (
-    )
+            importName,
+            runTime.constant(),
+            runTime,
+            IOobject::MUST_READ,
+            IOobject::NO_WRITE
+        )
+    );
+
+    Info<< "read surfMesh:\n  " << smesh.objectPath() << endl;
+
+
+    // Simply copy for now, but really should have a separate write method
+
+    MeshedSurface<face> surf(smesh);
+
+    if (args.options().found("clean"))
     {
-        return 1;
+        surf.cleanup(true);
+    }
+
+    scalar scaleIn = 0;
+    scalar scaleOut = 0;
+    if (args.options().found("scaleIn"))
+    {
+        IStringStream(args.options()["scaleIn"])() >> scaleIn;
+    }
+    if (args.options().found("scaleOut"))
+    {
+        IStringStream(args.options()["scaleOut"])() >> scaleOut;
     }
 
 
+    if (scaleIn > 0)
     {
-        MeshedSurface<face> surf(importName);
+        Info<< " -scaleIn " << scaleIn << endl;
-
+        surf.scalePoints(scaleIn);
-        if (args.options().found("clean"))
-        {
-            surf.cleanup(true);
-        }
-
-        if (fromCsys.valid())
-        {
-            tmp<pointField> tpf = fromCsys().localPosition(surf.points());
-            surf.movePoints(tpf());
-        }
-
-        if (toCsys.valid())
-        {
-            tmp<pointField> tpf = toCsys().globalPosition(surf.points());
-            surf.movePoints(tpf());
-        }
-
-        Info<< "writing " << exportName;
-        if (scaleFactor <= 0)
-        {
-            Info<< " without scaling" << endl;
-        }
-        else
-        {
-            Info<< " with scaling " << scaleFactor << endl;
-            surf.scalePoints(scaleFactor);
-        }
-        surf.write(exportName);
     }
 
+    if (fromCsys.valid())
+    {
+        Info<< " -from " << fromCsys().name() << endl;
+        tmp<pointField> tpf = fromCsys().localPosition(surf.points());
+        surf.movePoints(tpf());
+    }
+
+    if (toCsys.valid())
+    {
+        Info<< " -to " << toCsys().name() << endl;
+        tmp<pointField> tpf = toCsys().globalPosition(surf.points());
+        surf.movePoints(tpf());
+    }
+
+    if (scaleOut > 0)
+    {
+        Info<< " -scaleOut " << scaleOut << endl;
+        surf.scalePoints(scaleOut);
+    }
+
+
+    surf.writeStats(Info);
+    Info<< endl;
+
+    Info<< "writing " << exportName << endl;
+    surf.write(exportName);
+
     Info<< "\nEnd\n" << endl;
 
     return 0;

applications/utilities/surface/surfaceMeshImport/Make/files

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

applications/utilities/surface/surfaceMeshImport/Make/options

@@ -0,0 +1,5 @@
+EXE_INC = \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/surfMesh/lnInclude
+
+EXE_LIBS = -lmeshTools -lsurfMesh

applications/utilities/surface/surfaceMeshImport/surfaceMeshImport.C

@@ -0,0 +1,284 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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
+    surfaceMeshImport
+
+Description
+    Import from various third-party surface formats into surfMesh
+    with optional scaling or transformations (rotate/translate)
+    on a coordinateSystem.
+
+Usage
+    - surfaceMeshImport inputFile [OPTION]
+
+    @param -clean \n
+    Perform some surface checking/cleanup on the input surface.
+
+    @param -name \<name\> \n
+    Specify an alternative surface name when writing.
+
+    @param -scaleIn \<scale\> \n
+    Specify a scaling factor when reading files.
+
+    @param -scaleOut \<scale\> \n
+    Specify a scaling factor when writing files.
+
+    @param -dict \<dictionary\> \n
+    Specify an alternative dictionary for constant/coordinateSystems.
+
+    @param -from \<coordinateSystem\> \n
+    Specify a coordinate System when reading files.
+
+    @param -to \<coordinateSystem\> \n
+    Specify a coordinate System when writing files.
+
+Note
+    The filename extensions are used to determine the file format type.
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "timeSelector.H"
+#include "Time.H"
+
+#include "MeshedSurfaces.H"
+#include "coordinateSystems.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::noParallel();
+    argList::validArgs.append("inputFile");
+    argList::validOptions.insert("name",  "name");
+    argList::validOptions.insert("clean",  "scale");
+    argList::validOptions.insert("scaleIn",  "scale");
+    argList::validOptions.insert("scaleOut", "scale");
+    argList::validOptions.insert("dict", "coordinateSystemsDict");
+    argList::validOptions.insert("from", "sourceCoordinateSystem");
+    argList::validOptions.insert("to",   "targetCoordinateSystem");
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+
+    const stringList& params = args.additionalArgs();
+
+    // try for the latestTime, but create "constant" as needed
+    instantList Times = runTime.times();
+    if (Times.size())
+    {
+        label startTime = Times.size()-1;
+        runTime.setTime(Times[startTime], startTime);
+    }
+    else
+    {
+        runTime.setTime(instant(0, runTime.constant()), 0);
+    }
+
+
+    fileName importName(params[0]);
+    word exportName("default");
+
+    // check that reading is supported
+    if (!MeshedSurface<face>::canRead(importName, true))
+    {
+        return 1;
+    }
+
+    if (args.options().found("name"))
+    {
+        exportName = args.options()["name"];
+    }
+
+
+    // get the coordinate transformations
+    autoPtr<coordinateSystem> fromCsys;
+    autoPtr<coordinateSystem> toCsys;
+
+    if (args.options().found("from") || args.options().found("to"))
+    {
+        autoPtr<IOobject> ioPtr;
+
+        if (args.options().found("dict"))
+        {
+            fileName dictPath(args.options()["dict"]);
+
+            ioPtr.set
+            (
+                new IOobject
+                (
+                    (
+                        isDir(dictPath)
+                      ? dictPath/coordinateSystems::typeName
+                      : dictPath
+                    ),
+                    runTime,
+                    IOobject::MUST_READ,
+                    IOobject::NO_WRITE,
+                    false
+                )
+            );
+        }
+        else
+        {
+            ioPtr.set
+            (
+                new IOobject
+                (
+                    coordinateSystems::typeName,
+                    runTime.constant(),
+                    runTime,
+                    IOobject::MUST_READ,
+                    IOobject::NO_WRITE,
+                    false
+                )
+            );
+        }
+
+
+        if (!ioPtr->headerOk())
+        {
+            FatalErrorIn(args.executable())
+                << "Cannot open coordinateSystems file\n    "
+                << ioPtr->objectPath() << nl
+                << exit(FatalError);
+        }
+
+        coordinateSystems csLst(ioPtr());
+
+        if (args.options().found("from"))
+        {
+            const word csName(args.options()["from"]);
+
+            label csId = csLst.find(csName);
+            if (csId < 0)
+            {
+                FatalErrorIn(args.executable())
+                    << "Cannot find -from " << csName << nl
+                    << "available coordinateSystems: " << csLst.toc() << nl
+                    << exit(FatalError);
+            }
+
+            fromCsys.reset(new coordinateSystem(csLst[csId]));
+        }
+
+        if (args.options().found("to"))
+        {
+            const word csName(args.options()["to"]);
+
+            label csId = csLst.find(csName);
+            if (csId < 0)
+            {
+                FatalErrorIn(args.executable())
+                    << "Cannot find -to " << csName << nl
+                    << "available coordinateSystems: " << csLst.toc() << nl
+                    << exit(FatalError);
+            }
+
+            toCsys.reset(new coordinateSystem(csLst[csId]));
+        }
+
+
+        // maybe fix this later
+        if (fromCsys.valid() && toCsys.valid())
+        {
+            FatalErrorIn(args.executable())
+                << "Only allowed  '-from' or '-to' option at the moment."
+                << exit(FatalError);
+        }
+    }
+
+
+
+    MeshedSurface<face> surf(importName);
+
+    if (args.options().found("clean"))
+    {
+        surf.cleanup(true);
+    }
+
+
+    scalar scaleIn = 0;
+    scalar scaleOut = 0;
+    if (args.options().found("scaleIn"))
+    {
+        IStringStream(args.options()["scaleIn"])() >> scaleIn;
+    }
+    if (args.options().found("scaleOut"))
+    {
+        IStringStream(args.options()["scaleOut"])() >> scaleOut;
+    }
+
+
+    if (scaleIn > 0)
+    {
+        Info<< " -scaleIn " << scaleIn << endl;
+        surf.scalePoints(scaleIn);
+    }
+
+    if (fromCsys.valid())
+    {
+        Info<< " -from " << fromCsys().name() << endl;
+        tmp<pointField> tpf = fromCsys().localPosition(surf.points());
+        surf.movePoints(tpf());
+    }
+
+    if (toCsys.valid())
+    {
+        Info<< " -to " << toCsys().name() << endl;
+        tmp<pointField> tpf = toCsys().globalPosition(surf.points());
+        surf.movePoints(tpf());
+    }
+
+    if (scaleOut > 0)
+    {
+        Info<< " -scaleOut " << scaleOut << endl;
+        surf.scalePoints(scaleOut);
+    }
+
+    surfMesh smesh
+    (
+        IOobject
+        (
+            exportName,
+            runTime.constant(),
+            runTime
+        ),
+        surf.xfer()
+    );
+
+
+    Info<< "writing surfMesh:\n  " << smesh.objectPath() << endl;
+    smesh.write();
+
+    Info<< "\nEnd\n" << endl;
+
+    return 0;
+}
+
+// ************************************************************************* //

applications/utilities/surface/surfaceSplitNonManifolds/surfaceSplitNonManifolds.C

@@ -351,7 +351,7 @@ label otherEdge
 
     return -1;
 }
-    
+
 
 // Starting from startPoint on startEdge on startFace walk along border
 // and insert faces along the way. Walk keeps always one point or one edge
@@ -461,18 +461,8 @@ label sharedFace
 
     label startIndex = findIndex(f, e.start());
 
-    bool edgeOrder;
+    // points in face in same order as edge
-
+    bool edgeOrder = (f[f.fcIndex(startIndex)] == e.end());
-    if (f[(startIndex + 1) % f.size()] == e.end())
-    {
-        // points in face in same order as edge
-        edgeOrder = true;
-    }
-    else
-    {
-        // points in face in reverse order as edge
-        edgeOrder = false;
-    }
 
     // Get faces using edge in sorted order. (sorted such that walking
     // around them in anti-clockwise order corresponds to edge vector
@@ -485,25 +475,18 @@ label sharedFace
     if (edgeOrder)
     {
         // Get face before firstFaceI
-        if (faceIndex == 0)
+        return eFaces[eFaces.rcIndex(faceIndex)];
-        {
-            return eFaces[eFaces.size() - 1];
-        }
-        else
-        {
-            return eFaces[faceIndex - 1];
-        }
     }
     else
     {
         // Get face after firstFaceI
-        return eFaces[(faceIndex+1) % eFaces.size()];
+        return eFaces[eFaces.fcIndex(faceIndex)];
     }
 }
 
 
 // Calculate (inward pointing) normals on edges shared by faces in faceToEdge and
-// averages them to pointNormals. 
+// averages them to pointNormals.
 void calcPointVecs
 (
     const triSurface& surf,
@@ -602,7 +585,7 @@ void calcPointVecs
             }
 
             scalar magMidVec = mag(midVec);
-    
+
             if (magMidVec > SMALL)
             {
                 midVec /= magMidVec;
@@ -925,7 +908,7 @@ int main(int argc, char *argv[])
                 newPoints[newPointI] = newPoints[pointI] + 0.1 * minLen * n;
             }
         }
-        
+
 
         //
         // Renumber all faces in connectedFaces

src/OSspecific/Unix/Unix.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    UNIX versions of the functions declared in OSspecific.H.
+    UNIX versions of the functions declared in OSspecific.H
 
 \*---------------------------------------------------------------------------*/
 
@@ -218,7 +218,7 @@ Foam::fileName Foam::findEtcFile(const fileName& name, bool mandatory)
     // Search user files:
     // ~~~~~~~~~~~~~~~~~~
     fileName searchDir = home()/".OpenFOAM";
-    if (dir(searchDir))
+    if (isDir(searchDir))
     {
         // Check for user file in ~/.OpenFOAM/VERSION
         fileName fullName = searchDir/FOAMversion/name;
@@ -239,7 +239,7 @@ Foam::fileName Foam::findEtcFile(const fileName& name, bool mandatory)
     // Search site files:
     // ~~~~~~~~~~~~~~~~~~
     searchDir = getEnv("WM_PROJECT_INST_DIR");
-    if (dir(searchDir))
+    if (isDir(searchDir))
     {
         // Check for site file in $WM_PROJECT_INST_DIR/site/VERSION
         fileName fullName = searchDir/"site"/FOAMversion/name;
@@ -259,7 +259,7 @@ Foam::fileName Foam::findEtcFile(const fileName& name, bool mandatory)
     // Search installation files:
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~
     searchDir = getEnv("WM_PROJECT_DIR");
-    if (dir(searchDir))
+    if (isDir(searchDir))
     {
         // Check for shipped OpenFOAM file in $WM_PROJECT_DIR/etc
         fileName fullName = searchDir/"etc"/name;
@@ -432,7 +432,7 @@ bool Foam::mkDir(const fileName& pathName, mode_t mode)
 
 
 // Set the file mode
-bool Foam::chmod(const fileName& name, const mode_t m)
+bool Foam::chMod(const fileName& name, const mode_t m)
 {
     return ::chmod(name.c_str(), m) == 0;
 }
@@ -476,24 +476,24 @@ Foam::fileName::Type Foam::type(const fileName& name)
 // Does the name exist in the filing system?
 bool Foam::exists(const fileName& name)
 {
-    return mode(name) || file(name);
+    return mode(name) || isFile(name);
-}
-
-
-// Does the file exist
-bool Foam::file(const fileName& name)
-{
-    return S_ISREG(mode(name)) || S_ISREG(mode(name + ".gz"));
 }
 
 
 // Does the directory exist
-bool Foam::dir(const fileName& name)
+bool Foam::isDir(const fileName& name)
 {
     return S_ISDIR(mode(name));
 }
 
 
+// Does the file exist
+bool Foam::isFile(const fileName& name, const bool checkGzip)
+{
+    return S_ISREG(mode(name)) || (checkGzip && S_ISREG(mode(name + ".gz")));
+}
+
+
 // Return size of file
 off_t Foam::fileSize(const fileName& name)
 {
@@ -641,7 +641,7 @@ bool Foam::cp(const fileName& src, const fileName& dest)
         }
 
         // Make sure the destination directory exists.
-        if (!dir(destFile.path()) && !mkDir(destFile.path()))
+        if (!isDir(destFile.path()) && !mkDir(destFile.path()))
         {
             return false;
         }
@@ -681,7 +681,7 @@ bool Foam::cp(const fileName& src, const fileName& dest)
         }
 
         // Make sure the destination directory exists.
-        if (!dir(destFile) && !mkDir(destFile))
+        if (!isDir(destFile) && !mkDir(destFile))
         {
             return false;
         }
@@ -719,19 +719,19 @@ bool Foam::cp(const fileName& src, const fileName& dest)
 }
 
 
-// Create a softlink. destFile should not exist. Returns true if successful.
+// Create a softlink. dst should not exist. Returns true if successful.
-bool Foam::ln(const fileName& src, const fileName& dest)
+bool Foam::ln(const fileName& src, const fileName& dst)
 {
     if (Unix::debug)
     {
-        Info<< "Create softlink from : " << src << " to " << dest
+        Info<< "Create softlink from : " << src << " to " << dst
             << endl;
     }
 
-    if (exists(dest))
+    if (exists(dst))
     {
         WarningIn("ln(const fileName&, const fileName&)")
-            << "destination " << dest << " already exists. Not linking."
+            << "destination " << dst << " already exists. Not linking."
             << endl;
         return false;
     }
@@ -743,40 +743,40 @@ bool Foam::ln(const fileName& src, const fileName& dest)
         return false;
     }
 
-    if (symlink(src.c_str(), dest.c_str()) == 0)
+    if (symlink(src.c_str(), dst.c_str()) == 0)
     {
         return true;
     }
     else
     {
         WarningIn("ln(const fileName&, const fileName&)")
-            << "symlink from " << src << " to " << dest << " failed." << endl;
+            << "symlink from " << src << " to " << dst << " failed." << endl;
         return false;
     }
 }
 
 
-// Rename srcFile destFile
+// Rename srcFile dstFile
-bool Foam::mv(const fileName& srcFile, const fileName& destFile)
+bool Foam::mv(const fileName& srcFile, const fileName& dstFile)
 {
     if (Unix::debug)
     {
-        Info<< "Move : " << srcFile << " to " << destFile << endl;
+        Info<< "Move : " << srcFile << " to " << dstFile << endl;
     }
 
     if
     (
-        (destFile.type() == fileName::DIRECTORY)
+        dstFile.type() == fileName::DIRECTORY
-     && (srcFile.type() != fileName::DIRECTORY)
+     && srcFile.type() != fileName::DIRECTORY
     )
     {
-        const fileName destName(destFile/srcFile.name());
+        const fileName dstName(dstFile/srcFile.name());
 
-        return rename(srcFile.c_str(), destName.c_str()) == 0;
+        return rename(srcFile.c_str(), dstName.c_str()) == 0;
     }
     else
     {
-        return rename(srcFile.c_str(), destFile.c_str()) == 0;
+        return rename(srcFile.c_str(), dstFile.c_str()) == 0;
     }
 }
 
@@ -806,7 +806,7 @@ bool Foam::rmDir(const fileName& directory)
 {
     if (Unix::debug)
     {
-        Info<< "rmdir(const fileName&) : "
+        Info<< "rmDir(const fileName&) : "
             << "removing directory " << directory << endl;
     }
 
@@ -817,7 +817,7 @@ bool Foam::rmDir(const fileName& directory)
     // Attempt to open directory and set the structure pointer
     if ((source = opendir(directory.c_str())) == NULL)
     {
-        WarningIn("rmdir(const fileName&)")
+        WarningIn("rmDir(const fileName&)")
             << "cannot open directory " << directory << endl;
 
         return false;
@@ -837,7 +837,7 @@ bool Foam::rmDir(const fileName& directory)
                 {
                     if (!rmDir(path))
                     {
-                        WarningIn("rmdir(const fileName&)")
+                        WarningIn("rmDir(const fileName&)")
                             << "failed to remove directory " << fName
                             << " while removing directory " << directory
                             << endl;
@@ -851,7 +851,7 @@ bool Foam::rmDir(const fileName& directory)
                 {
                     if (!rm(path))
                     {
-                        WarningIn("rmdir(const fileName&)")
+                        WarningIn("rmDir(const fileName&)")
                             << "failed to remove file " << fName
                             << " while removing directory " << directory
                             << endl;
@@ -867,7 +867,7 @@ bool Foam::rmDir(const fileName& directory)
 
         if (!rm(directory))
         {
-            WarningIn("rmdir(const fileName&)")
+            WarningIn("rmDir(const fileName&)")
                 << "failed to remove directory " << directory << endl;
 
             closedir(source);

src/OpenFOAM/Make/files

@@ -45,6 +45,10 @@ $(strings)/fileName/fileNameIO.C
 $(strings)/keyType/keyTypeIO.C
 $(strings)/wordRe/wordReIO.C
 
+sha1 = primitives/hashes/SHA1
+$(sha1)/SHA1.C
+$(sha1)/SHA1Digest.C
+
 primitives/random/Random.C
 
 containers/HashTables/HashTable/HashTableName.C

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

@@ -226,7 +226,7 @@ bool Foam::HashTable<T, Key, Hash>::set
     const bool protect
 )
 {
-    if (tableSize_ == 0)
+    if (!tableSize_)
     {
         resize(2);
     }
@@ -556,7 +556,7 @@ void Foam::HashTable<T, Key, Hash>::operator=
     }
 
     // could be zero-sized from a previous transfer()
-    if (tableSize_ == 0)
+    if (!tableSize_)
     {
         resize(rhs.tableSize_);
     }

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

@@ -54,7 +54,7 @@ inline Foam::label Foam::HashTable<T, Key, Hash>::size() const
 template<class T, class Key, class Hash>
 inline bool Foam::HashTable<T, Key, Hash>::empty() const
 {
-    return (nElmts_ == 0);
+    return !nElmts_;
 }
 
 

src/OpenFOAM/containers/HashTables/StaticHashTable/StaticHashTableI.H

@@ -41,7 +41,7 @@ inline Foam::label Foam::StaticHashTable<T, Key, Hash>::size() const
 template<class T, class Key, class Hash>
 inline bool Foam::StaticHashTable<T, Key, Hash>::empty() const
 {
-    return (nElmts_ == 0);
+    return !nElmts_;
 }
 
 

src/OpenFOAM/containers/LinkedLists/linkTypes/DLListBase/DLListBaseI.H

@@ -83,7 +83,7 @@ inline Foam::label Foam::DLListBase::size() const
 
 inline bool Foam::DLListBase::empty() const
 {
-    return (nElmts_ == 0);
+    return !nElmts_;
 }
 
 

src/OpenFOAM/containers/LinkedLists/linkTypes/SLListBase/SLListBaseI.H

@@ -73,7 +73,7 @@ inline Foam::label Foam::SLListBase::size() const
 
 inline bool Foam::SLListBase::empty() const
 {
-    return (nElmts_ == 0);
+    return !nElmts_;
 }
 
 

src/OpenFOAM/containers/Lists/FixedList/FixedList.H

@@ -135,10 +135,21 @@ public:
             inline label fcIndex(const label i) const;
 
             //- Return the reverse circular index, i.e. the previous index
-            //  which returns to the last at the begining of the list
+            //  which returns to the last at the beginning of the list
             inline label rcIndex(const label i) const;
 
 
+            //- Return a const pointer to the first data element,
+            //  similar to the STL front() method and the string::data() method
+            //  This can be used (with caution) when interfacing with C code.
+            inline const T* cdata() const;
+
+            //- Return a pointer to the first data element,
+            //  similar to the STL front() method and the string::data() method
+            //  This can be used (with caution) when interfacing with C code.
+            inline T* data();
+
+
         // Check
 
             //- Check start is within valid range (0 ... size-1).
@@ -174,10 +185,10 @@ public:
 
     // Member operators
 
-        //- Return subscript-checked element of FixedList.
+        //- Return element of FixedList.
         inline T& operator[](const label);
 
-        //- Return subscript-checked element of constant FixedList.
+        //- Return element of constant FixedList.
         inline const T& operator[](const label) const;
 
         //- Assignment from array operator. Takes linear time.
@@ -282,7 +293,7 @@ public:
         //- Return size of the largest possible FixedList.
         inline label max_size() const;
 
-        //- Return true if the FixedList is empty (i.e., if size() == 0).
+        //- Return true if the FixedList is empty (ie, size() is zero).
         inline bool empty() const;
 
         //- Swap two FixedLists of the same type in constant time.

src/OpenFOAM/containers/Lists/FixedList/FixedListI.H

@@ -121,7 +121,7 @@ inline Foam::label Foam::FixedList<T, Size>::fcIndex(const label i) const
 template<class T, Foam::label Size>
 inline Foam::label Foam::FixedList<T, Size>::rcIndex(const label i) const
 {
-    return (i == 0 ? Size-1 : i-1);
+    return (i ? i-1 : Size-1);
 }
 
 
@@ -195,9 +195,26 @@ inline void Foam::FixedList<T, Size>::transfer(const FixedList<T, Size>& lst)
     }
 }
 
+
+template<class T, Foam::label Size>
+inline const T*
+Foam::FixedList<T, Size>::cdata() const
+{
+    return v_;
+}
+
+
+template<class T, Foam::label Size>
+inline T*
+Foam::FixedList<T, Size>::data()
+{
+    return v_;
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
-// Return subscript-checked element access
+// element access
 template<class T, Foam::label Size>
 inline T& Foam::FixedList<T, Size>::operator[](const label i)
 {
@@ -208,7 +225,7 @@ inline T& Foam::FixedList<T, Size>::operator[](const label i)
 }
 
 
-// Return subscript-checked const element access
+// const element access
 template<class T, Foam::label Size>
 inline const T& Foam::FixedList<T, Size>::operator[](const label i) const
 {

src/OpenFOAM/containers/Lists/FixedList/FixedListIO.C

@@ -119,7 +119,7 @@ Foam::Istream& Foam::operator>>(Foam::Istream& is, FixedList<T, Size>& L)
     }
     else
     {
-        is.read(reinterpret_cast<char*>(L.begin()), Size*sizeof(T));
+        is.read(reinterpret_cast<char*>(L.data()), Size*sizeof(T));
 
         is.fatalCheck
         (
@@ -231,7 +231,7 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const FixedList<T, Size>& L)
     }
     else
     {
-        os.write(reinterpret_cast<const char*>(L.v_), Size*sizeof(T));
+        os.write(reinterpret_cast<const char*>(L.cdata()), Size*sizeof(T));
     }
 
     // Check state of IOstream

src/OpenFOAM/containers/Lists/List/ListIO.C

@@ -117,7 +117,7 @@ Foam::Istream& Foam::operator>>(Istream& is, List<T>& L)
         {
             if (s)
             {
-                is.read(reinterpret_cast<char*>(L.begin()), s*sizeof(T));
+                is.read(reinterpret_cast<char*>(L.data()), s*sizeof(T));
 
                 is.fatalCheck
                 (

src/OpenFOAM/containers/Lists/ListOps/ListOps.H

@@ -90,17 +90,31 @@ void duplicateOrder(const UList<T>&, labelList& order);
 template<class T>
 void uniqueOrder(const UList<T>&, labelList& order);
 
-//- Extract elements of List whose region is certain value.
+//- Extract elements of List when select is a certain value.
-//  Use e.g. to extract all selected elements:
+//  eg, to extract all selected elements:
-//    subset<boolList, labelList>(selectedElems, true, lst);
+//    subset<bool, labelList>(selectedElems, true, lst);
 template<class T, class ListType>
-ListType subset(const UList<T>& regions, const T& region, const ListType&);
+ListType subset(const UList<T>& select, const T& value, const ListType&);
 
-//- Inplace extract elements of List whose region is certain value. Use e.g.
+//- Inplace extract elements of List when select is a certain value.
-//  to extract all selected elements:
+//  eg, to extract all selected elements:
-//  inplaceSubset<boolList, labelList>(selectedElems, true, lst);
+//    inplaceSubset<bool, labelList>(selectedElems, true, lst);
 template<class T, class ListType>
-void inplaceSubset(const UList<T>& regions, const T& region, ListType&);
+void inplaceSubset(const UList<T>& select, const T& value, ListType&);
+
+//- Extract elements of List when select is true
+//  eg, to extract all selected elements:
+//    subset<boolList, labelList>(selectedElems, lst);
+//  Note a labelHashSet could also be used for the bool-list
+template<class BoolListType, class ListType>
+ListType subset(const BoolListType& select, const ListType&);
+
+//- Inplace extract elements of List when select is true
+//  eg, to extract all selected elements:
+//    inplaceSubset<boolList, labelList>(selectedElems, lst);
+//  Note a labelHashSet could also be used for the bool-list
+template<class BoolListType, class ListType>
+void inplaceSubset(const BoolListType& select, ListType&);
 
 //- Invert one-to-one map. Unmapped elements will be -1.
 labelList invert(const label len, const UList<label>&);
@@ -108,8 +122,9 @@ labelList invert(const label len, const UList<label>&);
 //- Invert one-to-many map. Unmapped elements will be size 0.
 labelListList invertOneToMany(const label len, const UList<label>&);
 
-//- Invert many-to-many. Input and output types need to be inherited
+//- Invert many-to-many.
-//  from List. E.g. faces to pointFaces.
+//  Input and output types need to be inherited from List.
+//  eg, faces to pointFaces.
 template<class InList, class OutList>
 void invertManyToMany(const label len, const UList<InList>&, List<OutList>&);
 

src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C

@@ -243,16 +243,17 @@ void Foam::uniqueOrder
 template<class T, class ListType>
 ListType Foam::subset
 (
-    const UList<T>& regions,
+    const UList<T>& select,
-    const T& region,
+    const T& value,
     const ListType& lst
 )
 {
-    if (regions.size() < lst.size())
+    // select must at least cover the list range
+    if (select.size() < lst.size())
     {
         FatalErrorIn("subset(const UList<T>&, const T&, const ListType&)")
-            << "Regions is of size " << regions.size()
+            << "select is of size " << select.size()
-            << "; list it is supposed to index is of size " << lst.size()
+            << "; but it must index a list of size " << lst.size()
             << abort(FatalError);
     }
 
@@ -261,7 +262,7 @@ ListType Foam::subset
     label nElem = 0;
     forAll(lst, elemI)
     {
-        if (regions[elemI] == region)
+        if (select[elemI] == value)
         {
             newLst[nElem++] = lst[elemI];
         }
@@ -275,23 +276,77 @@ ListType Foam::subset
 template<class T, class ListType>
 void Foam::inplaceSubset
 (
-    const UList<T>& regions,
+    const UList<T>& select,
-    const T& region,
+    const T& value,
     ListType& lst
 )
 {
-    if (regions.size() < lst.size())
+    // select must at least cover the list range
+    if (select.size() < lst.size())
     {
         FatalErrorIn("inplaceSubset(const UList<T>&, const T&, ListType&)")
-            << "Regions is of size " << regions.size()
+            << "select is of size " << select.size()
-            << "; list it is supposed to index is of size " << lst.size()
+            << "; but it must index a list of size " << lst.size()
             << abort(FatalError);
     }
 
     label nElem = 0;
     forAll(lst, elemI)
     {
-        if (regions[elemI] == region)
+        if (select[elemI] == value)
+        {
+            if (nElem != elemI)
+            {
+                lst[nElem] = lst[elemI];
+            }
+            ++nElem;
+        }
+    }
+
+    lst.setSize(nElem);
+}
+
+
+template<class BoolListType, class ListType>
+ListType Foam::subset
+(
+    const BoolListType& select,
+    const ListType& lst
+)
+{
+    // select can have a different size
+    // eg, when it is a PackedBoolList or a labelHashSet
+
+    ListType newLst(lst.size());
+
+    label nElem = 0;
+    forAll(lst, elemI)
+    {
+        if (select[elemI])
+        {
+            newLst[nElem++] = lst[elemI];
+        }
+    }
+    newLst.setSize(nElem);
+
+    return newLst;
+}
+
+
+template<class BoolListType, class ListType>
+void Foam::inplaceSubset
+(
+    const BoolListType& select,
+    ListType& lst
+)
+{
+    // select can have a different size
+    // eg, when it is a PackedBoolList or a labelHashSet
+
+    label nElem = 0;
+    forAll(lst, elemI)
+    {
+        if (select[elemI])
         {
             if (nElem != elemI)
             {

src/OpenFOAM/containers/Lists/PackedList/PackedList.C

@@ -83,25 +83,25 @@ unsigned int Foam::PackedList<nBits>::count() const
 
     if (size_)
     {
-        // mask value for complete chunks
+        // mask value for complete segments
         unsigned int mask = maskLower(packing());
 
-        unsigned int endIdx = size_ / packing();
+        const unsigned int endSeg = size_ / packing();
-        unsigned int endOff = size_ % packing();
+        const unsigned int endOff = size_ % packing();
 
-        // count bits in complete elements
+        // count bits in complete segments
-        for (unsigned i = 0; i < endIdx; ++i)
+        for (unsigned i = 0; i < endSeg; ++i)
         {
             register unsigned int bits = StorageList::operator[](i) & mask;
             COUNT_PACKEDBITS(c, bits);
         }
 
-        // count bits in partial chunk
+        // count bits in partial segment
         if (endOff)
         {
             mask = maskLower(endOff);
 
-            register unsigned int bits = StorageList::operator[](endIdx) & mask;
+            register unsigned int bits = StorageList::operator[](endSeg) & mask;
             COUNT_PACKEDBITS(c, bits);
         }
     }
@@ -118,7 +118,7 @@ bool Foam::PackedList<nBits>::trim()
         return false;
     }
 
-    // mask value for complete chunks
+    // mask value for complete segments
     unsigned int mask = maskLower(packing());
 
     label currElem = packedLength(size_) - 1;
@@ -130,7 +130,7 @@ bool Foam::PackedList<nBits>::trim()
         StorageList::operator[](currElem) &= maskLower(endOff);
     }
 
-    // test entire chunk
+    // test entire segment
     while (currElem > 0 && !(StorageList::operator[](currElem) &= mask))
     {
         currElem--;
@@ -162,10 +162,22 @@ bool Foam::PackedList<nBits>::trim()
 }
 
 
+template<unsigned nBits>
+void Foam::PackedList<nBits>::flip()
+{
+    label packLen = packedLength(size_);
+
+    for (label i=0; i < packLen; i++)
+    {
+        StorageList::operator[](i) = ~StorageList::operator[](i);
+    }
+}
+
+
 template<unsigned nBits>
 Foam::labelList Foam::PackedList<nBits>::values() const
 {
-    labelList elems(size());
+    labelList elems(size_);
 
     forAll(*this, i)
     {
@@ -178,10 +190,11 @@ Foam::labelList Foam::PackedList<nBits>::values() const
 template<unsigned nBits>
 Foam::Ostream& Foam::PackedList<nBits>::iteratorBase::print(Ostream& os) const
 {
-    os  << "iterator<" << label(nBits) << "> ["
+    os  << "iterator<"  << label(nBits) << "> ["
-        << (index_ * packing() + offset_) << "]"
+        << this->index_ << "]"
-        << " index:" << index_ << " offset:" << offset_
+        << " segment:"  << label(this->index_ / packing())
-        << " value:" << unsigned(*this)
+        << " offset:"   << label(this->index_ % packing())
+        << " value:"    << this->get()
         << nl;
 
     return os;
@@ -194,7 +207,7 @@ Foam::Ostream& Foam::PackedList<nBits>::print(Ostream& os) const
     os  << "PackedList<" << label(nBits) << ">"
         << " max_value:" << max_value()
         << " packing:"   << packing() << nl
-        << "values: " << size() << "/" << capacity() << "( ";
+        << "values: " << size_ << "/" << capacity() << "( ";
     forAll(*this, i)
     {
         os << get(i) << ' ';
@@ -205,17 +218,17 @@ Foam::Ostream& Foam::PackedList<nBits>::print(Ostream& os) const
     os  << ")\n"
         << "storage: " << packLen << "/" << StorageList::size() << "( ";
 
-    // mask value for complete chunks
+    // mask value for complete segments
     unsigned int mask = maskLower(packing());
 
     for (label i=0; i < packLen; i++)
     {
         const StorageType& rawBits = StorageList::operator[](i);
 
-        // the final storage may not be full, modify mask accordingly
+        // the final segment may not be full, modify mask accordingly
         if (i+1 == packLen)
         {
-            unsigned endOff = size_ % packing();
+            unsigned int endOff = size_ % packing();
 
             if (endOff)
             {
@@ -229,7 +242,7 @@ Foam::Ostream& Foam::PackedList<nBits>::print(Ostream& os) const
 
         for (unsigned int testBit = (1 << max_bits()); testBit; testBit >>= 1)
         {
-            if (testBit & mask)
+            if (mask & testBit)
             {
                 if (rawBits & testBit)
                 {

src/OpenFOAM/containers/Lists/PackedList/PackedList.H

@@ -44,9 +44,9 @@ Note
     Using the iteratorBase as a proxy allows assignment of values
     between list elements. Thus the following bit of code works as expected:
     @code
-        blist[1] = blist[5];     // value assignment, not iterator position
+        list[1] = list[5];      // value assignment, not iterator position
-        blist[2] = blist[5] = 4; // propagates value
+        list[2] = list[5] = 4;  // propagates value
-        blist[1] = blist[5] = blist[6];  // propagates value
+        list[1] = list[5] = list[6];  // propagates value
     @endcode
 
     Using get() or the '[]' operator are similarly fast. Looping and reading
@@ -58,11 +58,21 @@ Note
     useful for branching on changed values.
 
     @code
-        blist[5] = 4;
+        list[5] = 4;
-        changed = blist.set(5, 8);
+        changed = list.set(5, 8);
         if (changed) ...
     @endcode
 
+    The lazy evaluation used means that reading an out-of-range element
+    returns zero, but does not affect the list size.  Even in a non-const
+    context, only the assigment causes the element to be created.
+    For example,
+    @code
+        list.resize(4);
+        Info<< list[10] << "\n";  // print zero, but doesn't adjust list
+        list[8] = 1;
+    @endcode
+
 SeeAlso
     Foam::DynamicList
 
@@ -120,9 +130,6 @@ class PackedList
         //- Calculate the list length when packed
         inline static label packedLength(const label);
 
-        //- Check index I is within valid range [ 0 .. max_value() ]
-        inline void checkIndex(const label) const;
-
 public:
 
     // Public data
@@ -172,22 +179,23 @@ public:
 
         // Access
 
-        //- The number of elements that can be stored before resizing
+        //- The number of elements that can be stored before reallocating
         inline label capacity() const;
 
         //- Number of entries.
         inline label size() const;
 
-        //- Return true if the list is empty (i.e., if size() == 0).
+        //- Return true if the list is empty (ie, size() is zero).
         inline bool empty() const;
 
         //- Get value at index I.
-        //  Does not auto-vivify entries.
+        //  Never auto-vivify entries.
         inline unsigned int get(const label) const;
 
         //- Set value at index I. Return true if value changed.
-        //  Does not auto-vivify entries.
+        //  Does auto-vivify for non-existent entries.
-        inline bool set(const label, const unsigned int val);
+        //  Default value set is the max_value.
+        inline bool set(const label, const unsigned int val = ~0u);
 
         //- Return the underlying packed storage
         inline List<unsigned int>& storage();
@@ -200,9 +208,6 @@ public:
         //  http://en.wikipedia.org/wiki/Hamming_weight
         unsigned int count() const;
 
-        //- Trim any trailing zero elements
-        bool trim();
-
         //- Return the values as a labelList
         labelList values() const;
 
@@ -211,6 +216,12 @@ public:
 
         // Edit
 
+        //- Trim any trailing zero elements
+        bool trim();
+
+        //- Invert the bits in the addressable region.
+        void flip();
+
         //- Alter the size of the underlying storage.
         //  The addressed size will be truncated if needed to fit, but will
         //  remain otherwise untouched.
@@ -255,12 +266,12 @@ public:
         inline unsigned int remove();
 
         //- Get value at index I
-        //  Does not auto-vivify entries.
+        //  Never auto-vivify entries.
         inline unsigned int operator[](const label) const;
 
         //- Set value at index I.
         //  Returns iterator to perform the actual operation.
-        //  Does not auto-vivify entries.
+        //  Does not auto-vivify entries, but will when assigned to.
         inline iteratorBase operator[](const label);
 
         //- Assignment of all entries to the given value. Takes linear time.
@@ -294,52 +305,27 @@ public:
                 //  This also lets us use the default bitwise copy/assignment
                 PackedList* list_;
 
-                //- Element index within storage
+                //- Element index
-                unsigned index_;
+                label index_;
-
-                //- Offset within storage element
-                unsigned offset_;
 
             // Protected Member Functions
 
-                //- Get value as unsigned
+                //- Get value as unsigned, no range-checking
                 inline unsigned int get() const;
 
-                //- Set value, returning true if changed
+                //- Set value, returning true if changed, no range-checking
                 inline bool set(unsigned int);
 
-                //- Increment to new position
-                inline void incr();
-
-                //- Decrement to new position
-                inline void decr();
-
-                //- Move to new position, but not beyond end()
-                inline void seek(const iteratorBase&);
-
-
             // Constructors
 
                 //- Construct null
                 inline iteratorBase();
 
-                //- Copy construct
-                inline iteratorBase(const iteratorBase&);
-
                 //- Construct from base list and position index
                 inline iteratorBase(const PackedList*, const label);
 
         public:
 
-            // Member Functions
-
-                //- Return true if the element is within addressable range
-                inline bool valid() const;
-
-                //- Move iterator to end() if it would otherwise be out-of-range
-                //  Returns true if the element was already ok
-                inline bool validate();
-
             // Member Operators
 
                 //- Compare positions
@@ -350,10 +336,12 @@ public:
                 //  This allows packed[0] = packed[3] for assigning values
                 inline unsigned int operator=(const iteratorBase&);
 
-                //- Assign value
+                //- Assign value.
+                //  A non-existent entry will be auto-vivified.
                 inline unsigned int operator=(const unsigned int val);
 
                 //- Conversion operator
+                //  Never auto-vivify entries.
                 inline operator unsigned int () const;
 
             //- Print value and information
@@ -378,6 +366,8 @@ public:
                 inline iterator();
 
                 //- Construct from iterator base, eg iter(packedlist[i])
+                //  but also  "iterator iter = packedlist[i];"
+                //  An out-of-range iterator is assigned end()
                 inline iterator(const iteratorBase&);
 
                 //- Construct from base list and position index
@@ -386,6 +376,7 @@ public:
             // Member Operators
 
                 //- Assign from iteratorBase, eg iter = packedlist[i]
+                //  An out-of-range iterator is assigned end()
                 inline iterator& operator=(const iteratorBase&);
 
                 //- Return value
@@ -427,7 +418,9 @@ public:
                 //- Construct null
                 inline const_iterator();
 
-                //- Construct from iterator base
+                //- Construct from iterator base, eg iter(packedlist[i])
+                //  but also  "const_iterator iter = packedlist[i];"
+                //  An out-of-range iterator is assigned end()
                 inline const_iterator(const iteratorBase&);
 
                 //- Construct from base list and position index
@@ -439,7 +432,7 @@ public:
             // Member operators
 
                 //- Assign from iteratorBase or derived
-                //  eg, iter = packedlist[i] or iter = [non-const]list.begin()
+                //  eg, iter = packedlist[i] or even iter = list.begin()
                 inline const_iterator& operator=(const iteratorBase&);
 
                 //- Return referenced value directly

src/OpenFOAM/containers/Lists/PackedList/PackedListI.H

@@ -65,24 +65,6 @@ inline Foam::label Foam::PackedList<nBits>::packedLength(const label nElem)
 }
 
 
-template<unsigned nBits>
-inline void Foam::PackedList<nBits>::checkIndex(const label i) const
-{
-    if (!size_)
-    {
-        FatalErrorIn("PackedList<nBits>::checkIndex(const label)")
-            << "attempt to access element from zero-sized list"
-            << abort(FatalError);
-    }
-    else if (i < 0 || i >= size_)
-    {
-        FatalErrorIn("PackedList<nBits>::checkIndex(const label)")
-            << "index " << i << " out of range 0 ... " << size_-1
-            << abort(FatalError);
-    }
-}
-
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<unsigned nBits>
@@ -105,7 +87,7 @@ template<unsigned nBits>
 inline Foam::PackedList<nBits>::PackedList(const PackedList<nBits>& lst)
 :
     StorageList(lst),
-    size_(lst.size())
+    size_(lst.size_)
 {}
 
 
@@ -132,20 +114,7 @@ template<unsigned nBits>
 inline Foam::PackedList<nBits>::iteratorBase::iteratorBase()
 :
     list_(0),
-    index_(0),
+    index_(0)
-    offset_(0)
-{}
-
-
-template<unsigned nBits>
-inline Foam::PackedList<nBits>::iteratorBase::iteratorBase
-(
-    const iteratorBase& iter
-)
-:
-    list_(iter.list_),
-    index_(iter.index_),
-    offset_(iter.offset_)
 {}
 
 
@@ -157,8 +126,7 @@ inline Foam::PackedList<nBits>::iteratorBase::iteratorBase
 )
 :
     list_(const_cast<PackedList<nBits>*>(lst)),
-    index_(i / packing()),
+    index_(i)
-    offset_(i % packing())
 {}
 
 
@@ -166,8 +134,11 @@ template<unsigned nBits>
 inline unsigned int
 Foam::PackedList<nBits>::iteratorBase::get() const
 {
-    const unsigned int& stored = list_->StorageList::operator[](index_);
+    const unsigned int seg = index_ / packing();
-    return (stored >> (nBits * offset_)) & max_value();
+    const unsigned int off = index_ % packing();
+
+    const unsigned int& stored = list_->StorageList::operator[](seg);
+    return (stored >> (nBits * off)) & max_value();
 }
 
 
@@ -175,114 +146,37 @@ template<unsigned nBits>
 inline bool
 Foam::PackedList<nBits>::iteratorBase::set(const unsigned int val)
 {
-    unsigned int& stored = list_->StorageList::operator[](index_);
+    const unsigned int seg = index_ / packing();
+    const unsigned int off = index_ % packing();
+
+    unsigned int& stored = list_->StorageList::operator[](seg);
     const unsigned int prev = stored;
 
-    const unsigned int startBit = nBits * offset_;
+    const unsigned int startBit = nBits * off;
     const unsigned int maskNew  = max_value() << startBit;
 
     if (val & ~max_value())
     {
-#       ifdef DEBUGList
+        // overflow is max_value, fill everything
-        FatalErrorIn("PackedList<T>::iteratorBase::set(const unsigned int)")
-            << "value " << label(val)
-w            << " out-of-range 0 ... " << label(max_value())
-            << " representable by " << nBits << " bits"
-            << abort(FatalError);
-#       endif
-
-        // treat overflow as max_value
         stored |= maskNew;
     }
     else
     {
-        stored = (stored & ~maskNew) | (maskNew & (val << startBit));
+        stored &= ~maskNew;
+        stored |= maskNew & (val << startBit);
     }
 
     return prev != stored;
 }
 
 
-
-template<unsigned nBits>
-inline void
-Foam::PackedList<nBits>::iteratorBase::incr()
-{
-    offset_++;
-    if (offset_ >= packing())
-    {
-        offset_ = 0;
-        index_++;
-    }
-}
-
-
-template<unsigned nBits>
-inline void
-Foam::PackedList<nBits>::iteratorBase::decr()
-{
-    if (!offset_)
-    {
-        offset_ = packing();
-        index_--;
-    }
-    offset_--;
-}
-
-
-template<unsigned nBits>
-inline void
-Foam::PackedList<nBits>::iteratorBase::seek
-(
-    const iteratorBase& iter
-)
-{
-    list_   = iter.list_;
-    index_  = iter.index_;
-    offset_ = iter.offset_;
-
-    this->validate();
-}
-
-
-template<unsigned nBits>
-inline bool
-Foam::PackedList<nBits>::iteratorBase::valid() const
-{
-    label elemI = offset_ + index_ * packing();
-    return (elemI < list_->size_);
-}
-
-
-template<unsigned nBits>
-inline bool
-Foam::PackedList<nBits>::iteratorBase::validate()
-{
-    // avoid going past end()
-    unsigned endIdx = list_->size_ / packing();
-    unsigned endOff = list_->size_ % packing();
-
-    if (index_ > endIdx || (index_ == endIdx && offset_ > endOff))
-    {
-        index_  = endIdx;
-        offset_ = endOff;
-
-        return false;
-    }
-    else
-    {
-        return true;
-    }
-}
-
-
 template<unsigned nBits>
 inline bool Foam::PackedList<nBits>::iteratorBase::operator==
 (
     const iteratorBase& iter
 ) const
 {
-    return this->index_ == iter.index_ && this->offset_ == iter.offset_;
+    return this->index_ == iter.index_;
 }
 
 
@@ -292,7 +186,7 @@ inline bool Foam::PackedList<nBits>::iteratorBase::operator!=
     const iteratorBase& iter
 ) const
 {
-    return this->index_ != iter.index_ || this->offset_ != iter.offset_;
+    return this->index_ != iter.index_;
 }
 
 
@@ -310,14 +204,11 @@ template<unsigned nBits>
 inline unsigned int
 Foam::PackedList<nBits>::iteratorBase::operator=(const unsigned int val)
 {
-#   ifdef DEBUGList
+    // lazy evaluation - increase size on assigment
-    // lazy evaluation would be nice to keep, but really slows things down
+    if (index_ >= list_->size_)
-    label minsize = 1 + offset_ + index_ * packing();
-    if (minsize > list_->size_)
     {
-        list_->resize(minsize);
+        list_->resize(index_ + 1);
     }
-#endif
 
     this->set(val);
     return val;
@@ -328,14 +219,11 @@ template<unsigned nBits>
 inline Foam::PackedList<nBits>::iteratorBase::operator
 unsigned int () const
 {
-#   ifdef DEBUGList
+    // lazy evaluation - return 0 for out-of-range
-    // lazy evaluation would be nice to keep, but really slows things down
+    if (index_ >= list_->size_)
-    label minsize = 1 + offset_ + index_ * packing();
-    if (minsize > list_->size_)
     {
         return 0;
     }
-#endif
 
     return this->get();
 }
@@ -365,7 +253,12 @@ inline Foam::PackedList<nBits>::iterator::iterator
 :
     iteratorBase(iter)
 {
-    this->validate();
+    // avoid going past end()
+    // eg, iter = iterator(list, Inf)
+    if (this->index_ > this->list_->size_)
+    {
+        this->index_ = this->list_->size_;
+    }
 }
 
 
@@ -377,7 +270,12 @@ inline Foam::PackedList<nBits>::const_iterator::const_iterator
 :
     iteratorBase(iter)
 {
-    this->validate();
+    // avoid going past end()
+    // eg, iter = iterator(list, Inf)
+    if (this->index_ > this->list_->size_)
+    {
+        this->index_ = this->list_->size_;
+    }
 }
 
 
@@ -417,7 +315,16 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::iterator&
 Foam::PackedList<nBits>::iterator::operator=(const iteratorBase& iter)
 {
-    this->seek(iter);
+    this->list_  = iter.list_;
+    this->index_ = iter.index_;
+
+    // avoid going past end()
+    // eg, iter = iterator(list, Inf)
+    if (this->index_ > this->list_->size_)
+    {
+        this->index_ = this->list_->size_;
+    }
+
     return *this;
 }
 
@@ -426,7 +333,16 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::const_iterator&
 Foam::PackedList<nBits>::const_iterator::operator=(const iteratorBase& iter)
 {
-    this->seek(iter);
+    this->list_  = iter.list_;
+    this->index_ = iter.index_;
+
+    // avoid going past end()
+    // eg, iter = iterator(list, Inf)
+    if (this->index_ > this->list_->size_)
+    {
+        this->index_ = this->list_->size_;
+    }
+
     return *this;
 }
 
@@ -435,7 +351,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::iterator&
 Foam::PackedList<nBits>::iterator::operator++()
 {
-    this->incr();
+    ++this->index_;
     return *this;
 }
 
@@ -444,7 +360,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::const_iterator&
 Foam::PackedList<nBits>::const_iterator::operator++()
 {
-    this->incr();
+    ++this->index_;
     return *this;
 }
 
@@ -454,7 +370,7 @@ inline typename Foam::PackedList<nBits>::iterator
 Foam::PackedList<nBits>::iterator::operator++(int)
 {
     iterator old = *this;
-    this->incr();
+    ++this->index_;
     return old;
 }
 
@@ -464,7 +380,7 @@ inline typename Foam::PackedList<nBits>::const_iterator
 Foam::PackedList<nBits>::const_iterator::operator++(int)
 {
     const_iterator old = *this;
-    this->incr();
+    ++this->index_;
     return old;
 }
 
@@ -473,7 +389,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::iterator&
 Foam::PackedList<nBits>::iterator::operator--()
 {
-    this->decr();
+    --this->index_;
     return *this;
 }
 
@@ -482,7 +398,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::const_iterator&
 Foam::PackedList<nBits>::const_iterator::operator--()
 {
-    this->decr();
+    --this->index_;
     return *this;
 }
 
@@ -492,7 +408,7 @@ inline typename Foam::PackedList<nBits>::iterator
 Foam::PackedList<nBits>::iterator::operator--(int)
 {
     iterator old = *this;
-    this->decr();
+    --this->index_;
     return old;
 }
 
@@ -502,7 +418,7 @@ inline typename Foam::PackedList<nBits>::const_iterator
 Foam::PackedList<nBits>::const_iterator::operator--(int)
 {
     const_iterator old = *this;
-    this->decr();
+    --this->index_;
     return old;
 }
 
@@ -567,7 +483,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::iterator
 Foam::PackedList<nBits>::end()
 {
-    return iterator(this, this->size());
+    return iterator(this, size_);
 }
 
 
@@ -575,7 +491,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::const_iterator
 Foam::PackedList<nBits>::end() const
 {
-    return const_iterator(this, this->size());
+    return const_iterator(this, size_);
 }
 
 
@@ -583,7 +499,7 @@ template<unsigned nBits>
 inline typename Foam::PackedList<nBits>::const_iterator
 Foam::PackedList<nBits>::cend() const
 {
-    return const_iterator(this, this->size());
+    return const_iterator(this, size_);
 }
 
 
@@ -617,20 +533,12 @@ inline void Foam::PackedList<nBits>::resize
         // fill new elements or newly exposed elements
         if (size_)
         {
-            // fill value for complete chunks
+            // fill value for complete segments
             unsigned int fill = val;
 
             if (fill & ~max_value())
             {
-#               ifdef DEBUGList
+                // overflow is max_value, fill everything
-                FatalErrorIn("PackedList<T>::resize(label, const unsigned int)")
-                    << "value " << label(val)
-                    << " out-of-range 0 ... " << label(max_value())
-                    << " representable by " << nBits << " bits"
-                    << abort(FatalError);
-#               endif
-
-                // treat overflow as max_value, fill everything
                 fill = ~0;
             }
             else
@@ -641,26 +549,26 @@ inline void Foam::PackedList<nBits>::resize
                 }
             }
 
-            unsigned begIdx = size_ / packing();
+            unsigned int seg = size_ / packing();
-            unsigned begOff = size_ % packing();
+            unsigned int off = size_ % packing();
-            unsigned endIdx = nElem / packing();
 
-            // partial chunk, preserve existing value
+            // partial segment, preserve existing value
-            if (begOff)
+            if (off)
             {
-                unsigned int maskOld = maskLower(begOff);
+                unsigned int maskOld = maskLower(off);
 
-                StorageList::operator[](begIdx) &= maskOld;
+                StorageList::operator[](seg) &= maskOld;
-                StorageList::operator[](begIdx) |= ~maskOld & fill;
+                StorageList::operator[](seg) |= ~maskOld & fill;
 
-                // continue with the next chunk
+                // continue with the next segment
-                begIdx++;
+                seg++;
             }
 
+            unsigned int endSeg = nElem / packing();
             // fill in complete elements
-            while (begIdx < endIdx)
+            while (seg < endSeg)
             {
-                StorageList::operator[](begIdx++) = fill;
+                StorageList::operator[](seg++) = fill;
             }
         }
         else
@@ -786,17 +694,31 @@ Foam::PackedList<nBits>::xfer()
 template<unsigned nBits>
 inline unsigned int Foam::PackedList<nBits>::get(const label i) const
 {
-#   ifdef DEBUGList
+#   ifdef FULLDEBUG
-    checkIndex(i);
+    if (i < 0)
+    {
+        FatalErrorIn("PackedList<nBits>::get(const label)")
+            << "negative index " << i << " max=" << size_-1
+            << abort(FatalError);
+    }
 #   endif
 
-    return iteratorBase(this, i).get();
+    // lazy evaluation - return 0 for out-of-range
+    if (i < size_)
+    {
+        return iteratorBase(this, i).get();
+    }
+    else
+    {
+        return 0;
+    }
 }
 
 
 template<unsigned nBits>
 inline unsigned int Foam::PackedList<nBits>::operator[](const label i) const
 {
+    // lazy evaluation - return 0 for out-of-range
     if (i < size_)
     {
         return iteratorBase(this, i).get();
@@ -815,18 +737,21 @@ inline bool Foam::PackedList<nBits>::set
     const unsigned int val
 )
 {
-#   ifdef DEBUGList
+#   ifdef FULLDEBUG
-    checkIndex(i);
+    if (i < 0)
-
-    if (val & ~max_value())
     {
-        FatalErrorIn("PackedList<T>::set(const label, const unsigned int)")
+        FatalErrorIn("PackedList<nBits>::set(const label)")
-            << "value " << label(val)
+            << "negative index " << i << " max=" << size_-1
-            << " out-of-range 0 ... " << label(max_value())
-            << " representable by " << nBits << " bits"
             << abort(FatalError);
     }
-#   endif
+#endif
+
+    // lazy evaluation - increase size on assigment
+    if (i >= size_)
+    {
+        resize(i + 1);
+    }
+
     return iteratorBase(this, i).set(val);
 }
 
@@ -879,14 +804,6 @@ inline void Foam::PackedList<nBits>::operator=(const unsigned int val)
 
         if (fill & ~max_value())
         {
-#           ifdef DEBUGList
-            FatalErrorIn("PackedList<T>::operator=(const unsigned int)")
-                << "value " << label(val)
-                << " out-of-range 0 ... " << label(max_value())
-                << " representable by " << nBits << " bits"
-                << abort(FatalError);
-#           endif
-
             // treat overflow as max_value
             fill = ~0;
         }

src/OpenFOAM/containers/Lists/PtrList/PtrList.H

@@ -158,7 +158,7 @@ public:
             //- Return the number of elements in the PtrList
             inline label size() const;
 
-            //- Return true if the PtrList is empty (i.e., if size() == 0).
+            //- Return true if the PtrList is empty (ie, size() is zero).
             inline bool empty() const;
 
 

src/OpenFOAM/containers/Lists/UList/UList.H

@@ -27,7 +27,7 @@ Class
 
 Description
     A 1D vector of objects of type \<T\>, where the size of the vector is
-    known and used for subscript bounds checking, etc.
+    known and can be used for subscript bounds checking, etc.
 
     Storage is not allocated during construction or use but is supplied to
     the constructor as an argument.  This type of list is particularly useful
@@ -140,6 +140,17 @@ public:
             label byteSize() const;
 
 
+            //- Return a const pointer to the first data element,
+            //  similar to the STL front() method and the string::data() method
+            //  This can be used (with caution) when interfacing with C code.
+            inline const T* cdata() const;
+
+            //- Return a pointer to the first data element,
+            //  similar to the STL front() method and the string::data() method
+            //  This can be used (with caution) when interfacing with C code.
+            inline T* data();
+
+
         // Check
 
             //- Check start is within valid range (0 ... size-1).
@@ -164,10 +175,12 @@ public:
 
     // Member operators
 
-        //- Return subscript-checked element of UList.
+        //- Return element of UList.
         inline T& operator[](const label);
 
-        //- Return subscript-checked element of constant UList.
+        //- Return element of constant UList.
+        //  Note that the bool specialization adds lazy evaluation so reading
+        //  an out-of-range element returns false without any ill-effects
         inline const T& operator[](const label) const;
 
         //- Allow cast to a const List<T>&
@@ -266,7 +279,7 @@ public:
         //- Return size of the largest possible UList.
         inline label max_size() const;
 
-        //- Return true if the UList is empty (i.e., if size() == 0).
+        //- Return true if the UList is empty (ie, size() is zero).
         inline bool empty() const;
 
         //- Swap two ULists of the same type in constant time.

src/OpenFOAM/containers/Lists/UList/UListI.H

@@ -25,6 +25,7 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "error.H"
+#include "pTraits.H"
 #include "Swap.H"
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
@@ -64,7 +65,7 @@ inline Foam::label Foam::UList<T>::fcIndex(const label i) const
 template<class T>
 inline Foam::label Foam::UList<T>::rcIndex(const label i) const
 {
-    return (i == 0 ? size()-1 : i-1);
+    return (i ? i-1 : size()-1);
 }
 
 
@@ -113,9 +114,24 @@ inline void Foam::UList<T>::checkIndex(const label i) const
 }
 
 
+template<class T>
+inline const T* Foam::UList<T>::cdata() const
+{
+    return v_;
+}
+
+
+template<class T>
+inline T* Foam::UList<T>::data()
+{
+    return v_;
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
-// Return subscript-checked element access
+
+// element access
 template<class T>
 inline T& Foam::UList<T>::operator[](const label i)
 {
@@ -126,7 +142,28 @@ inline T& Foam::UList<T>::operator[](const label i)
 }
 
 
-// Return subscript-checked const element access
+namespace Foam
+{
+
+    // Template specialization for bool
+    template<>
+    inline const bool& Foam::UList<bool>::operator[](const label i) const
+    {
+        // lazy evaluation - return false for out-of-range
+        if (i < size_)
+        {
+            return v_[i];
+        }
+        else
+        {
+            return Foam::pTraits<bool>::zero;
+        }
+    }
+
+} // end of namespace Foam
+
+
+// const element access
 template<class T>
 inline const T& Foam::UList<T>::operator[](const label i) const
 {
@@ -248,7 +285,7 @@ inline Foam::label Foam::UList<T>::max_size() const
 template<class T>
 inline bool Foam::UList<T>::empty() const
 {
-    return (size_ == 0);
+    return !size_;
 }
 
 

src/OpenFOAM/containers/Lists/UPtrList/UPtrList.H

@@ -124,7 +124,7 @@ public:
             //- Return the number of elements in the UPtrList
             inline label size() const;
 
-            //- Return true if the UPtrList is empty (i.e., if size() == 0).
+            //- Return true if the UPtrList is empty (ie, size() is zero).
             inline bool empty() const;
 
 

src/OpenFOAM/db/IOobject/IOobject.C

@@ -35,6 +35,85 @@ namespace Foam
     defineTypeNameAndDebug(IOobject, 0);
 }
 
+// * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * * //
+
+// Return components following the IOobject requirements
+//
+//  behaviour
+//    input               IOobject(instance, local, name)
+//    -----               ------
+//    "foo"               ("", "", "foo")
+//    "foo/bar"           ("foo", "", "bar")
+//    "/XXX"              ERROR - no absolute path
+//    "foo/bar/"          ERROR - no name
+//    "foo/xxx/bar"       ("foo", "xxx", "bar")
+//    "foo/xxx/yyy/bar"   ("foo", "xxx/yyy", "bar")
+bool Foam::IOobject::IOobject::fileNameComponents
+(
+    const fileName& path,
+    fileName& instance,
+    fileName& local,
+    word& name
+)
+{
+    instance.clear();
+    local.clear();
+    name.clear();
+
+    // called with directory
+    if (!isDir(path))
+    {
+        WarningIn("IOobject::fileNameComponents(const fileName&, ...)")
+            << " called with directory: " << path << "\n";
+        return false;
+    }
+
+    string::size_type first = path.find('/');
+
+    if (first == 0)
+    {
+        // called with absolute path
+        WarningIn("IOobject::fileNameComponents(const fileName&, ...)")
+            << "called with absolute path: " << path << "\n";
+        return false;
+    }
+
+    if (first == string::npos)
+    {
+        // no '/' found - no instance or local
+
+        // check afterwards
+        name.string::operator=(path);
+    }
+    else
+    {
+        instance = path.substr(0, first);
+
+        string::size_type last = path.rfind('/');
+        if (last > first)
+        {
+            // with local
+            local = path.substr(first+1, last-first-1);
+        }
+
+        // check afterwards
+        name.string::operator=(path.substr(last+1));
+    }
+
+
+    // check for valid (and stripped) name, regardless of the debug level
+    if (name.empty() || string::stripInvalid<word>(name))
+    {
+        WarningIn("IOobject::fileNameComponents(const fileName&, ...)")
+            << "has invalid word for name: \"" << name
+            << "\"\nwhile processing path: " << path << "\n";
+        return false;
+    }
+
+    return true;
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::IOobject::IOobject
@@ -118,7 +197,15 @@ Foam::IOobject::IOobject
     registerObject_(registerObject),
     objState_(GOOD)
 {
-    path.IOobjectComponents(instance_, local_, name_);
+    if (!fileNameComponents(path, instance_, local_, name_))
+    {
+        FatalErrorIn
+        (
+            "IOobject::IOobject" "(const fileName&, const objectRegistry&, ...)"
+        )
+            << " invalid path specification\n"
+            << exit(FatalError);
+    }
 
     if (objectRegistry::debug)
     {
@@ -182,7 +269,7 @@ Foam::fileName Foam::IOobject::filePath() const
     fileName path = this->path();
     fileName objectPath = path/name();
 
-    if (file(objectPath))
+    if (isFile(objectPath))
     {
         return objectPath;
     }
@@ -201,13 +288,13 @@ Foam::fileName Foam::IOobject::filePath() const
                 rootPath()/caseName()
                /".."/instance()/db_.dbDir()/local()/name();
 
-            if (file(parentObjectPath))
+            if (isFile(parentObjectPath))
             {
                 return parentObjectPath;
             }
         }
 
-        if (!dir(path))
+        if (!isDir(path))
         {
             word newInstancePath = time().findInstancePath(instant(instance()));
 
@@ -219,7 +306,7 @@ Foam::fileName Foam::IOobject::filePath() const
                    /newInstancePath/db_.dbDir()/local()/name()
                 );
 
-                if (file(fName))
+                if (isFile(fName))
                 {
                     return fName;
                 }
@@ -235,7 +322,7 @@ Foam::Istream* Foam::IOobject::objectStream()
 {
     fileName fName = filePath();
 
-    if (fName != fileName::null)
+    if (fName.size())
     {
         IFstream* isPtr = new IFstream(fName);
 

src/OpenFOAM/db/IOobject/IOobject.H

@@ -149,7 +149,6 @@ private:
         //- IOobject state
         objectState objState_;
 
-
 protected:
 
     // Protected member functions
@@ -168,6 +167,18 @@ public:
     TypeName("IOobject");
 
 
+    // Static Member Functions
+
+        //- Split path into instance, local, name components
+        static bool fileNameComponents
+        (
+            const fileName& path,
+            fileName& instance,
+            fileName& local,
+            word& name
+        );
+
+
     // Constructors
 
         //- Construct from name, instance, registry, io options
@@ -194,6 +205,7 @@ public:
         );
 
         //- Construct from path, registry, io options
+        //  Uses fileNameComponents() to split path into components.
         IOobject
         (
             const fileName& path,
@@ -215,7 +227,7 @@ public:
         virtual ~IOobject();
 
 
-    // Member functions
+    // Member Functions
 
         // General access
 

src/OpenFOAM/db/IOobjectList/IOobjectList.C

@@ -48,7 +48,7 @@ Foam::IOobjectList::IOobjectList
 {
     word newInstance = instance;
 
-    if (!dir(db.path(instance)))
+    if (!isDir(db.path(instance)))
     {
         newInstance = db.time().findInstancePath(instant(instance));
 
@@ -59,7 +59,7 @@ Foam::IOobjectList::IOobjectList
     }
 
     // Create list file names in directory
-    fileNameList ObjectNames = 
+    fileNameList ObjectNames =
         readDir(db.path(newInstance, db.dbDir()/local), fileName::FILE);
 
     forAll(ObjectNames, i)

src/OpenFOAM/db/IOstreams/Fstreams/IFstream.C

@@ -54,7 +54,7 @@ Foam::IFstreamAllocator::IFstreamAllocator(const fileName& pathname)
     ifPtr_ = new ifstream(pathname.c_str());
 
     // If the file is compressed, decompress it before reading.
-    if (!ifPtr_->good() && file(pathname + ".gz"))
+    if (!ifPtr_->good() && isFile(pathname + ".gz", false))
     {
         if (IFstream::debug)
         {
@@ -120,8 +120,8 @@ Foam::IFstream::IFstream
         if (debug)
         {
             Info<< "IFstream::IFstream(const fileName&,"
-                   "streamFormat format=ASCII,"
+                   "streamFormat=ASCII,"
-                   "versionNumber version=currentVersion) : "
+                   "versionNumber=currentVersion) : "
                    "could not open file for input"
                 << endl << info() << endl;
         }
@@ -159,17 +159,18 @@ Foam::IFstream& Foam::IFstream::operator()() const
 {
     if (!good())
     {
-        if (!file(pathname_) && !file(pathname_ + ".gz"))
+        // also checks .gz file
+        if (isFile(pathname_, true))
+        {
+            check("IFstream::operator()");
+            FatalIOError.exit();
+        }
+        else
         {
             FatalIOErrorIn("IFstream::operator()", *this)
                 << "file " << pathname_ << " does not exist"
                 << exit(FatalIOError);
         }
-        else
-        {
-            check("IFstream::operator()");
-            FatalIOError.exit();
-        }
     }
 
     return const_cast<IFstream&>(*this);

src/OpenFOAM/db/IOstreams/Fstreams/OFstream.C

@@ -57,7 +57,8 @@ Foam::OFstreamAllocator::OFstreamAllocator
 
     if (compression == IOstream::COMPRESSED)
     {
-        if (file(pathname))
+        // get identically named uncompressed version out of the way
+        if (isFile(pathname, false))
         {
             rm(pathname);
         }
@@ -66,7 +67,8 @@ Foam::OFstreamAllocator::OFstreamAllocator
     }
     else
     {
-        if (file(pathname + ".gz"))
+        // get identically named compressed version out of the way
+        if (isFile(pathname + ".gz", false))
         {
             rm(pathname + ".gz");
         }

src/OpenFOAM/db/IOstreams/hashes/OSHA1stream.H

@@ -0,0 +1,212 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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
+
+Class
+    Foam::OSHA1stream
+
+Description
+    An output stream for calculating SHA1 digests.
+
+SourceFiles
+    OSHA1stream.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef OSHA1stream_H
+#define OSHA1stream_H
+
+#include "OSstream.H"
+#include "SHA1.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+class osha1stream;
+class OSHA1stream;
+
+/*---------------------------------------------------------------------------*\
+                        Class sha1streambuf Declaration
+\*---------------------------------------------------------------------------*/
+
+//- A streambuf class for calculating SHA1 digests
+class sha1streambuf
+:
+    public std::streambuf
+{
+    // Private data
+
+    //- This does all the work and has its own buffering
+    SHA1 sha1_;
+
+    friend class osha1stream;
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        sha1streambuf()
+        {}
+
+    // Member Functions
+
+    // Write
+
+        //- Process unbuffered
+        virtual std::streamsize xsputn(const char* str, std::streamsize n)
+        {
+            sha1_.append(str, n);
+            return n;
+        }
+};
+
+
+/*---------------------------------------------------------------------------*\
+                         Class osha1stream Declaration
+\*---------------------------------------------------------------------------*/
+
+//- A basic output stream for calculating SHA1 digests
+class osha1stream
+:
+    virtual public std::ios,
+    public std::ostream
+{
+    // Private data
+
+    sha1streambuf sbuf_;
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        osha1stream()
+        :
+            std::ostream(&sbuf_)
+        {}
+
+    // Member Functions
+
+    // Access
+
+        //- This hides both signatures of std::basic_ios::rdbuf()
+        sha1streambuf* rdbuf()
+        {
+            return &sbuf_;
+        }
+
+        //- Full access to the sha1
+        SHA1& sha1()
+        {
+            return sbuf_.sha1_;
+        }
+
+};
+
+
+/*---------------------------------------------------------------------------*\
+                         Class OSHA1stream Declaration
+\*---------------------------------------------------------------------------*/
+
+//- The output stream for calculating SHA1 digests
+class OSHA1stream
+:
+    public OSstream
+{
+
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct
+        OSHA1stream(const OSHA1stream&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const OSHA1stream&);
+
+public:
+
+    // Constructors
+
+        //- Construct and set stream status
+        OSHA1stream
+        (
+            streamFormat format=ASCII,
+            versionNumber version=currentVersion
+        )
+        :
+            OSstream
+            (
+                *(new osha1stream),
+                "OSHA1stream.sinkFile_",
+                format,
+                version
+            )
+        {}
+
+
+    // Destructor
+
+        ~OSHA1stream()
+        {
+            delete &dynamic_cast<osha1stream&>(stream());
+        }
+
+
+    // Member functions
+
+    // Access
+
+        //- Full access to the sha1
+        Foam::SHA1& sha1()
+        {
+            return dynamic_cast<osha1stream&>(stream()).sha1();
+        }
+
+        //- Return SHA1::Digest for the data processed until now
+        Foam::SHA1Digest digest()
+        {
+            return sha1().digest();
+        }
+
+    // Edit
+
+        //- Clear the SHA1 calculation
+        void rewind()
+        {
+            sha1().clear();
+        }
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/OpenFOAM/db/Time/Time.C

@@ -31,11 +31,7 @@ License
 
 // * * * * * * * * * * * * * Static Member Data  * * * * * * * * * * * * * * //
 
-namespace Foam
+defineTypeNameAndDebug(Foam::Time, 0);
-{
-    defineTypeNameAndDebug(Time, 0);
-}
-
 
 template<>
 const char* Foam::NamedEnum<Foam::Time::stopAtControls, 4>::names[] =
@@ -100,9 +96,11 @@ void Foam::Time::adjustDeltaT()
 void Foam::Time::setControls()
 {
     // default is to resume calculation from "latestTime"
-    word startFrom("latestTime");
+    word startFrom = controlDict_.lookupOrDefault<word>
-
+    (
-    controlDict_.readIfPresent("startFrom", startFrom);
+        "startFrom",
+        "latestTime"
+    );
 
     if (startFrom == "startTime")
     {
@@ -421,7 +419,7 @@ Foam::instant Foam::Time::findClosestTime(const scalar t) const
     label nearestIndex = -1;
     scalar deltaT = GREAT;
 
-    for (label i=1; i<times.size(); i++)
+    for (label i=1; i < times.size(); i++)
     {
         scalar diff = mag(times[i].value() - t);
         if (diff < deltaT)

src/OpenFOAM/db/Time/Time.H

@@ -283,7 +283,7 @@ public:
 
             //- Return the location of "dir" containing the file "name".
             //  (Used in reading mesh data)
-            //  If name is null search for a directory "dir"
+            //  If name is null search for the directory "dir" only
             word findInstance
             (
                 const fileName& dir,

src/OpenFOAM/db/Time/findInstance.C

@@ -42,78 +42,74 @@ Foam::word Foam::Time::findInstance
     const IOobject::readOption rOpt
 ) const
 {
-    // Is the mesh data in the current time directory ?
+    // Note: if name is empty, just check the directory itself
+
+    // check the current time directory
     if
     (
-        (name.empty() && Foam::dir(path()/timeName()/dir))
+        name.empty()
-     ||
+      ? isDir(path()/timeName()/dir)
+      :
         (
-           !name.empty()
+            isFile(path()/timeName()/dir/name)
-         && file(path()/timeName()/dir/name)
          && IOobject(name, timeName(), dir, *this).headerOk()
         )
     )
     {
         if (debug)
         {
-            Info<< "Time::findInstance(const word&, const word&) : "
+            Info<< "Time::findInstance(const fileName&, const word&) : "
-                << "found " << name
+                << "found \"" << name
-                << " in " << timeName()/dir
+                << "\" in " << timeName()/dir
                 << endl;
         }
 
         return timeName();
     }
 
-    // Search back through the time directories list to find the time
+    // Search back through the time directories to find the time
     // closest to and lower than current time
 
     instantList ts = times();
-    label i;
+    label instanceI;
 
-    for (i=ts.size()-1; i>=0; i--)
+    for (instanceI = ts.size()-1; instanceI >= 0; --instanceI)
     {
-        if (ts[i].value() <= timeOutputValue())
+        if (ts[instanceI].value() <= timeOutputValue())
         {
             break;
         }
     }
 
-    // Noting that the current directory has already been searched
+    // continue searching from here
-    // for mesh data, start searching from the previously stored time directory
+    for (; instanceI >= 0; --instanceI)
-
-    if (i>=0)
     {
-        for (label j=i; j>=0; j--)
+        if
-        {
+        (
-            if
+            name.empty()
+          ? isDir(path()/ts[instanceI].name()/dir)
+          :
             (
-                (name.empty() && Foam::dir(path()/ts[j].name()/dir))
+                isFile(path()/ts[instanceI].name()/dir/name)
-             ||
+             && IOobject(name, ts[instanceI].name(), dir, *this).headerOk()
-                (
-                   !name.empty()
-                 && file(path()/ts[j].name()/dir/name)
-                 && IOobject(name, ts[j].name(), dir, *this).headerOk()
-                )
             )
+        )
+        {
+            if (debug)
             {
-                if (debug)
+                Info<< "Time::findInstance"
-                {
+                    "(const fileName&,const word&) : "
-                    Info<< "Time::findInstance(const word&, "
+                    << "found \"" << name
-                        << "const word&) : "
+                    << "\" in " << ts[instanceI].name()/dir
-                        << "found " << name
+                    << endl;
-                        << " in " << ts[j].name()/dir
-                        << endl;
-                }
-
-                return ts[j].name();
             }
+
+            return ts[instanceI].name();
         }
     }
 
 
-    // If the mesh data is not in any of the time directories
+    // not in any of the time directories, try constant
-    // Try in constant
 
     // Note. This needs to be a hard-coded constant, rather than the
     // constant function of the time, because the latter points to
@@ -121,20 +117,21 @@ Foam::word Foam::Time::findInstance
 
     if
     (
-        (name.empty() && Foam::dir(path()/constant()/dir))
+        name.empty()
-     || (
+      ? isDir(path()/constant()/dir)
-            !name.empty()
+      :
-         && file(path()/constant()/dir/name)
+        (
+            isFile(path()/constant()/dir/name)
          && IOobject(name, constant(), dir, *this).headerOk()
         )
     )
     {
         if (debug)
         {
-            Info<< "Time::findInstance(const word&, "
+            Info<< "Time::findInstance"
-                << "const word&) : "
+                   "(const fileName&,const word&) : "
-                << "found " << name
+                << "found \"" << name
-                << " in " << constant()/dir
+                << "\" in " << constant()/dir
                 << endl;
         }
 
@@ -143,7 +140,10 @@ Foam::word Foam::Time::findInstance
 
     if (rOpt == IOobject::MUST_READ)
     {
-        FatalErrorIn("Time::findInstance(const word&, const word&)")
+        FatalErrorIn
+            (
+                "Time::findInstance(const fileName&,const word&)"
+            )
             << "Cannot find file \"" << name << "\" in directory "
             << constant()/dir
             << exit(FatalError);

src/OpenFOAM/db/Time/timeSelector.C

@@ -103,7 +103,7 @@ Foam::List<Foam::instant> Foam::timeSelector::select
     const List<instant>& Times
 ) const
 {
-    return subset(selected(Times), true, Times);
+    return subset(selected(Times), Times);
 }
 
 
@@ -112,7 +112,7 @@ void Foam::timeSelector::inplaceSelect
     List<instant>& Times
 ) const
 {
-    inplaceSubset(selected(Times), true, Times);
+    inplaceSubset(selected(Times), Times);
 }
 
 
@@ -219,7 +219,7 @@ Foam::List<Foam::instant> Foam::timeSelector::select
             }
         }
 
-        return subset(selectTimes, true, timeDirs);
+        return subset(selectTimes, timeDirs);
     }
     else
     {

src/OpenFOAM/db/dictionary/dictionary.C

@@ -28,6 +28,7 @@ License
 #include "primitiveEntry.H"
 #include "dictionaryEntry.H"
 #include "regExp.H"
+#include "OSHA1stream.H"
 
 /* * * * * * * * * * * * * * * Static Member Data  * * * * * * * * * * * * * */
 
@@ -232,6 +233,25 @@ Foam::label Foam::dictionary::endLineNumber() const
 }
 
 
+Foam::SHA1Digest Foam::dictionary::digest() const
+{
+    OSHA1stream os;
+
+    // process entries
+    for
+    (
+        IDLList<entry>::const_iterator iter = begin();
+        iter != end();
+        ++iter
+    )
+    {
+        os << *iter;
+    }
+
+    return os.digest();
+}
+
+
 bool Foam::dictionary::found(const word& keyword, bool recursive) const
 {
     if (hashedEntries_.found(keyword))

src/OpenFOAM/db/dictionary/dictionary.H

@@ -69,6 +69,8 @@ namespace Foam
 // Forward declaration of friend functions and operators
 class regExp;
 class dictionary;
+class SHA1Digest;
+
 Istream& operator>>(Istream&, dictionary&);
 Ostream& operator<<(Ostream&, const dictionary&);
 
@@ -210,6 +212,9 @@ public:
         //- Return line number of last token in dictionary
         label endLineNumber() const;
 
+        //- Return the SHA1 digest of the dictionary contents
+        SHA1Digest digest() const;
+
 
         // Search and lookup
 

src/OpenFOAM/db/dictionary/dictionaryEntry/dictionaryEntryIO.C

@@ -45,7 +45,7 @@ Foam::dictionaryEntry::dictionaryEntry
     is.fatalCheck
     (
         "dictionaryEntry::dictionaryEntry"
-        "(const dictionary& parentDict, Istream& is)"
+        "(const dictionary& parentDict, Istream&)"
     );
 }
 
@@ -65,7 +65,7 @@ Foam::dictionaryEntry::dictionaryEntry
     is.fatalCheck
     (
         "dictionaryEntry::dictionaryEntry"
-        "(const keyType& keyword, const dictionary& parentDict, Istream& is)"
+        "(const keyType&, const dictionary& parentDict, Istream&)"
     );
 }
 
@@ -74,7 +74,9 @@ Foam::dictionaryEntry::dictionaryEntry
 
 void Foam::dictionaryEntry::write(Ostream& os) const
 {
-    os.writeKeyword(keyword());
+    // write keyword with indent but without trailing spaces
+    os.indent();
+    os.write(keyword());
     dictionary::write(os);
 }
 

src/OpenFOAM/db/regIOobject/regIOobjectRead.C

@@ -29,14 +29,10 @@ License
 #include "Time.H"
 #include "PstreamReduceOps.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Istream& regIOobject::readStream()
+Foam::Istream& Foam::regIOobject::readStream()
 {
     if (IFstream::debug)
     {
@@ -48,7 +44,7 @@ Istream& regIOobject::readStream()
 
     if (readOpt() == NO_READ)
     {
-        FatalErrorIn("regIOobject::readStream(const word&)")
+        FatalErrorIn("regIOobject::readStream()")
             << "NO_READ specified for read-constructor of object " << name()
             << " of class " << headerClassName()
             << abort(FatalError);
@@ -61,7 +57,7 @@ Istream& regIOobject::readStream()
         {
             FatalIOError
             (
-                "regIOobject::readStream(const word&)",
+                "regIOobject::readStream()",
                 __FILE__,
                 __LINE__,
                 objectPath(),
@@ -71,7 +67,7 @@ Istream& regIOobject::readStream()
         }
         else if (!readHeader(*isPtr_))
         {
-            FatalIOErrorIn("regIOobject::readStream(const word&)", *isPtr_)
+            FatalIOErrorIn("regIOobject::readStream()", *isPtr_)
                 << "problem while reading header for object " << name()
                 << exit(FatalIOError);
         }
@@ -86,7 +82,7 @@ Istream& regIOobject::readStream()
 }
 
 
-Istream& regIOobject::readStream(const word& aType)
+Foam::Istream& Foam::regIOobject::readStream(const word& expectName)
 {
     if (IFstream::debug)
     {
@@ -106,14 +102,14 @@ Istream& regIOobject::readStream(const word& aType)
         // instantiated is a dictionary
         if
         (
-            aType != word::null
+            expectName.size()
-         && headerClassName() != aType
+         && headerClassName() != expectName
          && headerClassName() != "dictionary"
         )
         {
             FatalIOErrorIn("regIOobject::readStream(const word&)", *isPtr_)
                 << "unexpected class name " << headerClassName()
-                << " expected " << aType << endl
+                << " expected " << expectName << endl
                 << "    while reading object " << name()
                 << exit(FatalIOError);
         }
@@ -123,7 +119,7 @@ Istream& regIOobject::readStream(const word& aType)
 }
 
 
-void regIOobject::close()
+void Foam::regIOobject::close()
 {
     if (IFstream::debug)
     {
@@ -140,13 +136,13 @@ void regIOobject::close()
 }
 
 
-bool regIOobject::readData(Istream&)
+bool Foam::regIOobject::readData(Istream&)
 {
     return false;
 }
 
 
-bool regIOobject::read()
+bool Foam::regIOobject::read()
 {
     bool ok = readData(readStream(type()));
     close();
@@ -154,7 +150,7 @@ bool regIOobject::read()
 }
 
 
-bool regIOobject::modified() const
+bool Foam::regIOobject::modified() const
 {
     return
     (
@@ -164,7 +160,7 @@ bool regIOobject::modified() const
 }
 
 
-bool regIOobject::readIfModified()
+bool Foam::regIOobject::readIfModified()
 {
     if (lastModified_)
     {
@@ -213,8 +209,4 @@ bool regIOobject::readIfModified()
 }
 
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/db/scalarRange/scalarRanges.C

@@ -123,7 +123,7 @@ Foam::List<Foam::scalar> Foam::scalarRanges::select
     const List<scalar>& values
 ) const
 {
-    return subset(selected(values), true, values);
+    return subset(selected(values), values);
 }
 
 
@@ -132,7 +132,7 @@ void Foam::scalarRanges::inplaceSelect
     List<scalar>& values
 ) const
 {
-    inplaceSubset(selected(values), true, values);
+    inplaceSubset(selected(values), values);
 }
 
 

src/OpenFOAM/dimensionSet/dimensionSet.H

@@ -123,7 +123,7 @@ public:
         enum dimensionType
         {
             MASS,               // kilogram   kg
-            LENGTH,             // meter      m
+            LENGTH,             // metre      m
             TIME,               // second     s
             TEMPERATURE,        // Kelvin     K
             MOLES,              // mole       mol

src/OpenFOAM/dimensionSet/dimensionSets.C

@@ -44,6 +44,7 @@ const Foam::dimensionSet Foam::dimVol(0, 3, 0, 0, 0, 0, 0);
 
 const Foam::dimensionSet Foam::dimDensity(1, -3, 0, 0, 0, 0, 0);
 const Foam::dimensionSet Foam::dimForce(1, 1, -2, 0, 0, 0, 0);
+const Foam::dimensionSet Foam::dimEnergy(1, 2, -2, 0, 0, 0, 0);
 
 const Foam::dimensionSet Foam::dimVelocity(0, 1, -1, 0, 0, 0, 0);
 const Foam::dimensionSet Foam::dimAcceleration(0, 1, -2, 0, 0, 0, 0);

src/OpenFOAM/dimensionSet/dimensionSets.H

@@ -60,6 +60,7 @@ extern const dimensionSet dimVol;
 
 extern const dimensionSet dimDensity;
 extern const dimensionSet dimForce;
+extern const dimensionSet dimEnergy;
 
 extern const dimensionSet dimVelocity;
 extern const dimensionSet dimAcceleration;

src/OpenFOAM/fields/pointPatchFields/pointPatchField/pointPatchField.C

@@ -105,7 +105,7 @@ void pointPatchField<Type>::write(Ostream& os) const
 {
     os.writeKeyword("type") << type() << token::END_STATEMENT << nl;
 
-    if (patchType_ != word::null)
+    if (patchType_.size())
     {
         os.writeKeyword("patchType") << patchType_
             << token::END_STATEMENT << nl;

src/OpenFOAM/global/JobInfo/JobInfo.C

@@ -65,14 +65,14 @@ Foam::JobInfo::JobInfo()
                 << Foam::exit(FatalError);
         }
 
-        if (!dir(runningDir) && !mkDir(runningDir))
+        if (!isDir(runningDir) && !mkDir(runningDir))
         {
             FatalErrorIn("JobInfo::JobInfo()")
                 << "Cannot make JobInfo directory " << runningDir
                 << Foam::exit(FatalError);
         }
 
-        if (!dir(finishedDir) && !mkDir(finishedDir))
+        if (!isDir(finishedDir) && !mkDir(finishedDir))
         {
             FatalErrorIn("JobInfo::JobInfo()")
                 << "Cannot make JobInfo directory " << finishedDir