Merge branch 'develop' of develop.openfoam.com:Development/OpenFOAM-plus into develop

.gitignore

@@ -75,9 +75,10 @@ doc/Doxygen/DTAGS
 # Ignore .tags in the main directory
 /.tags
 
-# Ignore eclipse project files in the main directory
+# Ignore project files in the main directory
 /.cproject
 /.project
+/.dir-locals.el
 
 # Ignore the test directory
 /tutorialsTest

applications/Allwmake

@@ -17,10 +17,7 @@ wmakeCheckPwd "$WM_PROJECT_DIR/applications" || {
     exit 1
 }
 
-set -x
-
 wmake -all $targetType solvers
 wmake -all $targetType utilities
 
-
 #------------------------------------------------------------------------------

applications/solvers/combustion/chemFoam/createFields.H

@@ -12,7 +12,7 @@
         (
             "initialConditions",
             runTime.constant(),
-            runTime,
+            mesh,
             IOobject::MUST_READ_IF_MODIFIED,
             IOobject::NO_WRITE
         )
@@ -37,7 +37,7 @@
         (
             "rho",
             runTime.timeName(),
-            runTime,
+            mesh,
             IOobject::NO_READ,
             IOobject::AUTO_WRITE
         ),
@@ -50,7 +50,7 @@
         (
             "Rspecific",
             runTime.timeName(),
-            runTime,
+            mesh,
             IOobject::NO_READ,
             IOobject::AUTO_WRITE
         ),
@@ -69,7 +69,7 @@
         (
             "U",
             runTime.timeName(),
-            runTime,
+            mesh,
             IOobject::NO_READ,
             IOobject::NO_WRITE
         ),

applications/solvers/compressible/rhoCentralFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso BCs
 wclean

applications/solvers/compressible/rhoCentralFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 (wmake $targetType BCs && wmake $targetType && wmake $targetType rhoCentralDyMFoam)
 

applications/solvers/lagrangian/DPMFoam/Allwclean

@@ -1,7 +1,6 @@
 #!/bin/sh
 
 cd ${0%/*} || exit 1
-set -x
 
 wclean libso DPMTurbulenceModels
 wclean

applications/solvers/lagrangian/DPMFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType DPMTurbulenceModels
 

applications/solvers/multiphase/compressibleInterFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso twoPhaseMixtureThermo
 wclean

applications/solvers/multiphase/compressibleInterFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType twoPhaseMixtureThermo
 

applications/solvers/multiphase/compressibleMultiphaseInterFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso multiphaseMixtureThermo
 wclean

applications/solvers/multiphase/compressibleMultiphaseInterFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType multiphaseMixtureThermo
 wmake $targetType

applications/solvers/multiphase/driftFluxFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso mixtureViscosityModels
 wclean libso relativeVelocityModels

applications/solvers/multiphase/driftFluxFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType mixtureViscosityModels
 wmake $targetType relativeVelocityModels

applications/solvers/multiphase/driftFluxFoam/relativeVelocityModels/relativeVelocityModel/relativeVelocityModel.C

@@ -24,6 +24,9 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "relativeVelocityModel.H"
+#include "fixedValueFvPatchFields.H"
+#include "slipFvPatchFields.H"
+#include "partialSlipFvPatchFields.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
@@ -33,6 +36,34 @@ namespace Foam
     defineRunTimeSelectionTable(relativeVelocityModel, dictionary);
 }
 
+// * * * * * * * * * * * * * Private Member Functions   * * * * * * * * * * * //
+
+Foam::wordList Foam::relativeVelocityModel::UdmPatchFieldTypes() const
+{
+    const volVectorField& U = mixture_.U();
+
+    wordList UdmTypes
+    (
+        U.boundaryField().size(),
+        calculatedFvPatchScalarField::typeName
+    );
+
+    forAll(U.boundaryField(), i)
+    {
+        if
+        (
+            isA<fixedValueFvPatchVectorField>(U.boundaryField()[i])
+         || isA<slipFvPatchVectorField>(U.boundaryField()[i])
+         || isA<partialSlipFvPatchVectorField>(U.boundaryField()[i])
+        )
+        {
+            UdmTypes[i] = fixedValueFvPatchVectorField::typeName;
+        }
+    }
+
+    return UdmTypes;
+}
+
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -55,11 +86,12 @@ Foam::relativeVelocityModel::relativeVelocityModel
             "Udm",
             alphac_.time().timeName(),
             alphac_.mesh(),
-            IOobject::NO_READ,
+            IOobject::READ_IF_PRESENT,
             IOobject::AUTO_WRITE
         ),
         alphac_.mesh(),
-        dimensionedVector("Udm", dimVelocity, Zero)
+        dimensionedVector("Udm", dimVelocity, Zero),
+        UdmPatchFieldTypes()
     )
 {}
 

applications/solvers/multiphase/driftFluxFoam/relativeVelocityModels/relativeVelocityModel/relativeVelocityModel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2014 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2014-2016 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -52,12 +52,16 @@ class relativeVelocityModel
 {
     // Private Member Functions
 
+        //- Return the list of patchFieldTypes for Udm derived from U
+        wordList UdmPatchFieldTypes() const;
+
         //- Disallow default bitwise copy construct
         relativeVelocityModel(const relativeVelocityModel&);
 
         //- Disallow default bitwise assignment
         void operator=(const relativeVelocityModel&);
 
+
 protected:
 
     // Protected data

applications/solvers/multiphase/interCondensingEvaporatingFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso temperaturePhaseChangeTwoPhaseMixtures
 wclean

applications/solvers/multiphase/interPhaseChangeFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso phaseChangeTwoPhaseMixtures
 wclean

applications/solvers/multiphase/interPhaseChangeFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType phaseChangeTwoPhaseMixtures
 wmake $targetType

applications/solvers/multiphase/multiphaseEulerFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso multiphaseSystem
 wclean libso interfacialModels

applications/solvers/multiphase/multiphaseEulerFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmakeLnInclude interfacialModels
 wmake $targetType multiphaseSystem

applications/solvers/multiphase/multiphaseInterFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso multiphaseMixture
 wclean

applications/solvers/multiphase/multiphaseInterFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType multiphaseMixture
 wmake $targetType

applications/solvers/multiphase/reactingEulerFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso phaseSystems
 wclean libso interfacialModels

applications/solvers/multiphase/reactingEulerFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmakeLnInclude interfacialModels
 wmakeLnInclude interfacialCompositionModels

applications/solvers/multiphase/reactingEulerFoam/phaseSystems/phaseModel/AnisothermalPhaseModel/AnisothermalPhaseModel.C

@@ -77,11 +77,39 @@ void Foam::AnisothermalPhaseModel<BasePhaseModel>::correctThermo()
 }
 
 
+template<class BasePhaseModel>
+Foam::tmp<Foam::volScalarField>
+Foam::AnisothermalPhaseModel<BasePhaseModel>::filterPressureWork
+(
+    const tmp<volScalarField>& pressureWork
+) const
+{
+    const volScalarField& alpha = *this;
+
+    scalar pressureWorkAlphaLimit =
+        this->thermo_->lookupOrDefault("pressureWorkAlphaLimit", 0.0);
+
+    if (pressureWorkAlphaLimit > 0)
+    {
+        return
+        (
+            max(alpha - pressureWorkAlphaLimit, scalar(0))
+           /max(alpha - pressureWorkAlphaLimit, pressureWorkAlphaLimit)
+        )*pressureWork;
+    }
+    else
+    {
+        return pressureWork;
+    }
+}
+
+
 template<class BasePhaseModel>
 Foam::tmp<Foam::fvScalarMatrix>
 Foam::AnisothermalPhaseModel<BasePhaseModel>::heEqn()
 {
     const volScalarField& alpha = *this;
+    const volVectorField& U = this->U();
     const surfaceScalarField& alphaPhi = this->alphaPhi();
     const surfaceScalarField& alphaRhoPhi = this->alphaRhoPhi();
 
@@ -93,7 +121,8 @@ Foam::AnisothermalPhaseModel<BasePhaseModel>::heEqn()
 
     tmp<fvScalarMatrix> tEEqn
     (
-        fvm::ddt(alpha, this->rho(), he) + fvm::div(alphaRhoPhi, he)
+        fvm::ddt(alpha, this->rho(), he)
+      + fvm::div(alphaRhoPhi, he)
       - fvm::Sp(contErr, he)
 
       + fvc::ddt(alpha, this->rho(), K_) + fvc::div(alphaRhoPhi, K_)
@@ -112,13 +141,15 @@ Foam::AnisothermalPhaseModel<BasePhaseModel>::heEqn()
     // Add the appropriate pressure-work term
     if (he.name() == this->thermo_->phasePropertyName("e"))
     {
-        tEEqn.ref() +=
+        tEEqn.ref() += filterPressureWork
-            fvc::ddt(alpha)*this->thermo().p()
+        (
-          + fvc::div(alphaPhi, this->thermo().p());
+            fvc::div(fvc::absolute(alphaPhi, alpha, U), this->thermo().p())
+          + this->thermo().p()*fvc::ddt(alpha)
+        );
     }
     else if (this->thermo_->dpdt())
     {
-        tEEqn.ref() -= alpha*this->fluid().dpdt();
+        tEEqn.ref() -= filterPressureWork(alpha*this->fluid().dpdt());
     }
 
     return tEEqn;

applications/solvers/multiphase/reactingEulerFoam/phaseSystems/phaseModel/AnisothermalPhaseModel/AnisothermalPhaseModel.H

@@ -58,6 +58,15 @@ class AnisothermalPhaseModel
         volScalarField K_;
 
 
+    // Private member functions
+
+        //- Optionally filter the pressure work term as the phase-fraction -> 0
+        tmp<volScalarField> filterPressureWork
+        (
+            const tmp<volScalarField>& pressureWork
+        ) const;
+
+
 public:
 
     // Constructors

applications/solvers/multiphase/reactingEulerFoam/phaseSystems/phaseModel/ReactingPhaseModel/ReactingPhaseModel.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2015-2016 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -40,7 +40,12 @@ Foam::ReactingPhaseModel<BasePhaseModel, ReactionType>::ReactingPhaseModel
     BasePhaseModel(fluid, phaseName, index, false),
     reaction_
     (
-        ReactionType::New(fluid.mesh(), this->name())
+        ReactionType::New
+        (
+            fluid.mesh(),
+            combustionModel::combustionPropertiesName,
+            this->name()
+        )
     )
 {
     this->thermo_ = &reaction_->thermo();

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso multiphaseSystem
 wclean libso multiphaseCompressibleTurbulenceModels

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType multiphaseSystem
 wmake $targetType multiphaseCompressibleTurbulenceModels

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/EEqns.H

@@ -35,6 +35,7 @@ for (int Ecorr=0; Ecorr<nEnergyCorrectors; Ecorr++)
     }
 
     fluid.correctThermo();
+    fluid.correct();
 }
 
 

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/pU/pEqn.H

@@ -89,9 +89,6 @@ PtrList<surfaceScalarField> phiFs(phases.size());
 // --- Pressure corrector loop
 while (pimple.correct())
 {
-    // Update continuity errors due to temperature changes
-    fluid.correct();
-
     volScalarField rho("rho", fluid.rho());
 
     // Correct p_rgh for consistency with p and the updated densities

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/reactingMultiphaseEulerFoam.C

@@ -77,11 +77,6 @@ int main(int argc, char *argv[])
 
     //#include "pUf/createDDtU.H"
 
-    int nEnergyCorrectors
-    (
-        pimple.dict().lookupOrDefault<int>("nEnergyCorrectors", 1)
-    );
-
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;
@@ -90,6 +85,11 @@ int main(int argc, char *argv[])
     {
         #include "readTimeControls.H"
 
+        int nEnergyCorrectors
+        (
+            pimple.dict().lookupOrDefault<int>("nEnergyCorrectors", 1)
+        );
+
         if (LTS)
         {
             #include "setRDeltaT.H"

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso twoPhaseSystem
 wclean libso twoPhaseCompressibleTurbulenceModels

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType twoPhaseSystem
 wmake $targetType twoPhaseCompressibleTurbulenceModels

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/EEqns.H

@@ -29,36 +29,25 @@ for (int Ecorr=0; Ecorr<nEnergyCorrectors; Ecorr++)
     }
 
     {
-        tmp<fvScalarMatrix> E2eqn(phase2.heEqn());
+        tmp<fvScalarMatrix> E2Eqn(phase2.heEqn());
 
-        if (E2eqn.valid())
+        if (E2Eqn.valid())
         {
-            E2eqn =
+            E2Eqn =
             (
-                E2eqn
+                E2Eqn
              ==
                *heatTransfer[phase2.name()]
               + alpha2*rho2*(U2&g)
               + fvOptions(alpha2, rho2, phase2.thermo().he())
             );
 
-            E2eqn->relax();
+            E2Eqn->relax();
-            fvOptions.constrain(E2eqn.ref());
+            fvOptions.constrain(E2Eqn.ref());
-            E2eqn->solve();
+            E2Eqn->solve();
         }
     }
 
     fluid.correctThermo();
+    fluid.correct();
 }
-
-Info<< phase1.name() << " min/max T "
-    << min(phase1.thermo().T()).value()
-    << " - "
-    << max(phase1.thermo().T()).value()
-    << endl;
-
-Info<< phase2.name() << " min/max T "
-    << min(phase2.thermo().T()).value()
-    << " - "
-    << max(phase2.thermo().T()).value()
-    << endl;

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/createRDeltaTf.H

@@ -0,0 +1,21 @@
+tmp<surfaceScalarField> trDeltaTf;
+
+if (LTS && faceMomentum)
+{
+    trDeltaTf = tmp<surfaceScalarField>
+    (
+        new surfaceScalarField
+        (
+            IOobject
+            (
+                fv::localEulerDdt::rDeltaTfName,
+                runTime.timeName(),
+                mesh,
+                IOobject::READ_IF_PRESENT,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimensionedScalar("one", dimless/dimTime, 1)
+        )
+    );
+}

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/pU/pEqn.H

@@ -83,9 +83,6 @@ tmp<surfaceScalarField> phiF2;
 // --- Pressure corrector loop
 while (pimple.correct())
 {
-    // Update continuity errors due to temperature changes
-    fluid.correct();
-
     volScalarField rho("rho", fluid.rho());
 
     // Correct p_rgh for consistency with p and the updated densities

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/pUf/DDtU.H

@@ -1,9 +1,2 @@
-    ddtPhi1 =
+ddtPhi1 = fvc::ddt(phi1);
-    (
+ddtPhi2 = fvc::ddt(phi2);
-        (phi1 - phi1.oldTime())/runTime.deltaT()
-    );
-
-    ddtPhi2 =
-    (
-        (phi2 - phi2.oldTime())/runTime.deltaT()
-    );

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/pUf/createDDtU.H

@@ -1,9 +1,2 @@
-    surfaceScalarField ddtPhi1
+surfaceScalarField ddtPhi1(fvc::ddt(phi1));
-    (
+surfaceScalarField ddtPhi2(fvc::ddt(phi2));
-        (phi1 - phi1.oldTime())/runTime.deltaT()
-    );
-
-    surfaceScalarField ddtPhi2
-    (
-        (phi2 - phi2.oldTime())/runTime.deltaT()
-    );

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/pUf/pEqn.H

@@ -32,10 +32,10 @@ surfaceScalarField rAUf1
     IOobject::groupName("rAUf", phase1.name()),
     1.0
    /(
-        (alphaRhof10 + Vmf)/runTime.deltaT()
+        byDt(alphaRhof10 + Vmf)
       + fvc::interpolate(U1Eqn.A())
       + Kdf
-   )
+    )
 );
 
 surfaceScalarField rAUf2
@@ -43,10 +43,10 @@ surfaceScalarField rAUf2
     IOobject::groupName("rAUf", phase2.name()),
     1.0
    /(
-        (alphaRhof20 + Vmf)/runTime.deltaT()
+        byDt(alphaRhof20 + Vmf)
       + fvc::interpolate(U2Eqn.A())
       + Kdf
-   )
+    )
 );
 
 
@@ -93,9 +93,6 @@ tmp<surfaceScalarField> Ff2;
 
 while (pimple.correct())
 {
-    // Update continuity errors due to temperature changes
-    fluid.correct();
-
     volScalarField rho("rho", fluid.rho());
 
     // Correct p_rgh for consistency with p and the updated densities
@@ -160,7 +157,7 @@ while (pimple.correct())
         rAUf1
        *(
             (alphaRhof10 + Vmf)
-           *MRF.absolute(phi1.oldTime())/runTime.deltaT()
+           *byDt(MRF.absolute(phi1.oldTime()))
           + fvc::flux(U1Eqn.H())
           + Vmf*ddtPhi2
           + Kdf*MRF.absolute(phi2)
@@ -178,7 +175,7 @@ while (pimple.correct())
         rAUf2
        *(
             (alphaRhof20 + Vmf)
-           *MRF.absolute(phi2.oldTime())/runTime.deltaT()
+           *byDt(MRF.absolute(phi2.oldTime()))
           + fvc::flux(U2Eqn.H())
           + Vmf*ddtPhi1
           + Kdf*MRF.absolute(phi1)

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/reactingTwoPhaseEulerFoam.C

@@ -43,6 +43,22 @@ Description
 #include "localEulerDdtScheme.H"
 #include "fvcSmooth.H"
 
+namespace Foam
+{
+    tmp<surfaceScalarField> byDt(const surfaceScalarField& sf)
+    {
+        if (fv::localEulerDdt::enabled(sf.mesh()))
+        {
+            return fv::localEulerDdt::localRDeltaTf(sf.mesh())*sf;
+        }
+        else
+        {
+            return sf/sf.mesh().time().deltaT();
+        }
+    }
+}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 int main(int argc, char *argv[])
@@ -76,13 +92,9 @@ int main(int argc, char *argv[])
         )
     );
 
+    #include "createRDeltaTf.H"
     #include "pUf/createDDtU.H"
 
-    int nEnergyCorrectors
-    (
-        pimple.dict().lookupOrDefault<int>("nEnergyCorrectors", 1)
-    );
-
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;
@@ -91,9 +103,18 @@ int main(int argc, char *argv[])
     {
         #include "readTimeControls.H"
 
+        int nEnergyCorrectors
+        (
+            pimple.dict().lookupOrDefault<int>("nEnergyCorrectors", 1)
+        );
+
         if (LTS)
         {
             #include "setRDeltaT.H"
+            if (faceMomentum)
+            {
+                #include "setRDeltaTf.H"
+            }
         }
         else
         {

applications/solvers/multiphase/reactingEulerFoam/reactingTwoPhaseEulerFoam/setRDeltaTf.H

@@ -0,0 +1 @@
+trDeltaTf.ref() = fvc::interpolate(fv::localEulerDdt::localRDeltaT(mesh));

applications/solvers/multiphase/twoPhaseEulerFoam/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso twoPhaseSystem
 wclean libso interfacialModels

applications/solvers/multiphase/twoPhaseEulerFoam/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmakeLnInclude interfacialModels
 wmake $targetType twoPhaseSystem

applications/solvers/multiphase/twoPhaseEulerFoam/EEqns.H

@@ -16,7 +16,8 @@
       - contErr1*K1
       + (
             he1.name() == thermo1.phasePropertyName("e")
-          ? fvc::ddt(alpha1)*p + fvc::div(alphaPhi1, p)
+          ? fvc::div(fvc::absolute(alphaPhi1, alpha1, U1), p)
+          + p*fvc::ddt(alpha1)
           : -alpha1*dpdt
         )
 
@@ -48,7 +49,8 @@
       - contErr2*K2
       + (
             he2.name() == thermo2.phasePropertyName("e")
-          ? fvc::ddt(alpha2)*p + fvc::div(alphaPhi2, p)
+          ? fvc::div(fvc::absolute(alphaPhi2, alpha2, U2), p)
+          + p*fvc::ddt(alpha1)
           : -alpha2*dpdt
         )
 

applications/solvers/multiphase/twoPhaseEulerFoam/twoPhaseSystem/phaseModel/phaseModel.C

@@ -248,4 +248,30 @@ bool Foam::phaseModel::read(const dictionary& phaseProperties)
 }
 
 
+void Foam::phaseModel::correctInflowFlux(surfaceScalarField& alphaPhi) const
+{
+    surfaceScalarField::Boundary& alphaPhiBf = alphaPhi.boundaryFieldRef();
+
+    // Ensure that the flux at inflow BCs is preserved
+    forAll(alphaPhiBf, patchi)
+    {
+        fvsPatchScalarField& alphaPhip = alphaPhiBf[patchi];
+
+        if (!alphaPhip.coupled())
+        {
+            const scalarField& phip = phi().boundaryField()[patchi];
+            const scalarField& alphap = boundaryField()[patchi];
+
+            forAll(alphaPhip, facei)
+            {
+                if (phip[facei] < SMALL)
+                {
+                    alphaPhip[facei] = alphap[facei]*phip[facei];
+                }
+            }
+        }
+    }
+}
+
+
 // ************************************************************************* //

applications/solvers/multiphase/twoPhaseEulerFoam/twoPhaseSystem/phaseModel/phaseModel.H

@@ -319,6 +319,9 @@ public:
             return alphaRhoPhi_;
         }
 
+        //- Ensure that the flux at inflow BCs is preserved
+        void correctInflowFlux(surfaceScalarField& alphaPhi) const;
+
         //- Correct the phase properties
         //  other than the thermodynamics and turbulence
         //  which have special treatment

applications/solvers/multiphase/twoPhaseEulerFoam/twoPhaseSystem/twoPhaseSystem.C

@@ -444,28 +444,7 @@ void Foam::twoPhaseSystem::solve()
             )
         );
 
-        surfaceScalarField::Boundary& alphaPhic1Bf =
+        phase1_.correctInflowFlux(alphaPhic1);
-            alphaPhic1.boundaryFieldRef();
-
-        // Ensure that the flux at inflow BCs is preserved
-        forAll(alphaPhic1Bf, patchi)
-        {
-            fvsPatchScalarField& alphaPhic1p = alphaPhic1Bf[patchi];
-
-            if (!alphaPhic1p.coupled())
-            {
-                const scalarField& phi1p = phi1.boundaryField()[patchi];
-                const scalarField& alpha1p = alpha1.boundaryField()[patchi];
-
-                forAll(alphaPhic1p, facei)
-                {
-                    if (phi1p[facei] < 0)
-                    {
-                        alphaPhic1p[facei] = alpha1p[facei]*phi1p[facei];
-                    }
-                }
-            }
-        }
 
         if (nAlphaSubCycles > 1)
         {
@@ -537,6 +516,7 @@ void Foam::twoPhaseSystem::solve()
 
         phase2_.alphaPhi() = phi_ - phase1_.alphaPhi();
         alpha2 = scalar(1) - alpha1;
+        phase2_.correctInflowFlux(phase2_.alphaPhi());
         phase2_.alphaRhoPhi() =
             fvc::interpolate(phase2_.rho())*phase2_.alphaPhi();
 

applications/test/objectRegistry/Test-objectRegistry.C

@@ -76,9 +76,8 @@ void printRegistry
     Foam::label indent
 )
 {
-    hashedWordList regs = obr.names<objectRegistry>();
-    regs.sort();
     wordList names = obr.sortedNames();
+    hashedWordList regs = obr.sortedNames<objectRegistry>();
 
     std::string prefix;
     for (label i=indent; i; --i)
@@ -121,7 +120,8 @@ void printRegistry
         const word& name = regs[i];
         const objectRegistry& next = obr.lookupObject<objectRegistry>
         (
-            name
+            name,
+            recursive
         );
 
         os  << prefix.c_str()
@@ -158,13 +158,13 @@ int main(int argc, char *argv[])
         "skip",
         "skip some parts"
     );
-    // argList::validArgs.append("recursive (true|false)");
+    argList::validArgs.append("recursive (true|false)");
 
     #include "setRootCase.H"
     #include "createTime.H"
     #include "createPolyMesh.H"
 
-    // recursive = Switch(args[1]);
+    recursive = Switch(args[1]);
 
     const bool optMesh   = args.optionFound("mesh");
     const bool optSkip   = args.optionFound("skip");
@@ -183,7 +183,8 @@ int main(int argc, char *argv[])
         db.subRegistry
         (
             entryName,
-            true
+            true,
+            recursive
         );
     }
 
@@ -200,7 +201,8 @@ int main(int argc, char *argv[])
         const objectRegistry& subreg = db.subRegistry
         (
             regName,
-            true
+            true,
+            recursive
         );
 
         for (label j = 0; j < 3; ++j)
@@ -210,12 +212,14 @@ int main(int argc, char *argv[])
             subreg.subRegistry
             (
                 entryName,
-                true
+                true,
+                recursive
             );
             subreg.subRegistry
             (
                 "$" + entryName, // qualified to avoid collisions
-                true
+                true,
+                recursive
             );
         }
     }
@@ -231,7 +235,8 @@ int main(int argc, char *argv[])
         db.subRegistry
         (
             entryName,
-            true
+            true,
+            recursive
         );
     }
 
@@ -249,7 +254,8 @@ int main(int argc, char *argv[])
         const objectRegistry& subreg = db.subRegistry
         (
             regName,
-            false
+            false,
+            recursive
         );
 
         if (!optSkip)
@@ -261,7 +267,8 @@ int main(int argc, char *argv[])
                 subreg.subRegistry
                 (
                     entryName,
-                    true
+                    true,
+                    recursive
                 );
             }
         }

applications/utilities/mesh/advanced/PDRMesh/PDRMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -56,7 +56,9 @@ Description
 #include "mapPolyMesh.H"
 #include "faceSet.H"
 #include "cellSet.H"
+#include "pointSet.H"
 #include "syncTools.H"
+#include "ReadFields.H"
 #include "polyTopoChange.H"
 #include "polyModifyFace.H"
 #include "polyAddFace.H"
@@ -315,6 +317,59 @@ void initCreatedPatches
 }
 
 
+template<class TopoSet>
+void subsetTopoSets
+(
+    const fvMesh& mesh,
+    const IOobjectList& objectsList,
+    const labelList& map,
+    const fvMesh& subMesh,
+    PtrList<TopoSet>& subSets
+)
+{
+    // Read original sets
+    PtrList<TopoSet> sets;
+    ReadFields<TopoSet>(objectsList, sets);
+
+    subSets.setSize(sets.size());
+    forAll(sets, i)
+    {
+        TopoSet& set = sets[i];
+
+        Info<< "Subsetting " << set.type() << " " << set.name() << endl;
+
+        // Map the data
+        PackedBoolList isSet(set.maxSize(mesh));
+        forAllConstIter(labelHashSet, set, iter)
+        {
+            isSet[iter.key()] = true;
+        }
+        label nSet = 0;
+        forAll(map, i)
+        {
+            if (isSet[map[i]])
+            {
+                nSet++;
+            }
+        }
+
+        subSets.set
+        (
+            i,
+            new TopoSet(subMesh, set.name(), nSet, IOobject::AUTO_WRITE)
+        );
+        TopoSet& subSet = subSets[i];
+        forAll(map, i)
+        {
+            if (isSet[map[i]])
+            {
+                subSet.insert(i);
+            }
+        }
+    }
+}
+
+
 void createCoupledBaffles
 (
     fvMesh& mesh,
@@ -923,6 +978,41 @@ int main(int argc, char *argv[])
         surfTensorFlds
     );
 
+
+    // Set handling
+    PtrList<cellSet> cellSets;
+    PtrList<faceSet> faceSets;
+    PtrList<pointSet> pointSets;
+    {
+        IOobjectList objects(mesh, mesh.facesInstance(), "polyMesh/sets");
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.cellMap(),
+            subsetter.subMesh(),
+            cellSets
+        );
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.faceMap(),
+            subsetter.subMesh(),
+            faceSets
+        );
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.pointMap(),
+            subsetter.subMesh(),
+            pointSets
+        );
+    }
+
+
+
     if (!overwrite)
     {
         runTime++;
@@ -1134,6 +1224,11 @@ int main(int argc, char *argv[])
         Zero
     );
 
+    // Update numbering of topoSets
+    topoSet::updateMesh(subsetter.subMesh().facesInstance(), map, cellSets);
+    topoSet::updateMesh(subsetter.subMesh().facesInstance(), map, faceSets);
+    topoSet::updateMesh(subsetter.subMesh().facesInstance(), map, pointSets);
+
 
     // Move mesh (since morphing might not do this)
     if (map().hasMotionPoints())

applications/utilities/mesh/advanced/combinePatchFaces/Make/options

@@ -1,9 +1,11 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
 
 
 EXE_LIBS = \
     -lfiniteVolume \
+    -lreconstruct \
     -ldynamicMesh

applications/utilities/mesh/advanced/combinePatchFaces/combinePatchFaces.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -60,6 +60,8 @@ Description
 #include "mapPolyMesh.H"
 #include "unitConversion.H"
 #include "motionSmoother.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -450,6 +452,8 @@ int main(int argc, char *argv[])
         Info<< "Writing morphed mesh to time " << runTime.timeName() << endl;
 
         mesh.write();
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
     }
     else
     {

applications/utilities/mesh/advanced/modifyMesh/Make/options

@@ -1,7 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
+    -lreconstruct \
     -ldynamicMesh

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

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -62,6 +62,8 @@ Description
 #include "meshTools.H"
 #include "Pair.H"
 #include "globalIndex.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -567,6 +569,8 @@ int main(int argc, char *argv[])
         // Write resulting mesh
         Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
         mesh.write();
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
     }
     else if (edgeToPos.size())
     {
@@ -641,6 +645,8 @@ int main(int argc, char *argv[])
         // Write resulting mesh
         Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
         mesh.write();
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
     }
     else
     {
@@ -684,6 +690,8 @@ int main(int argc, char *argv[])
         // Write resulting mesh
         Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
         mesh.write();
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
     }
 
 

applications/utilities/mesh/advanced/refineHexMesh/Make/options

@@ -1,11 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
-
 EXE_LIBS = \
+    -lreconstruct \
     -ldynamicMesh \
-    -lmeshTools \
-    -lfiniteVolume \
     -lgenericPatchFields

applications/utilities/mesh/advanced/refineHexMesh/refineHexMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -49,6 +49,7 @@ Description
 #include "surfaceFields.H"
 #include "pointFields.H"
 #include "ReadFields.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -197,6 +198,8 @@ int main(int argc, char *argv[])
 
     mesh.write();
     meshCutter.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/advanced/refineWallLayer/Make/options

@@ -1,7 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
+    -lreconstruct \
     -lmeshTools

applications/utilities/mesh/advanced/refineWallLayer/refineWallLayer.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -53,6 +53,7 @@ Description
 #include "cellCuts.H"
 #include "cellSet.H"
 #include "meshCutter.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -257,6 +258,8 @@ int main(int argc, char *argv[])
     Info<< "Writing refined mesh to time " << runTime.timeName() << endl;
 
     mesh.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/advanced/removeFaces/Make/options

@@ -1,10 +1,12 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
     -ldynamicMesh \
     -lfiniteVolume \
+    -lreconstruct \
     -lgenericPatchFields

applications/utilities/mesh/advanced/removeFaces/removeFaces.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -44,6 +44,7 @@ Description
 #include "ReadFields.H"
 #include "volFields.H"
 #include "surfaceFields.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -179,6 +180,8 @@ int main(int argc, char *argv[])
     // Take over refinement levels and write to new time directory.
     Pout<< "Writing mesh to time " << runTime.timeName() << endl;
     mesh.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Pout<< "End\n" << endl;
 

applications/utilities/mesh/conversion/Optional/Allwmake

@@ -11,7 +11,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 . $WM_PROJECT_DIR/etc/config.sh/functions
 _foamSource $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/ccmio)
 
-set -x
 
 # Build libccmio (.a|.so)
 $WM_THIRD_PARTY_DIR/makeCCMIO lib # libso

applications/utilities/mesh/generation/extrude/extrudeMesh/Make/options

@@ -4,6 +4,7 @@ EXE_INC = \
     -I$(LIB_SRC)/surfMesh/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/mesh/extrudeModel/lnInclude
 
 EXE_LIBS = \
@@ -11,4 +12,5 @@ EXE_LIBS = \
     -lsurfMesh \
     -lmeshTools \
     -ldynamicMesh \
+    -lreconstruct \
     -lextrudeModel

applications/utilities/mesh/generation/extrude/extrudeMesh/extrudeMesh.C

@@ -56,6 +56,7 @@ Description
 #include "wedgePolyPatch.H"
 #include "planeExtrusion.H"
 #include "emptyPolyPatch.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -1058,6 +1059,8 @@ int main(int argc, char *argv[])
         FatalErrorInFunction
             << exit(FatalError);
     }
+    // Remove any left-over files
+    processorMeshes::removeFiles(mesh);
 
     // Need writing cellSet
     label nAdded = returnReduce(addedCellsSet.size(), sumOp<label>());

applications/utilities/mesh/generation/extrude/extrudeToRegionMesh/Make/options

@@ -3,6 +3,7 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/mesh/extrudeModel/lnInclude
 
 EXE_LIBS = \
@@ -10,4 +11,5 @@ EXE_LIBS = \
     -lfiniteVolume \
     -lmeshTools \
     -ldynamicMesh \
+    -lreconstruct \
     -lextrudeModel

applications/utilities/mesh/generation/extrude/extrudeToRegionMesh/extrudeToRegionMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -141,6 +141,7 @@ Notes:
 #include "fvMeshTools.H"
 #include "OBJstream.H"
 #include "PatchTools.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -2646,6 +2647,8 @@ int main(int argc, char *argv[])
             << " at location " << regionMesh.facesInstance()
             << exit(FatalError);
     }
+    topoSet::removeFiles(regionMesh);
+    processorMeshes::removeFiles(regionMesh);
 
 
     // See if we need to extrude coordinates as well
@@ -2847,6 +2850,8 @@ int main(int argc, char *argv[])
                 << " at location " << mesh.facesInstance()
                 << exit(FatalError);
         }
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
     }
 
     Info << "End\n" << endl;

applications/utilities/mesh/generation/extrude2DMesh/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean libso extrude2DMesh
 wclean

applications/utilities/mesh/generation/extrude2DMesh/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType extrude2DMesh
 wmake $targetType

applications/utilities/mesh/generation/extrude2DMesh/Make/options

@@ -2,11 +2,14 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/surfMesh/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -Iextrude2DMesh/lnInclude \
     -I$(LIB_SRC)/mesh/extrudeModel/lnInclude
 
 EXE_LIBS = \
     -lsurfMesh \
     -ldynamicMesh \
+    -lreconstruct \
     -lextrude2DMesh \
     -lextrudeModel

applications/utilities/mesh/generation/extrude2DMesh/extrude2DMeshApp.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -47,6 +47,8 @@ Note
 #include "addPatchCellLayer.H"
 #include "patchToPoly2DMesh.H"
 #include "globalIndex.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -323,6 +325,8 @@ int main(int argc, char *argv[])
         << nl << endl;
 
     mesh().write();
+    topoSet::removeFiles(mesh());
+    processorMeshes::removeFiles(mesh());
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/generation/foamyMesh/Allwclean

@@ -1,6 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
-set -x
 
 wclean conformalVoronoiMesh
 wclean conformalVoronoi2DMesh

applications/utilities/mesh/generation/foamyMesh/foamyHexMeshSurfaceSimplify/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for compilation (at least for error catching)
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 if [ -d "${FASTDUALOCTREE_SRC_PATH}" ]
 then

applications/utilities/mesh/generation/snappyHexMesh/Make/options

@@ -9,6 +9,7 @@ EXE_INC = \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
     -I$(LIB_SRC)/edgeMesh/lnInclude \
     -I$(LIB_SRC)/parallel/decompose/decompose/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
@@ -22,4 +23,5 @@ EXE_LIBS = \
     -lfileFormats \
     -ldynamicMesh \
     -ldecompose \
+    -lreconstruct \
     -lsnappyHexMesh

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C

@@ -63,6 +63,7 @@ Description
 #include "decompositionModel.H"
 #include "fvMeshTools.H"
 #include "profiling.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -658,6 +659,13 @@ void writeMesh
     meshRefiner.printMeshInfo(debugLevel, msg);
     Info<< "Writing mesh to time " << meshRefiner.timeName() << endl;
 
+    processorMeshes::removeFiles(mesh);
+    if (!debugLevel)
+    {
+        topoSet::removeFiles(mesh);
+    }
+    refinementHistory::removeFiles(mesh);
+
     //label flag = meshRefinement::MESH;
     //if (writeLevel)
     //{

applications/utilities/mesh/manipulation/createBaffles/Make/options

@@ -2,10 +2,12 @@ EXE_INC = \
     -IfaceSelection \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
     -lmeshTools \
     -lfiniteVolume \
+    -lreconstruct \
     -lgenericPatchFields

applications/utilities/mesh/manipulation/createBaffles/createBaffles.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -53,6 +53,8 @@ Description
 #include "faceSelection.H"
 
 #include "fvMeshTools.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -978,6 +980,8 @@ int main(int argc, char *argv[])
     Info<< "Writing mesh to " << runTime.timeName() << endl;
 
     mesh.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/manipulation/createPatch/Make/options

@@ -1,7 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
+    -lreconstruct \
     -lmeshTools

applications/utilities/mesh/manipulation/createPatch/createPatch.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -52,6 +52,7 @@ Description
 #include "polyTopoChange.H"
 #include "polyModifyFace.H"
 #include "wordReList.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -900,6 +901,8 @@ int main(int argc, char *argv[])
     // Write resulting mesh
     Info<< "Writing repatched mesh to " << runTime.timeName() << nl << endl;
     mesh.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/manipulation/mergeMeshes/Make/options

@@ -1,6 +1,9 @@
 EXE_INC = \
-    -I$(LIB_SRC)/dynamicMesh/lnInclude
+    -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
-    -lmeshTools
+    -lreconstruct

applications/utilities/mesh/manipulation/mergeMeshes/mergeMeshes.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -35,6 +35,8 @@ Description
 #include "argList.H"
 #include "Time.H"
 #include "mergePolyMesh.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -163,6 +165,8 @@ int main(int argc, char *argv[])
     }
 
     masterMesh.write();
+    topoSet::removeFiles(masterMesh);
+    processorMeshes::removeFiles(masterMesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/manipulation/mergeOrSplitBaffles/Make/options

@@ -1,10 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
     -lgenericPatchFields \
-    -lmeshTools \
+    -lreconstruct \
     -ldynamicMesh

applications/utilities/mesh/manipulation/mergeOrSplitBaffles/mergeOrSplitBaffles.C

@@ -79,6 +79,7 @@ Note
 #include "ReadFields.H"
 #include "volFields.H"
 #include "surfaceFields.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -537,6 +538,8 @@ int main(int argc, char *argv[])
         Info<< "Writing mesh to time " << runTime.timeName() << endl;
         mesh.write();
 
+        topoSet::removeFiles(mesh);
+        processorMeshes::removeFiles(mesh);
 
         // Dump duplicated points (if any)
         const labelList& pointMap = map().pointMap();

applications/utilities/mesh/manipulation/polyDualMesh/Make/options

@@ -1,10 +1,12 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \
     -lgenericPatchFields \
     -ldynamicMesh \
+    -lreconstruct \
     -lmeshTools

applications/utilities/mesh/manipulation/polyDualMesh/polyDualMeshApp.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -74,6 +74,8 @@ Note
 #include "ReadFields.H"
 #include "volFields.H"
 #include "surfaceFields.H"
+#include "topoSet.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -552,6 +554,8 @@ int main(int argc, char *argv[])
     Info<< "Writing dual mesh to " << runTime.timeName() << endl;
 
     mesh.write();
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/manipulation/renumberMesh/Make/options

@@ -6,7 +6,8 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/renumber/renumberMethods/lnInclude \
     -I$(LIB_SRC)/renumber/zoltanRenumber/lnInclude \
-    -I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude
+    -I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
@@ -14,5 +15,6 @@ EXE_LIBS = \
     -lfiniteVolume \
     -lgenericPatchFields \
     -lrenumberMethods \
+    -lreconstruct \
     $(LINK_FLAGS) \
     -ldecompositionMethods -L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp

applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -52,6 +52,8 @@ Description
 #include "cellSet.H"
 #include "faceSet.H"
 #include "pointSet.H"
+#include "processorMeshes.H"
+#include "hexRef8.H"
 
 #ifdef FOAM_USE_ZOLTAN
     #include "zoltanRenumber.H"
@@ -696,7 +698,6 @@ int main(int argc, char *argv[])
     bool writeMaps = false;
     bool orderPoints = false;
     label blockSize = 0;
-    bool renumberSets = true;
 
     // Construct renumberMethod
     autoPtr<IOdictionary> renumberDictPtr;
@@ -756,8 +757,6 @@ int main(int argc, char *argv[])
             Info<< "Writing renumber maps (new to old) to polyMesh." << nl
                 << endl;
         }
-
-        renumberSets = renumberDict.lookupOrDefault("renumberSets", true);
     }
     else
     {
@@ -884,46 +883,12 @@ int main(int argc, char *argv[])
     PtrList<cellSet> cellSets;
     PtrList<faceSet> faceSets;
     PtrList<pointSet> pointSets;
-    if (renumberSets)
     {
         // Read sets
         IOobjectList objects(mesh, mesh.facesInstance(), "polyMesh/sets");
-        {
+        ReadFields(objects, cellSets);
-            IOobjectList cSets(objects.lookupClass(cellSet::typeName));
+        ReadFields(objects, faceSets);
-            if (cSets.size())
+        ReadFields(objects, pointSets);
-            {
-                Info<< "Reading cellSets:" << endl;
-                forAllConstIter(IOobjectList, cSets, iter)
-                {
-                    cellSets.append(new cellSet(*iter()));
-                    Info<< "    " << cellSets.last().name() << endl;
-                }
-            }
-        }
-        {
-            IOobjectList fSets(objects.lookupClass(faceSet::typeName));
-            if (fSets.size())
-            {
-                Info<< "Reading faceSets:" << endl;
-                forAllConstIter(IOobjectList, fSets, iter)
-                {
-                    faceSets.append(new faceSet(*iter()));
-                    Info<< "    " << faceSets.last().name() << endl;
-                }
-            }
-        }
-        {
-            IOobjectList pSets(objects.lookupClass(pointSet::typeName));
-            if (pSets.size())
-            {
-                Info<< "Reading pointSets:" << endl;
-                forAllConstIter(IOobjectList, pSets, iter)
-                {
-                    pointSets.append(new pointSet(*iter()));
-                    Info<< "    " << pointSets.last().name() << endl;
-                }
-            }
-        }
     }
 
 
@@ -1183,6 +1148,7 @@ int main(int argc, char *argv[])
     }
 
 
+
     // Move mesh (since morphing might not do this)
     if (map().hasMotionPoints())
     {
@@ -1288,9 +1254,20 @@ int main(int argc, char *argv[])
     {
         mesh.setInstance(oldInstance);
     }
+    else
+    {
+        mesh.setInstance(runTime.timeName());
+    }
+
 
     Info<< "Writing mesh to " << mesh.facesInstance() << endl;
 
+    processorMeshes::removeFiles(mesh);
+    hexRef8::removeFiles(mesh);
+    topoSet::updateMesh(mesh.facesInstance(), map(), cellSets);
+    topoSet::updateMesh(mesh.facesInstance(), map(), faceSets);
+    topoSet::updateMesh(mesh.facesInstance(), map(), pointSets);
+
     mesh.write();
 
     if (cellProcAddressing.headerOk())
@@ -1437,27 +1414,6 @@ int main(int argc, char *argv[])
         ).write();
     }
 
-    if (renumberSets)
-    {
-        forAll(cellSets, i)
-        {
-            cellSets[i].updateMesh(map());
-            cellSets[i].instance() = mesh.facesInstance();
-            cellSets[i].write();
-        }
-        forAll(faceSets, i)
-        {
-            faceSets[i].updateMesh(map());
-            faceSets[i].instance() = mesh.facesInstance();
-            faceSets[i].write();
-        }
-        forAll(pointSets, i)
-        {
-            pointSets[i].updateMesh(map());
-            pointSets[i].instance() = mesh.facesInstance();
-            pointSets[i].write();
-        }
-    }
 
     Info<< "End\n" << endl;
 

applications/utilities/mesh/manipulation/renumberMesh/renumberMeshDict

@@ -34,9 +34,6 @@ sortCoupledFaceCells false;
 // Optional entry: sort points into internal and boundary points
 //orderPoints false;
 
-// Optional: suppress renumbering cellSets,faceSets,pointSets
-//renumberSets false;
-
 
 method          CuthillMcKee;
 //method          Sloan;

applications/utilities/mesh/manipulation/setSet/Allwmake

@@ -11,7 +11,7 @@ unset COMP_FLAGS LINK_FLAGS
 #
 if [ -f /usr/include/readline/readline.h ]
 then
-    echo "Found <readline/readline.h>  --  enabling readline support."
+    echo "    found <readline/readline.h>  --  enabling readline support."
     export COMP_FLAGS="-DHAS_READLINE"
     export LINK_FLAGS="-lreadline"
 fi

applications/utilities/mesh/manipulation/splitMesh/Make/options

@@ -1,7 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
+    -lreconstruct \
     -lmeshTools

applications/utilities/mesh/manipulation/splitMesh/splitMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -56,6 +56,7 @@ Description
 #include "attachPolyTopoChanger.H"
 #include "regionSide.H"
 #include "primitiveFacePatch.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -287,6 +288,9 @@ int main(int argc, char *argv[])
             << "Failed writing polyMesh."
             << exit(FatalError);
     }
+    topoSet::removeFiles(mesh);
+    processorMeshes::removeFiles(mesh);
+
 
     Info<< nl << "End" << nl << endl;
 

applications/utilities/mesh/manipulation/splitMeshRegions/Make/options

@@ -1,10 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lreconstruct \
-    -lgenericPatchFields \
     -ldynamicMesh \
-    -lmeshTools
+    -lgenericPatchFields

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

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -107,6 +107,7 @@ Description
 #include "mappedWallPolyPatch.H"
 #include "fvMeshTools.H"
 #include "zeroGradientFvPatchFields.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -941,6 +942,8 @@ void createAndWriteRegion
 
     newMesh().setInstance(newMeshInstance);
     newMesh().write();
+    topoSet::removeFiles(newMesh());
+    processorMeshes::removeFiles(newMesh());
 
     // Write addressing files like decomposePar
     Info<< "Writing addressing to base mesh" << endl;

applications/utilities/mesh/manipulation/subsetMesh/Make/options

@@ -1,9 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
-    -I$(LIB_SRC)/meshTools/lnInclude
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/parallel/reconstruct/reconstruct/lnInclude
 
 EXE_LIBS = \
     -ldynamicMesh \
-    -ldynamicMesh \
+    -lreconstruct \
     -lgenericPatchFields

applications/utilities/mesh/manipulation/subsetMesh/subsetMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -41,11 +41,15 @@ Description
 
 #include "fvMeshSubset.H"
 #include "argList.H"
-#include "cellSet.H"
 #include "IOobjectList.H"
 #include "volFields.H"
 #include "topoDistanceData.H"
 #include "FaceCellWave.H"
+#include "cellSet.H"
+#include "faceSet.H"
+#include "pointSet.H"
+#include "ReadFields.H"
+#include "processorMeshes.H"
 
 using namespace Foam;
 
@@ -262,6 +266,59 @@ void subsetDimensionedFields
 }
 
 
+template<class TopoSet>
+void subsetTopoSets
+(
+    const fvMesh& mesh,
+    const IOobjectList& objectsList,
+    const labelList& map,
+    const fvMesh& subMesh,
+    PtrList<TopoSet>& subSets
+)
+{
+    // Read original sets
+    PtrList<TopoSet> sets;
+    ReadFields<TopoSet>(objectsList, sets);
+
+    subSets.setSize(sets.size());
+    forAll(sets, i)
+    {
+        TopoSet& set = sets[i];
+
+        Info<< "Subsetting " << set.type() << " " << set.name() << endl;
+
+        // Map the data
+        PackedBoolList isSet(set.maxSize(mesh));
+        forAllConstIter(labelHashSet, set, iter)
+        {
+            isSet[iter.key()] = true;
+        }
+        label nSet = 0;
+        forAll(map, i)
+        {
+            if (isSet[map[i]])
+            {
+                nSet++;
+            }
+        }
+
+        subSets.set
+        (
+            i,
+            new TopoSet(subMesh, set.name(), nSet, IOobject::AUTO_WRITE)
+        );
+        TopoSet& subSet = subSets[i];
+        forAll(map, i)
+        {
+            if (isSet[map[i]])
+            {
+                subSet.insert(i);
+            }
+        }
+    }
+}
+
+
 
 int main(int argc, char *argv[])
 {
@@ -557,6 +614,43 @@ int main(int argc, char *argv[])
     subsetDimensionedFields(subsetter, tensorDimNames, tensorDimFlds);
 
 
+    // topoSets and subset
+    // ~~~~~~~~~~~~~~~~~~~
+
+    PtrList<cellSet> cellSets;
+    PtrList<faceSet> faceSets;
+    PtrList<pointSet> pointSets;
+    {
+        IOobjectList objects(mesh, mesh.facesInstance(), "polyMesh/sets");
+        objects.remove(currentSet);
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.cellMap(),
+            subsetter.subMesh(),
+            cellSets
+        );
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.faceMap(),
+            subsetter.subMesh(),
+            faceSets
+        );
+        subsetTopoSets
+        (
+            mesh,
+            objects,
+            subsetter.pointMap(),
+            subsetter.subMesh(),
+            pointSets
+        );
+    }
+
+
+
     // Write mesh and fields to new time
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -564,15 +658,22 @@ int main(int argc, char *argv[])
     {
         runTime.setTime(instant(fieldsInstance), 0);
         subsetter.subMesh().setInstance(meshInstance);
+        topoSet::setInstance(meshInstance, cellSets);
+        topoSet::setInstance(meshInstance, faceSets);
+        topoSet::setInstance(meshInstance, pointSets);
     }
     else
     {
         runTime++;
+        subsetter.subMesh().setInstance(runTime.timeName());
     }
 
+
+
     Info<< "Writing subsetted mesh and fields to time " << runTime.timeName()
         << endl;
     subsetter.subMesh().write();
+    processorMeshes::removeFiles(subsetter.subMesh());
 
 
     // Subsetting adds 'subset' prefix. Rename field to be like original.

applications/utilities/mesh/manipulation/topoSet/topoSet.C

@@ -36,9 +36,6 @@ Description
 #include "Time.H"
 #include "polyMesh.H"
 #include "topoSetSource.H"
-#include "cellSet.H"
-#include "faceSet.H"
-#include "pointSet.H"
 #include "globalMeshData.H"
 #include "timeSelector.H"
 #include "IOobjectList.H"

applications/utilities/mesh/manipulation/topoSet/topoSetDict

@@ -342,8 +342,12 @@ FoamFile
 //
 // cellZoneSet
 // ~~~~~~~~~~~
-// (mirrors operations on a cellSet into a cellZone)
+// Manipulates a cellZone (as well as a cellSet)
+// Takes any cellSet source. The difference with a cellSet is
+// - reads the cells from the cellZone, not the cellSet
+// - write to the cellZone as well as the cellSet
 //
+// For backwards compatibility:
 //    // Select based on cellSet
 //    source setToCellZone;
 //    sourceInfo
@@ -355,6 +359,9 @@ FoamFile
 //
 // faceZoneSet
 // ~~~~~~~~~~~
+// Manipulates a faceZone (as well as a faceSet). It can only be used
+// with two special sources:
+//
 //    // Select based on faceSet without orientation
 //    source setToFaceZone;
 //    sourceInfo
@@ -394,17 +401,19 @@ FoamFile
 //
 // pointZoneSet
 // ~~~~~~~~~~~~
-// (mirrors operations on a pointSet into a pointZone)
+// Manipulates a pointZone (as well as a pointSet)
+// Takes any pointSet source. The difference with a pointSet is
+// - reads the cells from the pointZone, not the pointSet
+// - write to the pointZone as well as the pointSet
 //
+// For backwards compatibility:
 //    // Select based on pointSet
 //    source setToPointZone;
 //    sourceInfo
 //    {
 //        set p0;           // name of pointSet
 //    }
-//
+
-//
-//
 
 actions
 (
@@ -465,6 +474,19 @@ actions
             option  all;
         }
     }
+
+
+    // Example: create cellZone from geometric region
+    {
+        name    c0;
+        type    cellZoneSet;
+        action  new;
+        source  boxToCell;
+        sourceInfo
+        {
+            box   (0.04 0 0)(0.06 100 100);
+        }
+    }
 );
 
 // ************************************************************************* //

applications/utilities/miscellaneous/foamDictionary/foamDictionary.C

@@ -57,6 +57,9 @@ Usage
       - \par -includes
         List the \c #include and \c #includeIfPresent files to standard output
 
+      - \par -disableFunctionEntries
+        Do not expand macros or directives (#include etc)
+
     Example usage:
       - Change simulation to run for one timestep only:
         \verbatim
@@ -97,6 +100,15 @@ Usage
             -entry boundaryField
         \endverbatim
 
+      - Change patch type:
+        \verbatim
+          foamDictionary constant/polyMesh/boundary \
+            -entry entry0.fixedWalls.type -set patch
+        \endverbatim
+        This uses special parsing of Lists which stores these in the
+        dictionary with keyword 'entryDDD' where DDD is the position
+        in the dictionary (after ignoring the FoamFile entry).
+
 \*---------------------------------------------------------------------------*/
 
 #include "argList.H"
@@ -271,6 +283,11 @@ int main(int argc, char *argv[])
         "Read the specified dictionary file, expand the macros etc. and write "
         "the resulting dictionary to standard output"
     );
+    argList::addBoolOption
+    (
+        "disableFunctionEntries",
+        "Disable expansion of dictionary directives - #include, #codeStream etc"
+    );
 
     argList args(argc, argv);
 
@@ -281,6 +298,15 @@ int main(int argc, char *argv[])
         Foam::functionEntries::includeEntry::log = true;
     }
 
+    const bool disableEntries = args.optionFound("disableFunctionEntries");
+    if (disableEntries)
+    {
+        Info<< "Not expanding variables or dictionary directives"
+            << endl;
+        entry::disableFunctionEntries = true;
+    }
+
+
     fileName dictFileName(args[1]);
 
     autoPtr<IFstream> dictFile(new IFstream(dictFileName));
@@ -460,7 +486,7 @@ int main(int argc, char *argv[])
             {
                 FatalIOErrorInFunction(dictFile)
                     << "Cannot find entry " << entryName
-                    << exit(FatalError, 2);
+                    << exit(FatalIOError, 2);
             }
         }
     }

applications/utilities/miscellaneous/foamHelp/Allwmake

@@ -3,7 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for library compilation
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
 wmake $targetType helpTypes
 wmake $targetType

applications/utilities/miscellaneous/foamList/Make/options

@@ -1,4 +1,5 @@
 EXE_INC = \
+    -DFULLDEBUG -g -O0 \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \
     -I$(LIB_SRC)/transportModels \
@@ -16,11 +17,8 @@ EXE_LIBS = \
     -lcoalCombustion \
     -lcombustionModels \
     -lcompressibleEulerianInterfacialModels \
-    -lcompressibleMultiphaseEulerianInterfacialModels \
     -lcompressibleTurbulenceModels \
     -lCompressibleTwoPhaseMixtureTurbulenceModels \
-    -lcompressibleTwoPhaseSystem \
-    -lconformalVoronoiMesh \
     -ldecompositionMethods \
     -ldistributed \
     -ldistributionModels \
@@ -54,12 +52,7 @@ EXE_LIBS = \
     -lliquidPropertiesFvPatchFields \
     -lliquidProperties \
     -lmeshTools \
-    -lmultiphaseInterFoam \
-    -lmultiphaseMixtureThermo \
-    -lmultiphaseReactingTurbulenceModels \
-    -lmultiphaseSystem \
     -lODE \
-    -lOpenFOAM \
     -lphaseChangeTwoPhaseMixtures \
     -lphaseCompressibleTurbulenceModels \
     -lphaseTemperatureChangeTwoPhaseMixtures \
@@ -67,11 +60,6 @@ EXE_LIBS = \
     -lpyrolysisModels \
     -lradiationModels \
     -lrandomProcesses \
-    -lreactingEulerianInterfacialCompositionModels \
-    -lreactingEulerianInterfacialModels \
-    -lreactingMultiphaseSystem \
-    -lreactingPhaseSystem \
-    -lreactingTwoPhaseSystem \
     -lreactionThermophysicalModels \
     -lregionCoupled \
     -lregionCoupling \
@@ -101,5 +89,4 @@ EXE_LIBS = \
     -lturbulenceModelSchemes \
     -lturbulenceModels \
     -ltwoPhaseProperties \
-    -ltwoPhaseReactingTurbulenceModels \
     -lutilityFunctionObjects

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -53,6 +53,7 @@ Description
 #include "fvMeshAdder.H"
 #include "polyTopoChange.H"
 #include "extrapolatedCalculatedFvPatchFields.H"
+#include "topoSet.H"
 
 using namespace Foam;
 
@@ -731,6 +732,7 @@ int main(int argc, char *argv[])
                     << "Failed writing polyMesh."
                     << exit(FatalError);
             }
+            topoSet::removeFiles(masterMesh);
 
             if (writeCellDist)
             {