COMP: Multiple changes - first clean build after latest merge - UNTESTED

applications/solvers/basic/potentialFoam/potentialFoam.C

@@ -28,9 +28,9 @@ Group
     grpBasicSolvers
 
 Description
-    Potential flow solver which solves for the velocity potential
+    Potential flow solver which solves for the velocity potential, to
-    from which the flux-field is obtained and velocity field by reconstructing
+    calculate the flux-field, from which the velocity field is obtained by
-    the flux.
+    reconstructing the flux.
 
     \heading Solver details
     The potential flow solution is typically employed to generate initial fields

applications/solvers/combustion/XiFoam/XiDyMFoam/XiDyMFoam.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  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -67,25 +67,26 @@ Description
 
 int main(int argc, char *argv[])
 {
-    #include "setRootCase.H"
+    #include "postProcess.H"
 
+    #include "setRootCase.H"
     #include "createTime.H"
     #include "createDynamicFvMesh.H"
-    #include "initContinuityErrs.H"
+    #include "createControl.H"
-
-    pimpleControl pimple(mesh);
-
     #include "readCombustionProperties.H"
     #include "readGravitationalAcceleration.H"
     #include "createFields.H"
-    #include "createMRF.H"
+    #include "createFieldRefs.H"
     #include "createFvOptions.H"
+    #include "initContinuityErrs.H"
     #include "createRhoUf.H"
     #include "createControls.H"
     #include "initContinuityErrs.H"
     #include "compressibleCourantNo.H"
     #include "setInitialDeltaT.H"
 
+    turbulence->validate();
+
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;

applications/solvers/combustion/XiFoam/XiDyMFoam/readControls.H

@@ -1,7 +1,6 @@
-    #include "readTimeControls.H"
+#include "readTimeControls.H"
 
-    bool correctPhi =
+correctPhi = pimple.dict().lookupOrDefault<Switch>("correctPhi", true);
-        pimple.dict().lookupOrDefault<Switch>("correctPhi", true);
 
-    bool checkMeshCourantNo =
+checkMeshCourantNo =
-        pimple.dict().lookupOrDefault<Switch>("checkMeshCourantNo", false);
+    pimple.dict().lookupOrDefault<Switch>("checkMeshCourantNo", false);

applications/solvers/heatTransfer/buoyantPimpleFoam/createFields.H

@@ -18,8 +18,6 @@ volScalarField rho
 );
 
 volScalarField& p = thermo.p();
-const volScalarField& psi = thermo.psi();
-
 
 Info<< "Reading field U\n" << endl;
 volVectorField U

applications/solvers/heatTransfer/buoyantPimpleFoam/pEqn.H

@@ -41,8 +41,6 @@
         p_rghDDtEqn =
         (
             fvc::ddt(rho) + psi*correction(fvm::ddt(p_rgh))
-        ==
-            fvOptions(psi, p_rgh, rho.name())
         );
     }
 
@@ -53,6 +51,8 @@
             p_rghDDtEqn()
           + fvc::div(phiHbyA)
           - fvm::laplacian(rhorAUf, p_rgh)
+        ==
+            fvOptions(psi, p_rgh, rho.name())
         );
 
         p_rghEqn.solve(mesh.solver(p_rgh.select(pimple.finalInnerIter())));

applications/solvers/heatTransfer/thermoFoam/setAlphaEff.H

@@ -11,7 +11,7 @@ IOobject turbulencePropertiesHeader
     false
 );
 
-if (turbulencePropertiesHeader.headerOk())
+if (turbulencePropertiesHeader.typeHeaderOk<IOdictionary>(false))
 {
     autoPtr<compressible::turbulenceModel> turbulence
     (

applications/solvers/lagrangian/simpleCoalParcelFoam/EEqn.H

@@ -0,0 +1,33 @@
+{
+    volScalarField& he = thermo.he();
+
+    fvScalarMatrix EEqn
+    (
+        mvConvection->fvmDiv(phi, he)
+      + (
+            he.name() == "e"
+          ? fvc::div(phi, volScalarField("Ekp", 0.5*magSqr(U) + p/rho))
+          : fvc::div(phi, volScalarField("K", 0.5*magSqr(U)))
+        )
+      - fvm::laplacian(turbulence->alphaEff(), he)
+     ==
+        rho*(U&g)
+      + parcels.Sh(he)
+      + radiation->Sh(thermo)
+      + combustion->Sh()
+      + fvOptions(rho, he)
+    );
+
+    EEqn.relax();
+
+    fvOptions.constrain(EEqn);
+
+    EEqn.solve();
+
+    fvOptions.correct(he);
+    thermo.correct();
+    radiation->correct();
+
+    Info<< "T gas min/max   = " << min(T).value() << ", "
+        << max(T).value() << endl;
+}

applications/solvers/lagrangian/simpleCoalParcelFoam/Make/options

@@ -24,8 +24,7 @@ EXE_INC = \
     -I$(LIB_SRC)/regionModels/surfaceFilmModels/lnInclude \
     -I$(LIB_SRC)/combustionModels/lnInclude \
     -I$(LIB_SRC)/fvOptions/lnInclude \
-    -I$(LIB_SRC)/sampling/lnInclude \
+    -I$(LIB_SRC)/sampling/lnInclude
-    -I$(FOAM_SOLVERS)/lagrangian/reactingParcelFoam/simpleReactingParcelFoam
 
 
 EXE_LIBS = \

applications/solvers/lagrangian/simpleCoalParcelFoam/UEqn.H

@@ -0,0 +1,21 @@
+    MRF.correctBoundaryVelocity(U);
+
+    tmp<fvVectorMatrix> tUEqn
+    (
+        fvm::div(phi, U)
+      + MRF.DDt(rho, U)
+      + turbulence->divDevRhoReff(U)
+     ==
+        rho()*g
+      + parcels.SU(U)
+      + fvOptions(rho, U)
+    );
+    fvVectorMatrix& UEqn = tUEqn.ref();
+
+    UEqn.relax();
+
+    fvOptions.constrain(UEqn);
+
+    solve(UEqn == -fvc::grad(p));
+
+    fvOptions.correct(U);

applications/solvers/lagrangian/simpleCoalParcelFoam/YEqn.H

@@ -0,0 +1,48 @@
+tmp<fv::convectionScheme<scalar>> mvConvection
+(
+    fv::convectionScheme<scalar>::New
+    (
+        mesh,
+        fields,
+        phi,
+        mesh.divScheme("div(phi,Yi_h)")
+    )
+);
+
+{
+    combustion->correct();
+    dQ = combustion->dQ();
+    volScalarField Yt(0.0*Y[0]);
+
+    forAll(Y, i)
+    {
+        if (i != inertIndex && composition.active(i))
+        {
+            volScalarField& Yi = Y[i];
+
+            fvScalarMatrix YEqn
+            (
+                mvConvection->fvmDiv(phi, Yi)
+              - fvm::laplacian(turbulence->muEff(), Yi)
+             ==
+                parcels.SYi(i, Yi)
+              + combustion->R(Yi)
+              + fvOptions(rho, Yi)
+            );
+
+            YEqn.relax();
+
+            fvOptions.constrain(YEqn);
+
+            YEqn.solve(mesh.solver("Yi"));
+
+            fvOptions.correct(Yi);
+
+            Yi.max(0.0);
+            Yt += Yi;
+        }
+    }
+
+    Y[inertIndex] = scalar(1) - Yt;
+    Y[inertIndex].max(0.0);
+}

applications/solvers/lagrangian/simpleCoalParcelFoam/createFieldRefs.H

@@ -0,0 +1,3 @@
+const volScalarField& psi = thermo.psi();
+const volScalarField& T = thermo.T();
+const label inertIndex(composition.species()[inertSpecie]);

applications/solvers/lagrangian/simpleCoalParcelFoam/createFields.H

@@ -0,0 +1,122 @@
+#include "readGravitationalAcceleration.H"
+
+Info<< "Creating combustion model\n" << endl;
+
+autoPtr<combustionModels::rhoCombustionModel> combustion
+(
+    combustionModels::rhoCombustionModel::New(mesh)
+);
+
+rhoReactionThermo& thermo = combustion->thermo();
+thermo.validate(args.executable(), "h", "e");
+
+SLGThermo slgThermo(mesh, thermo);
+
+basicSpecieMixture& composition = thermo.composition();
+PtrList<volScalarField>& Y = composition.Y();
+
+const word inertSpecie(thermo.lookup("inertSpecie"));
+if (!composition.species().found(inertSpecie))
+{
+    FatalIOErrorIn(args.executable().c_str(), thermo)
+        << "Inert specie " << inertSpecie << " not found in available species "
+        << composition.species()
+        << exit(FatalIOError);
+}
+
+volScalarField& p = thermo.p();
+
+volScalarField rho
+(
+    IOobject
+    (
+        "rho",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    thermo.rho()
+);
+
+Info<< "\nReading field U\n" << endl;
+volVectorField U
+(
+    IOobject
+    (
+        "U",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+#include "compressibleCreatePhi.H"
+
+mesh.setFluxRequired(p.name());
+
+dimensionedScalar rhoMax
+(
+    dimensionedScalar::lookupOrDefault
+    (
+        "rhoMax",
+        simple.dict(),
+        dimDensity,
+        GREAT
+    )
+);
+
+dimensionedScalar rhoMin
+(
+    dimensionedScalar::lookupOrDefault
+    (
+        "rhoMin",
+        simple.dict(),
+        dimDensity,
+        0
+    )
+);
+
+Info<< "Creating turbulence model\n" << endl;
+autoPtr<compressible::turbulenceModel> turbulence
+(
+    compressible::turbulenceModel::New
+    (
+        rho,
+        U,
+        phi,
+        thermo
+    )
+);
+
+// Set the turbulence into the combustion model
+combustion->setTurbulence(turbulence());
+
+Info<< "Creating multi-variate interpolation scheme\n" << endl;
+multivariateSurfaceInterpolationScheme<scalar>::fieldTable fields;
+
+forAll(Y, i)
+{
+    fields.add(Y[i]);
+}
+fields.add(thermo.he());
+
+volScalarField dQ
+(
+    IOobject
+    (
+        "dQ",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimensionedScalar("dQ", dimEnergy/dimTime, 0.0)
+);
+
+#include "createMRF.H"
+#include "createRadiationModel.H"
+#include "createClouds.H"

applications/solvers/lagrangian/simpleCoalParcelFoam/pEqn.H

@@ -0,0 +1,57 @@
+{
+    // Thermodynamic density needs to be updated by psi*d(p) after the
+    // pressure solution - done in 2 parts. Part 1:
+    thermo.rho() -= psi*p;
+
+    volScalarField rAU(1.0/UEqn.A());
+    surfaceScalarField rhorAUf("rhorAUf", fvc::interpolate(rho*rAU));
+    volVectorField HbyA(constrainHbyA(rAU*UEqn.H(), U, p));
+    tUEqn.clear();
+    surfaceScalarField phiHbyA
+    (
+        "phiHbyA",
+        fvc::interpolate(rho)*fvc::flux(HbyA)
+    );
+
+    MRF.makeRelative(fvc::interpolate(rho), phiHbyA);
+
+    // Update the pressure BCs to ensure flux consistency
+    constrainPressure(p, rho, U, phiHbyA, rhorAUf, MRF);
+
+    while (simple.correctNonOrthogonal())
+    {
+        fvScalarMatrix pEqn
+        (
+            fvc::div(phiHbyA)
+          - fvm::laplacian(rhorAUf, p)
+         ==
+            parcels.Srho()
+          + fvOptions(psi, p, rho.name())
+        );
+
+        pEqn.solve();
+
+        if (simple.finalNonOrthogonalIter())
+        {
+            phi = phiHbyA + pEqn.flux();
+        }
+    }
+
+    p.relax();
+
+    // Second part of thermodynamic density update
+    thermo.rho() += psi*p;
+
+    #include "compressibleContinuityErrs.H"
+
+    U = HbyA - rAU*fvc::grad(p);
+    U.correctBoundaryConditions();
+    fvOptions.correct(U);
+
+    rho = thermo.rho();
+    rho = max(rho, rhoMin);
+    rho = min(rho, rhoMax);
+    rho.relax();
+
+    Info<< "p min/max = " << min(p).value() << ", " << max(p).value() << endl;
+}

applications/solvers/lagrangian/simpleCoalParcelFoam/simpleCoalParcelFoam.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2015 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2015-2016 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -24,13 +24,12 @@ License
 Application
     simpleReactingParcelFoam
 
-Description
+Group
-    Steady state SIMPLE solver for laminar or turbulent flow with coal
+    grpLagrangianSolvers
-    Lagrangian parcels.
 
-    Note:
+Description
-    - including run-time selectable finite volume options,e.g. sources,
+    Steady state solver for compressible, turbulent flow with coal particle
-      constraints
+    clouds and optional sources/constraints.
 
 \*---------------------------------------------------------------------------*/
 
@@ -49,21 +48,19 @@ Description
 
 int main(int argc, char *argv[])
 {
-    #include "setRootCase.H"
+    #include "postProcess.H"
 
+    #include "setRootCase.H"
     #include "createTime.H"
     #include "createMesh.H"
-    #include "readGravitationalAcceleration.H"
+    #include "createControl.H"
-
-    simpleControl simple(mesh);
-
     #include "createFields.H"
-    #include "createRadiationModel.H"
+    #include "createFieldRefs.H"
-    #include "createClouds.H"
-    #include "createMRF.H"
     #include "createFvOptions.H"
     #include "initContinuityErrs.H"
 
+    turbulence->validate();
+
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;

applications/solvers/multiphase/MPPICInterFoam/CompressibleTwoPhaseMixtureTurbulenceModels/CompressibleTwoPhaseMixtureTurbulenceModels.C

@@ -32,6 +32,15 @@ License
 #include "turbulentTransportModel.H"
 #include "LESModel.H"
 
+makeTurbulenceModelTypes
+(
+    volScalarField,
+    geometricOneField,
+    incompressibleTurbulenceModel,
+    PhaseCompressibleTurbulenceModel,
+    immiscibleIncompressibleTwoPhaseMixture
+);
+
 makeBaseTurbulenceModel
 (
     volScalarField,

applications/solvers/multiphase/MPPICInterFoam/MPPICInterFoam.C

@@ -30,7 +30,7 @@ Description
     The momentum and other fluid properties are of the "mixture" and a single
     momentum equation is solved.
 
-    It includes MRF and MPPIC clouds
+    It includes MRF and an MPPIC cloud.
 
     Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected.
 
@@ -53,26 +53,22 @@ Description
 
 int main(int argc, char *argv[])
 {
+    #include "postProcess.H"
+
     #include "setRootCase.H"
     #include "createTime.H"
     #include "createMesh.H"
-
+    #include "createControl.H"
-    pimpleControl pimple(mesh);
-
-    #include "createTimeControls.H"
     #include "initContinuityErrs.H"
     #include "createFields.H"
-    #include "createMRF.H"
     #include "createFvOptions.H"
+    #include "createTimeControls.H"
     #include "correctPhi.H"
-
-    turbulence->validate();
-
-
-    #include "readTimeControls.H"
     #include "CourantNo.H"
     #include "setInitialDeltaT.H"
 
+    turbulence->validate();
+
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;
@@ -126,7 +122,7 @@ int main(int argc, char *argv[])
             zeroGradientFvPatchVectorField::typeName
         );
 
-        cloudVolSUSu.internalField() = -cloudSU.source()/mesh.V();
+        cloudVolSUSu.primitiveFieldRef() = -cloudSU.source()/mesh.V();
         cloudVolSUSu.correctBoundaryConditions();
 
         cloudSU.source() = vector::zero;

applications/solvers/multiphase/MPPICInterFoam/Make/options

@@ -1,6 +1,7 @@
 interFoamPath = $(FOAM_SOLVERS)/multiphase/interFoam
 
 EXE_INC =  \
+    -I. \
     -I./IncompressibleTwoPhaseMixtureTurbulenceModels/lnInclude \
     -I$(interFoamPath) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \

applications/solvers/multiphase/MPPICInterFoam/alphaEqn.H

@@ -17,9 +17,10 @@
 
     // Do not compress interface at non-coupled boundary faces
     // (inlets, outlets etc.)
+    surfaceScalarField::Boundary& phicBf = phic.boundaryFieldRef();
     forAll(phic.boundaryField(), patchi)
     {
-        fvsPatchScalarField& phicp = phic.boundaryField()[patchi];
+        fvsPatchScalarField& phicp = phicBf[patchi];
 
         if (!phicp.coupled())
         {

applications/solvers/multiphase/MPPICInterFoam/createFields.H

@@ -217,3 +217,5 @@
             mixture
         )
     );
+
+    #include "createMRF.H"

applications/solvers/multiphase/interCondensingEvaporatingFoam/temperaturePhaseChangeTwoPhaseMixtures/twoPhaseMixtureEThermo/twoPhaseMixtureEThermo.C

@@ -42,7 +42,7 @@ namespace Foam
 
 void Foam::twoPhaseMixtureEThermo::eBoundaryCorrection(volScalarField& h)
 {
-    volScalarField::GeometricBoundaryField& hbf = h.boundaryField();
+    volScalarField::Boundary& hbf = h.boundaryFieldRef();
 
     forAll(hbf, patchi)
     {
@@ -59,6 +59,7 @@ void Foam::twoPhaseMixtureEThermo::eBoundaryCorrection(volScalarField& h)
     }
 }
 
+
 void Foam::twoPhaseMixtureEThermo::init()
 {
     const volScalarField alpha1Rho1(alpha1()*rho1());
@@ -74,6 +75,7 @@ void Foam::twoPhaseMixtureEThermo::init()
     e_.correctBoundaryConditions();
 }
 
+
 // * * * * * * * * * * * * * * * * Constructor * * * * * * * * * * * * * * * //
 
 Foam::twoPhaseMixtureEThermo::twoPhaseMixtureEThermo
@@ -117,11 +119,13 @@ Foam::twoPhaseMixtureEThermo::twoPhaseMixtureEThermo
     init();
 }
 
+
 // * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
 
 Foam::twoPhaseMixtureEThermo::~twoPhaseMixtureEThermo()
 {}
 
+
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 void Foam::twoPhaseMixtureEThermo::correct()
@@ -226,10 +230,8 @@ Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::he
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::hc() const
-Foam::twoPhaseMixtureEThermo::hc() const
 {
-
     const fvMesh& mesh = this->T_.mesh();
 
     return tmp<volScalarField>
@@ -277,8 +279,7 @@ Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::THE
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::Cp() const
-Foam::twoPhaseMixtureEThermo::Cp() const
 {
     const volScalarField limitedAlpha1
     (
@@ -317,8 +318,7 @@ Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::Cp
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::rho() const
-Foam::twoPhaseMixtureEThermo::rho() const
 {
     const volScalarField limitedAlpha1
     (
@@ -337,8 +337,7 @@ Foam::twoPhaseMixtureEThermo::rho() const
 }
 
 
-Foam::tmp<Foam::scalarField>
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::rho
-Foam::twoPhaseMixtureEThermo::rho
 (
     const label patchi
 ) const
@@ -357,8 +356,7 @@ Foam::twoPhaseMixtureEThermo::rho
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::Cv() const
-Foam::twoPhaseMixtureEThermo::Cv() const
 {
     const volScalarField limitedAlpha1
     (
@@ -376,8 +374,7 @@ Foam::twoPhaseMixtureEThermo::Cv() const
 }
 
 
-Foam::tmp<Foam::scalarField>
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::Cv
-Foam::twoPhaseMixtureEThermo::Cv
 (
     const scalarField& p,
     const scalarField& T,
@@ -398,8 +395,7 @@ Foam::twoPhaseMixtureEThermo::Cv
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::gamma() const
-Foam::twoPhaseMixtureEThermo::gamma() const
 {
     return tmp<volScalarField>
     (
@@ -422,8 +418,7 @@ Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::gamma
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::Cpv() const
-Foam::twoPhaseMixtureEThermo::Cpv() const
 {
      // This is an e thermo (Cpv = Cv)
      return Cv();
@@ -442,16 +437,14 @@ Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::Cpv
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::CpByCpv() const
-Foam::twoPhaseMixtureEThermo::CpByCpv() const
 {
      NotImplemented;
      return tmp<Foam::volScalarField>();
 }
 
 
-Foam::tmp<Foam::scalarField>
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::CpByCpv
-Foam::twoPhaseMixtureEThermo::CpByCpv
 (
     const scalarField& p,
     const scalarField& T,
@@ -463,8 +456,7 @@ Foam::twoPhaseMixtureEThermo::CpByCpv
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::kappa() const
-Foam::twoPhaseMixtureEThermo::kappa() const
 {
     const volScalarField limitedAlpha1
     (
@@ -482,8 +474,10 @@ Foam::twoPhaseMixtureEThermo::kappa() const
 }
 
 
-Foam::tmp<Foam::scalarField>
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::kappa
-Foam::twoPhaseMixtureEThermo::kappa(const label patchi) const
+(
+    const label patchi
+) const
 {
     const volScalarField limitedAlpha1
     (
@@ -496,8 +490,7 @@ Foam::twoPhaseMixtureEThermo::kappa(const label patchi) const
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::kappaEff
-Foam::twoPhaseMixtureEThermo::kappaEff
 (
     const volScalarField& kappat
 ) const
@@ -508,8 +501,7 @@ Foam::twoPhaseMixtureEThermo::kappaEff
 }
 
 
-Foam::tmp<Foam::scalarField>
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::kappaEff
-Foam::twoPhaseMixtureEThermo::kappaEff
 (
     const scalarField& kappat,
     const label patchi
@@ -528,8 +520,7 @@ Foam::twoPhaseMixtureEThermo::kappaEff
 }
 
 
-Foam::tmp<Foam::volScalarField>
+Foam::tmp<Foam::volScalarField> Foam::twoPhaseMixtureEThermo::alphaEff
-Foam::twoPhaseMixtureEThermo::alphaEff
 (
     const volScalarField& alphat
 ) const
@@ -539,12 +530,11 @@ Foam::twoPhaseMixtureEThermo::alphaEff
         alpha1_*rho1() + (1.0 - alpha1_)*rho2()
     );
 
-
     return (kappa()/Cp()/rho + alphat);
 }
 
-Foam::tmp<Foam::scalarField>
+
-Foam::twoPhaseMixtureEThermo::alphaEff
+Foam::tmp<Foam::scalarField> Foam::twoPhaseMixtureEThermo::alphaEff
 (
     const scalarField& alphat,
     const label patchi
@@ -575,6 +565,7 @@ Foam::twoPhaseMixtureEThermo::alphaEff
     return kappa/Cp/rho + alphat;
 }
 
+
 bool Foam::twoPhaseMixtureEThermo::read()
 {
     if (basicThermo::read() && thermoIncompressibleTwoPhaseMixture::read())
@@ -589,4 +580,5 @@ bool Foam::twoPhaseMixtureEThermo::read()
     }
 }
 
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/solvers/multiphase/reactingEulerFoam/reactingMultiphaseEulerFoam/multiphaseCompressibleTurbulenceModels/Make/options

@@ -12,7 +12,7 @@ EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 LIB_LIBS = \
-    -lcompressibleTurbulenceModels
+    -lcompressibleTurbulenceModels \
     -lreactingPhaseSystem \
     -lreactingMultiphaseSystem \
     -lreactingEulerianInterfacialModels \

applications/utilities/mesh/advanced/snappyRefineMesh/Make/files

@@ -1,4 +1,4 @@
-autoRefineMesh.C
+snappyRefineMesh.C
 
-EXE = $(FOAM_APPBIN)/autoRefineMesh
+EXE = $(FOAM_APPBIN)/snappyRefineMesh
 

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

@@ -1316,14 +1316,14 @@ int main(int argc, char *argv[])
 
             Info<< surfaces.names()[surfi] << ':' << nl << nl;
 
-            const word& fzName = surfaces.surfZones()[surfI].faceZoneName();
+            const word& fzName = surfaces.surfZones()[surfi].faceZoneName();
 
             if (fzName.empty())
             {
                 // 'Normal' surface
                 forAll(regNames, i)
                 {
-                    label globalRegioni = surfaces.globalRegion(surfI, i);
+                    label globalRegioni = surfaces.globalRegion(surfi, i);
 
                     label patchi;
 

applications/utilities/mesh/manipulation/checkMesh/checkTopology.C

@@ -392,7 +392,7 @@ Foam::label Foam::checkTopology
                             // Already marked
                             regionDisconnected[regioni] = false;
                         }
-                        else if (pRegion != regionI)
+                        else if (pRegion != regioni)
                         {
                             // Multiple regions
                             regionDisconnected[regioni] = false;

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

@@ -326,7 +326,7 @@ int main(int argc, char *argv[])
     // Create mesh subsetting engine
     fvMeshSubset subsetter(mesh);
 
-    label patchi = -1;
+    labelList exposedPatchIDs;
 
     if (args.optionFound("patch"))
     {

applications/utilities/miscellaneous/foamDebugSwitches/Allwmake

@@ -1,11 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # run from this directory
-
-if [ -f "$FFTW_ARCH_PATH/include/fftw3.h" ] || \
-   [ "${FFTW_ARCH_PATH##*-}" = system -a -f "/usr/include/fftw3.h" ]
-then
-    export LINK_FLAGS="-lrandomProcesses"
-fi
-wmake
-
-#------------------------------------------------------------------------------

applications/utilities/parallelProcessing/decomposePar/decomposePar.C

@@ -1151,10 +1151,6 @@ int main(int argc, char *argv[])
                 // For the first region of a multi-region case additionally
                 // decompose the "uniform" directory in the time directory
                 if (regionNames.size() > 1 && regioni == 0)
-
-                    // If no fields have been decomposed the destination
-                    // directory will not have been created so make sure.
-                    mkDir(timePath);
                 {
                     decomposeUniform(copyUniform, mesh, processorDb);
                 }

applications/utilities/parallelProcessing/decomposePar/domainDecomposition.C

@@ -615,7 +615,7 @@ bool Foam::domainDecomposition::writeDecomposition(const bool decomposeSets)
 
                 label zonei = faceToZone[curF];
 
-                if (zoneI >= 0)
+                if (zonei >= 0)
                 {
                     // Single zone. Add the face
                     zoneFaces[zonei].append(facei);

applications/utilities/parallelProcessing/redistributePar/parFvFieldReconstructorReconstructFields.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -125,12 +125,8 @@ Foam::parFvFieldReconstructor::reconstructFvVolumeField
 
     PtrList<fvPatchField<Type>> patchFields(fld.mesh().boundary().size());
 
-    const typename GeometricField
+    const typename GeometricField<Type, fvPatchField, volMesh>::Boundary&
-    <
+        bfld = fld.boundaryField();
-        Type,
-        fvPatchField,
-        volMesh
-    >::GeometricBoundaryField& bfld = fld.boundaryField();
 
     forAll(bfld, patchI)
     {
@@ -292,12 +288,8 @@ Foam::parFvFieldReconstructor::reconstructFvSurfaceField
 
     PtrList<fvsPatchField<Type>> patchFields(fld.mesh().boundary().size());
 
-    const typename GeometricField
+    const typename GeometricField<Type, fvsPatchField, surfaceMesh>::Boundary&
-    <
+        bfld = fld.boundaryField();
-        Type,
-        fvsPatchField,
-        surfaceMesh
-    >::GeometricBoundaryField& bfld = fld.boundaryField();
 
     forAll(bfld, patchI)
     {

applications/utilities/parallelProcessing/redistributePar/redistributePar.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.
@@ -716,8 +716,7 @@ void correctCoupledBoundaryConditions(fvMesh& mesh)
     {
         GeoField& fld = *iter();
 
-        typename GeoField::GeometricBoundaryField& bfld =
+        typename GeoField::Boundary& bfld = fld.boundaryFieldRef();
-            fld.boundaryField();
         if
         (
             Pstream::defaultCommsType == Pstream::blocking
@@ -728,7 +727,7 @@ void correctCoupledBoundaryConditions(fvMesh& mesh)
 
             forAll(bfld, patchi)
             {
-                typename GeoField::PatchFieldType& pfld = bfld[patchi];
+                typename GeoField::Patch& pfld = bfld[patchi];
 
                 //if (pfld.coupled())
                 //if (isA<CoupledPatchType>(pfld))
@@ -750,7 +749,7 @@ void correctCoupledBoundaryConditions(fvMesh& mesh)
 
             forAll(bfld, patchi)
             {
-                typename GeoField::PatchFieldType& pfld = bfld[patchi];
+                typename GeoField::Patch& pfld = bfld[patchi];
 
                 //if (pfld.coupled())
                 //if (isA<CoupledPatchType>(pfld))
@@ -768,7 +767,7 @@ void correctCoupledBoundaryConditions(fvMesh& mesh)
             forAll(patchSchedule, patchEvali)
             {
                 label patchi = patchSchedule[patchEvali].patch;
-                typename GeoField::PatchFieldType& pfld = bfld[patchi];
+                typename GeoField::Patch& pfld = bfld[patchi];
 
                 //if (pfld.coupled())
                 //if (isA<CoupledPatchType>(pfld))

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

@@ -70,12 +70,7 @@ tmp<GeometricField<Type, fvPatchField, volMesh>>
 volField
 (
     const fvMeshSubset& meshSubsetter,
-    const typename GeometricField
+    const typename GeometricField<Type, fvPatchField, volMesh>::Internal& df
-    <
-        Type,
-        fvPatchField,
-        volMesh
-    >::DimensionedInternalField& df
 )
 {
     // Construct volField (with zeroGradient) from dimensioned field
@@ -93,7 +88,7 @@ volField
             zeroGradientFvPatchField<scalar>::typeName
         )
     );
-    tvf.ref().internalField() = df;
+    tvf.ref().primitiveFieldRef() = df;
     tvf.ref().correctBoundaryConditions();
     const GeometricField<Type, fvPatchField, volMesh>& vf = tvf();
 

applications/utilities/postProcessing/dataConversion/foamToEnsight/ensightField.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -60,7 +60,7 @@ volField
         Type,
         Foam::fvPatchField,
         Foam::volMesh
-    >::DimensionedInternalField& df
+    >::Internal& df
 );
 
 

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

@@ -186,11 +186,11 @@ int main(int argc, char *argv[])
         volSymmTensorField::typeName,
         volTensorField::typeName,
 
-        volScalarField::DimensionedInternalField::typeName,
+        volScalarField::Internal::typeName,
-        volVectorField::DimensionedInternalField::typeName,
+        volVectorField::Internal::typeName,
-        volSphericalTensorField::DimensionedInternalField::typeName,
+        volSphericalTensorField::Internal::typeName,
-        volSymmTensorField::DimensionedInternalField::typeName,
+        volSymmTensorField::Internal::typeName,
-        volTensorField::DimensionedInternalField::typeName
+        volTensorField::Internal::typeName
     };
 
     // Path to EnSight directory at case level only
@@ -562,15 +562,10 @@ int main(int argc, char *argv[])
                 // DimensionedFields
                 else if
                 (
-                    volFieldTypes[i]
+                    volFieldTypes[i] == volScalarField::Internal::typeName
-                 == volScalarField::DimensionedInternalField::typeName
                 )
                 {
-                    volScalarField::DimensionedInternalField df
+                    volScalarField::Internal df(fieldObject, mesh);
-                    (
-                        fieldObject,
-                        mesh
-                    );
                     ensightField<scalar>
                     (
                         volField<scalar>(meshSubsetter, df),
@@ -585,15 +580,10 @@ int main(int argc, char *argv[])
                 }
                 else if
                 (
-                    volFieldTypes[i]
+                    volFieldTypes[i] == volVectorField::Internal::typeName
-                 == volVectorField::DimensionedInternalField::typeName
                 )
                 {
-                    volVectorField::DimensionedInternalField df
+                    volVectorField::Internal df(fieldObject, mesh);
-                    (
-                        fieldObject,
-                        mesh
-                    );
                     ensightField<vector>
                     (
                         volField<vector>(meshSubsetter, df),
@@ -609,14 +599,10 @@ int main(int argc, char *argv[])
                 else if
                 (
                     volFieldTypes[i]
-                 == volSphericalTensorField::DimensionedInternalField::typeName
+                 == volSphericalTensorField::Internal::typeName
                 )
                 {
-                    volSphericalTensorField::DimensionedInternalField df
+                    volSphericalTensorField::Internal df(fieldObject, mesh);
-                    (
-                        fieldObject,
-                        mesh
-                    );
                     ensightField<sphericalTensor>
                     (
                         volField<sphericalTensor>(meshSubsetter, df),
@@ -631,15 +617,10 @@ int main(int argc, char *argv[])
                 }
                 else if
                 (
-                    volFieldTypes[i]
+                    volFieldTypes[i] == volSymmTensorField::Internal::typeName
-                 == volSymmTensorField::DimensionedInternalField::typeName
                 )
                 {
-                    volSymmTensorField::DimensionedInternalField df
+                    volSymmTensorField::Internal df(fieldObject, mesh);
-                    (
-                        fieldObject,
-                        mesh
-                    );
                     ensightField<symmTensor>
                     (
                         volField<symmTensor>(meshSubsetter, df),
@@ -654,15 +635,10 @@ int main(int argc, char *argv[])
                 }
                 else if
                 (
-                    volFieldTypes[i]
+                    volFieldTypes[i] == volTensorField::Internal::typeName
-                 == volTensorField::DimensionedInternalField::typeName
                 )
                 {
-                    volTensorField::DimensionedInternalField df
+                    volTensorField::Internal df(fieldObject, mesh);
-                    (
-                        fieldObject,
-                        mesh
-                    );
                     ensightField<tensor>
                     (
                         volField<tensor>(meshSubsetter, df),

applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.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.
@@ -618,11 +618,11 @@ int main(int argc, char *argv[])
 
 
         // Construct dimensioned fields
-        PtrList<volScalarField::DimensionedInternalField> dsf;
+        PtrList<const volScalarField::Internal> dsf;
-        PtrList<volVectorField::DimensionedInternalField> dvf;
+        PtrList<const volVectorField::Internal> dvf;
-        PtrList<volSphericalTensorField::DimensionedInternalField> dSpheretf;
+        PtrList<const volSphericalTensorField::Internal> dSpheretf;
-        PtrList<volSymmTensorField::DimensionedInternalField> dSymmtf;
+        PtrList<const volSymmTensorField::Internal> dSymmtf;
-        PtrList<volTensorField::DimensionedInternalField> dtf;
+        PtrList<const volTensorField::Internal> dtf;
 
         if (!specifiedFields || selectedFields.size())
         {

applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK/internalWriter.H

@@ -98,7 +98,7 @@ public:
         template<class Type, class GeoMesh>
         void write
         (
-            const PtrList<DimensionedField<Type, volMesh>>& flds
+            const PtrList<const DimensionedField<Type, volMesh>>& flds
         );
 
         //- Interpolate and write volFields
@@ -114,7 +114,7 @@ public:
         void write
         (
             const volPointInterpolation&,
-            const PtrList<DimensionedField<Type, volMesh>>&
+            const PtrList<const DimensionedField<Type, volMesh>>&
         );
 };
 

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

@@ -44,7 +44,7 @@ void Foam::internalWriter::write
 template<class Type, class GeoMesh>
 void Foam::internalWriter::write
 (
-    const PtrList<DimensionedField<Type, volMesh>>& flds
+    const PtrList<const DimensionedField<Type, volMesh>>& flds
 )
 {
     forAll(flds, i)
@@ -79,7 +79,7 @@ template<class Type, class GeoMesh>
 void Foam::internalWriter::write
 (
     const volPointInterpolation& pInterp,
-    const PtrList<DimensionedField<Type, volMesh>>& flds
+    const PtrList<const DimensionedField<Type, volMesh>>& flds
 )
 {
     forAll(flds, i)

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

@@ -64,7 +64,7 @@ void Foam::writeFuns::write
 (
     std::ostream& os,
     const bool binary,
-    const DimensionedField<Type, volMesh>& vvf,
+    const DimensionedField<Type, volMesh>& df,
     const vtkMesh& vMesh
 )
 {
@@ -74,19 +74,19 @@ void Foam::writeFuns::write
 
     label nValues = mesh.nCells() + superCells.size();
 
-    os  << vvf.name() << ' '
+    os  << df.name() << ' '
         << int(pTraits<Type>::nComponents) << ' '
         << nValues << " float" << std::endl;
 
     DynamicList<floatScalar> fField(pTraits<Type>::nComponents*nValues);
 
-    insert(vvf.primitiveField(), fField);
+    insert(df.field(), fField);
 
     forAll(superCells, superCelli)
     {
         label origCelli = superCells[superCelli];
 
-        insert(vvf[origCelli], fField);
+        insert(df[origCelli], fField);
     }
     write(os, binary, fField);
 }

applications/utilities/postProcessing/lagrangian/steadyParticleTracks/steadyParticleTracksTemplates.C

@@ -116,11 +116,11 @@ void Foam::writeVTKFields
         Info<< "        writing field " << fieldNames[fieldi] << endl;
         os  << nl << fieldNames[fieldi] << ' '
             << int(pTraits<Type>::nComponents) << ' '
-            << values[fieldI].size() << " float" << nl;
+            << values[fieldi].size() << " float" << nl;
         label offset = 0;
-        forAll(addr, trackI)
+        forAll(addr, tracki)
         {
-            const List<label> ids(addr[trackI]);
+            const List<label> ids(addr[tracki]);
 
             List<Type> data(UIndirectList<Type>(values[fieldi], ids));
             label nData = data.size() - 1;

applications/utilities/preProcessing/applyBoundaryLayer/applyBoundaryLayer.C

@@ -93,7 +93,7 @@ void correctProcessorPatches(volScalarField& vf)
     // Not possible to use correctBoundaryConditions on fields as they may
     // use local info as opposed to the constraint values employed here,
     // but still need to update processor patches
-    volScalarField::GeometricBoundaryField& bf = vf.boundaryField();
+    volScalarField::Boundary& bf = vf.boundaryFieldRef();
 
     forAll(bf, patchI)
     {
@@ -134,8 +134,8 @@ void blendField
     if (fieldHeader.typeHeaderOk<volScalarField>(true))
     {
         volScalarField fld(fieldHeader, mesh);
-        scalarField& internalField = fld.internalField();
+        scalarField& pf = fld.primitiveFieldRef();
-        internalField = (1 - mask)*internalField + mask*boundaryLayerField;
+        pf = (1 - mask)*pf + mask*boundaryLayerField;
         fld.max(SMALL);
 
         // Do not correct BC
@@ -172,10 +172,9 @@ void calcOmegaField
     if (omegaHeader.typeHeaderOk<volScalarField>(true))
     {
         volScalarField omega(omegaHeader, mesh);
-        scalarField& internalField = omega.internalField();
+        scalarField& pf = omega.primitiveFieldRef();
 
-        internalField =
+        pf = (1 - mask)*pf + mask*epsilonBL/(Cmu*kBL + SMALL);
-            (1 - mask)*internalField + mask*epsilonBL/(Cmu*kBL + SMALL);
         omega.max(SMALL);
 
         // Do not correct BC

applications/utilities/preProcessing/applyBoundaryLayer/createFields.H

@@ -52,7 +52,7 @@ volScalarField y
     dimensionedScalar("zero", dimLength, 0.0),
     zeroGradientFvPatchScalarField::typeName
 );
-y.internalField() = wallDist::New(mesh).y().internalField();
+y.primitiveFieldRef() = wallDist::New(mesh).y().primitiveField();
 y.correctBoundaryConditions();
 
 

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/Make/options

@@ -1,8 +1,8 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(LIB_SRC)/postProcessing/functionObjects/jobControl/lnInclude
+    -I$(LIB_SRC)/functionObjects/field/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \
-    -ljobControl
+    -lfieldFunctionObjects

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/createExternalCoupledPatchGeometry.C

@@ -56,12 +56,12 @@ Note:
     used for face addressing starts at index 0.
 
 See also
-    externalCoupledFunctionObject
+    functionObjects::externalCoupled
 
 \*---------------------------------------------------------------------------*/
 
 #include "fvCFD.H"
-#include "externalCoupledFunctionObject.H"
+#include "externalCoupled.H"
 #include "IOobjectList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -119,7 +119,7 @@ int main(int argc, char *argv[])
     }
 
 
-    externalCoupledFunctionObject::writeGeometry
+    functionObjects::externalCoupled::writeGeometry
     (
         UPtrList<const fvMesh>(meshes),
         commsDir,

applications/utilities/preProcessing/viewFactorsGen/viewFactorsGen.C

@@ -786,6 +786,8 @@ int main(int argc, char *argv[])
         );
 
         label compactI = 0;
+
+        volScalarField::Boundary& vfbf = viewFactorField.boundaryFieldRef();
         forAll(viewFactorsPatches, i)
         {
             label patchID = viewFactorsPatches[i];
@@ -805,7 +807,7 @@ int main(int argc, char *argv[])
                     forAll(fineFaces, fineId)
                     {
                         const label faceID = fineFaces[fineId];
-                        viewFactorField.boundaryField()[patchID][faceID] = Fij;
+                        vfbf[patchID][faceID] = Fij;
                     }
                     compactI++;
                 }

applications/utilities/surface/surfaceCheck/surfaceCheck.C

@@ -230,7 +230,7 @@ void writeParts
     {
         boolList includeMap(surf.size(), false);
 
-        forAll(faceZone, faceI)
+        forAll(faceZone, facei)
         {
             if (faceZone[facei] == zone)
             {
@@ -651,7 +651,7 @@ int main(int argc, char *argv[])
                 {
                     Info<< "    close unconnected points "
                         << pti << ' ' << localPoints[pti]
-                        << " and " << prevPtI << ' '
+                        << " and " << prevPti << ' '
                         << localPoints[prevPti]
                         << " distance:"
                         << mag(localPoints[pti] - localPoints[prevPti])
@@ -660,8 +660,8 @@ int main(int argc, char *argv[])
                 else
                 {
                     Info<< "    small edge between points "
-                        << ptI << ' ' << localPoints[pti]
+                        << pti << ' ' << localPoints[pti]
-                        << " and " << prevPtI << ' '
+                        << " and " << prevPti << ' '
                         << localPoints[prevPti]
                         << " distance:"
                         << mag(localPoints[pti] - localPoints[prevPti])
@@ -837,7 +837,7 @@ int main(int argc, char *argv[])
 
         label nInt = 0;
 
-        forAll(surf.edges(), edgeI)
+        forAll(surf.edges(), edgei)
         {
             const edge& e = surf.edges()[edgei];
 

doc/Doxygen/Doxyfile

@@ -44,14 +44,14 @@ PROJECT_NUMBER         = $(WM_PROJECT_VERSION)
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "The OpenFOAM Foundation"
+PROJECT_BRIEF          = "The open source CFD toolbox"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           = CFDFoundation55x55.png
+PROJECT_LOGO           = OpenFOAM-logo2-55x55.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -168,7 +168,8 @@ STRIP_FROM_INC_PATH    =
 # support long names like on DOS, Mac, or CD-ROM.
 # The default value is: NO.
 
-SHORT_NAMES            = YES
+#SHORT_NAMES            = YES
+SHORT_NAMES            = NO
 
 # If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
 # first line (until the first dot) of a Javadoc-style comment as the brief
@@ -1128,7 +1129,7 @@ HTML_EXTRA_FILES       =
 # Minimum value: 0, maximum value: 359, default value: 220.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_HUE    = 120
+HTML_COLORSTYLE_HUE    = 220
 
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
 # in the HTML output. For a value of 0 the output will use grayscales only. A
@@ -1426,7 +1427,7 @@ EXT_LINKS_IN_WINDOW    = NO
 # Minimum value: 8, maximum value: 50, default value: 10.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-FORMULA_FONTSIZE       = 12
+FORMULA_FONTSIZE       = 14
 
 # Use the FORMULA_TRANPARENT tag to determine whether or not the images
 # generated for formulas are transparent PNGs. Transparent PNGs are not

doc/Doxygen/footer.html

@@ -11,11 +11,27 @@
 </div>
 <!--END GENERATE_TREEVIEW-->
 <!--BEGIN !GENERATE_TREEVIEW-->
-<hr class="footer"/><address class="footer"><small>
+<hr class="footer"/>
-$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+  <address class="footer">
-<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+    <small>
-</a> $doxygenversion
+      <p>
-</small></address>
+        Copyright&nbsp;&copy;&nbsp;2011-2016&nbsp;
+        <a href="http://www.openfoam.com">OpenFOAM</a>
+        |
+        OPENFOAM&reg; is a registered
+        <a href="http://www.openfoam.com/legal/trademark-policy.php">trademark
+        </a> of OpenCFD Ltd.
+      </p>
+      <p>
+        $generatedby &#160;<a href="http://www.doxygen.org/index.html">
+        <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+        </a> $doxygenversion
+      </p>
+    </small>
+  </address>
 <!--END !GENERATE_TREEVIEW-->
+<!-- BEGIN MATHJAX-->
+$mathjax
+<!-- END MATHJAX-->
 </body>
 </html>

doc/Doxygen/header.html

@@ -32,7 +32,7 @@ $extrastylesheet
    <div id="projectname"><a href="http://openfoam.com">$projectname</a>
    <!--BEGIN PROJECT_NUMBER-->&#160;<span id="projectnumber"><a href="http://openfoam.com/download/source">$projectnumber</a></span><!--END PROJECT_NUMBER-->
    </div>
-   <!--BEGIN PROJECT_BRIEF--><div id="projectbrief"><a href="http://openfoam.com/dev">$projectbrief</a></div><!--END PROJECT_BRIEF-->
+   <!--BEGIN PROJECT_BRIEF--><div id="projectbrief"><a href="https://develop.openfoam.com">$projectbrief</a></div><!--END PROJECT_BRIEF-->
   </td>
   <!--END PROJECT_NAME-->
   <!--BEGIN !PROJECT_NAME-->

src/Allwmake

@@ -47,11 +47,7 @@ wmake $targetType lagrangian/basic
 wmake $targetType lagrangian/distributionModels
 wmake $targetType genericPatchFields
 
-<<<<<<< HEAD
 conversion/Allwmake $targetType $*
-=======
-wmake $targetType conversion
->>>>>>> foundation-github
 wmake $targetType mesh/extrudeModel
 wmake $targetType dynamicMesh
 wmake $targetType sampling

src/OpenFOAM/db/Time/Time.C

@@ -1316,8 +1316,6 @@ Foam::Time& Foam::Time::operator++()
                 }
             }
         }
-
-        functionObjects_.timeSet();
     }
 
     return *this;

src/OpenFOAM/db/error/messageStream.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -281,6 +281,15 @@ extern messageStream Info;
 //  for FUNCTION_NAME in file __FILE__ at line __LINE__
 #define InfoInFunction InfoIn(FUNCTION_NAME)
 
+//- Report an information message using Foam::Pout
+//  for functionName in file __FILE__ at line __LINE__
+#define PoutIn(functionName)                                                   \
+    ::Foam::Pout((functionName), __FILE__, __LINE__)
+
+//- Report an information message using Foam::Pout
+//  for FUNCTION_NAME in file __FILE__ at line __LINE__
+#define PoutInFunction PoutIn(FUNCTION_NAME)
+
 //- Report write to Foam::Info if the local log switch is true
 #define Log                                                                    \
     if (log) Info
@@ -309,6 +318,17 @@ extern messageStream Info;
 #define DebugInFunction                                                        \
     if (debug) InfoInFunction
 
+//- Report an information message using Foam::Pout
+//  if the local debug switch is true
+#define DebugPout                                                              \
+    if (debug) Pout
+
+//- Report an information message using Foam::Pout
+//  for FUNCTION_NAME in file __FILE__ at line __LINE__
+//  if the local debug switch is true
+#define DebugPoutInFunction                                                        \
+    if (debug) PoutInFunction
+
 //- Report a variable name and value
 //  using Foam::Pout in file __FILE__ at line __LINE__
 #define DebugVar(var)                                                          \

src/OpenFOAM/db/functionObjects/IOOutputFilter/IOOutputFilter.C

@@ -1,147 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     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 3 of the License, or
-    (at your option) any later version.
-
-    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-    for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
-\*---------------------------------------------------------------------------*/
-
-#include "IOOutputFilter.H"
-#include "Time.H"
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-template<class OutputFilter>
-Foam::IOOutputFilter<OutputFilter>::IOOutputFilter
-(
-    const word& outputFilterName,
-    const IOobject& ioDict,
-    const bool readFromFiles
-)
-:
-    IOdictionary(ioDict),
-    OutputFilter(outputFilterName, ioDict.db(), *this, readFromFiles)
-{}
-
-
-template<class OutputFilter>
-Foam::IOOutputFilter<OutputFilter>::IOOutputFilter
-(
-    const word& outputFilterName,
-    const objectRegistry& obr,
-    const word& dictName,
-    const IOobject::readOption rOpt,
-    const bool readFromFiles
-)
-:
-    IOdictionary
-    (
-        IOobject
-        (
-            dictName,
-            obr.time().system(),
-            obr,
-            rOpt,
-            IOobject::NO_WRITE
-        )
-    ),
-    OutputFilter(outputFilterName, obr, *this, readFromFiles)
-{}
-
-
-template<class OutputFilter>
-Foam::IOOutputFilter<OutputFilter>::IOOutputFilter
-(
-    const word& outputFilterName,
-    const objectRegistry& obr,
-    const fileName& dictName,
-    const IOobject::readOption rOpt,
-    const bool readFromFiles
-)
-:
-    IOdictionary
-    (
-        IOobject
-        (
-            dictName,
-            obr,
-            rOpt,
-            IOobject::NO_WRITE
-        )
-    ),
-    OutputFilter(outputFilterName, obr, *this, readFromFiles)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-template<class OutputFilter>
-Foam::IOOutputFilter<OutputFilter>::~IOOutputFilter()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-template<class OutputFilter>
-const Foam::word& Foam::IOOutputFilter<OutputFilter>::name() const
-{
-    return IOdictionary::name();
-}
-
-
-template<class OutputFilter>
-bool Foam::IOOutputFilter<OutputFilter>::read()
-{
-    if (regIOobject::read())
-    {
-        OutputFilter::read(*this);
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-
-template<class OutputFilter>
-bool Foam::IOOutputFilter<OutputFilter>::write()
-{
-    return OutputFilter::write();
-}
-
-
-template<class OutputFilter>
-void Foam::IOOutputFilter<OutputFilter>::updateMesh(const mapPolyMesh& mpm)
-{
-    read();
-    OutputFilter::updateMesh(mpm);
-}
-
-
-template<class OutputFilter>
-void Foam::IOOutputFilter<OutputFilter>::movePoints(const polyMesh& mesh)
-{
-    read();
-    OutputFilter::movePoints(mesh);
-}
-
-
-// ************************************************************************* //

src/OpenFOAM/db/functionObjects/IOOutputFilter/IOOutputFilter.H

@@ -1,153 +0,0 @@
-/*---------------------------------------------------------------------------* \
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     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 3 of the License, or
-    (at your option) any later version.
-
-    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-    for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
-Class
-    Foam::IOOutputFilter
-
-Description
-    IOdictionary wrapper around OutputFilter to allow them to read from
-    their associated dictionaries.
-
-Note
-    The IOobject or the objectRegistry will normally have to be
-    derived from a fvMesh for a subsequent cast (within OutputFilter)
-    to work correctly.
-
-SourceFiles
-    IOOutputFilter.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef IOOutputFilter_H
-#define IOOutputFilter_H
-
-#include "IOdictionary.H"
-#include "pointFieldFwd.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// Forward declaration of classes
-class mapPolyMesh;
-
-/*---------------------------------------------------------------------------*\
-                       Class IOOutputFilter Declaration
-\*---------------------------------------------------------------------------*/
-
-template<class OutputFilter>
-class IOOutputFilter
-:
-    public IOdictionary,
-    public OutputFilter
-{
-    // Private Member Functions
-
-        // Disallow default bitwise copy construct and assignment
-        IOOutputFilter(const IOOutputFilter&);
-        void operator=(const IOOutputFilter&);
-
-
-public:
-
-    // Constructors
-
-        //- Construct from an IOobject for IOdictionary
-        //  Allow the possibility to load fields from files
-        IOOutputFilter
-        (
-            const word& outputFilterName,
-            const IOobject& ioDict,
-            const bool loadFromFile = false
-        );
-
-        //- Construct for given objectRegistry and dictionary
-        //  Allow dictionary to be optional
-        //  Allow the possibility to load fields from files
-        IOOutputFilter
-        (
-            const word& outputFilterName,
-            const objectRegistry&,
-            const word& dictName = OutputFilter::typeName() + "Dict",
-            const IOobject::readOption rOpt = IOobject::MUST_READ_IF_MODIFIED,
-            const bool loadFromFile = false
-        );
-
-        //- Construct for given objectRegistry and dictionary
-        //  Dictionary read from full path.
-        //  Allow the possibility to load fields from files
-        IOOutputFilter
-        (
-            const word& outputFilterName,
-            const objectRegistry&,
-            const fileName& dictName,
-            const IOobject::readOption rOpt = IOobject::MUST_READ_IF_MODIFIED,
-            const bool loadFromFile = false
-        );
-
-
-    //- Destructor
-    virtual ~IOOutputFilter();
-
-
-    // Member Functions
-
-        //- Return name
-        virtual const word& name() const;
-
-        //- Inherit read from OutputFilter
-        using OutputFilter::read;
-
-        //- Read output filter properties
-        virtual bool read();
-
-        //- Inherit write from regIOobject
-        using regIOobject::write;
-
-        //- Sample and write
-        virtual bool write();
-
-        //- Update for changes of mesh
-        virtual void updateMesh(const mapPolyMesh& mpm);
-
-        //- Update for changes of mesh
-        virtual void movePoints(const polyMesh& mesh);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#ifdef NoRepository
-    #include "IOOutputFilter.C"
-#endif
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //

src/OpenFOAM/db/functionObjects/functionObjectList/functionObjectList.C

@@ -520,11 +520,6 @@ bool Foam::functionObjectList::execute()
 
     if (execution_)
     {
-        if (forceWrite)
-        {
-            resetState();
-        }
-
         if (!updated_)
         {
             read();
@@ -532,21 +527,18 @@ bool Foam::functionObjectList::execute()
 
         forAll(*this, objectI)
         {
-            addProfiling
+            const word& objName = operator[](objectI).name();
-            (
+            {
-                fo,
+                addProfiling(fo, "functionObject::" + objName + "::execute");
-                "functionObject::" + operator[](objectI).name() + "::execute"
-            );
 
-            ok = operator[](objectI).execute() && ok;
+                ok = operator[](objectI).execute() && ok;
+            }
 
-            addProfiling
+            {
-            (
+                addProfiling(fo, "functionObject::" + objName + "::write");
-                fo,
-                "functionObject::" + operator[](objectI).name() + "::write"
-            );
 
-            ok = operator[](objectI).write() && ok;
+                ok = operator[](objectI).write() && ok;
+            }
         }
     }
 
@@ -583,11 +575,9 @@ bool Foam::functionObjectList::end()
 
         forAll(*this, objectI)
         {
-            addProfiling
+            const word& objName = operator[](objectI).name();
-            (
+
-                fo,
+            addProfiling(fo, "functionObject::" + objName + "::end");
-                "functionObject::" + operator[](objectI).name() + "::end"
-            );
 
             ok = operator[](objectI).end() && ok;
         }
@@ -610,12 +600,9 @@ bool Foam::functionObjectList::adjustTimeStep()
 
         forAll(*this, objectI)
         {
-            addProfiling
+            const word& objName = operator[](objectI).name();
-            (
+
-                fo,
+            addProfiling(fo, "functionObject::" + objName + "::adjustTimeStep");
-                "functionObject::" + operator[](objectI).name()
-             + "::adjustTimeStep"
-            );
 
             ok = operator[](objectI).adjustTimeStep() && ok;
         }

src/OpenFOAM/db/functionObjects/logFiles/logFiles.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2012-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -40,7 +40,7 @@ void Foam::functionObjects::logFiles::createFiles()
         {
             if (!filePtrs_.set(i))
             {
-                filePtrs_.set(i, createFile(names_[i]);
+                filePtrs_.set(i, createFile(names_[i]));
 
                 initStream(filePtrs_[i]);
             }
@@ -67,7 +67,7 @@ void Foam::functionObjects::logFiles::resetName(const word& name)
     names_.clear();
     names_.append(name);
 
-    resetFile(name);
+    writeFile::resetFile(name);
 }
 
 
@@ -85,6 +85,21 @@ Foam::functionObjects::logFiles::logFiles
 {}
 
 
+Foam::functionObjects::logFiles::logFiles
+(
+    const objectRegistry& obr,
+    const word& prefix,
+    const dictionary& dict
+)
+:
+    writeFile(obr, prefix),
+    names_(),
+    filePtrs_()
+{
+    writeFile::read(dict);
+}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 Foam::functionObjects::logFiles::~logFiles()

src/OpenFOAM/db/functionObjects/logFiles/logFiles.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2012-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -41,7 +41,6 @@ SourceFiles
 #define functionObjects_logFiles_H
 
 #include "writeFile.H"
-#include "OFstream.H"
 #include "PtrList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -82,9 +81,6 @@ protected:
         //- Reset the list of names to a single name entry
         virtual void resetName(const word& name);
 
-        //- File header information
-        virtual void writeFileHeader(const label i = 0) = 0;
-
 
 private:
 
@@ -109,6 +105,16 @@ public:
         );
 
 
+        //- Construct from objectRegistry and prefix, and read options
+        //  from dictionary
+        logFiles
+        (
+            const objectRegistry& obr,
+            const word& prefix,
+            const dictionary& dict
+        );
+
+
     //- Destructor
     virtual ~logFiles();
 

src/OpenFOAM/db/functionObjects/regionFunctionObject/regionFunctionObject.C

@@ -97,8 +97,7 @@ Foam::functionObjects::regionFunctionObject::regionFunctionObject
     const dictionary& dict
 )
 :
-    functionObject(name),
+    stateFunctionObject(name, runTime),
-    time_(runTime),
     obr_
     (
         runTime.lookupObject<objectRegistry>
@@ -116,8 +115,7 @@ Foam::functionObjects::regionFunctionObject::regionFunctionObject
     const dictionary& dict
 )
 :
-    functionObject(name),
+    stateFunctionObject(name, obr.time()),
-    time_(obr.time()),
     obr_(obr)
 {}
 

src/OpenFOAM/db/functionObjects/regionFunctionObject/regionFunctionObject.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -29,7 +29,7 @@ Description
     reference to the region Foam::objectRegistry.
 
 See also
-    Foam::functionObject
+    Foam::functionObjects::stateFunctionObject
 
 SourceFiles
     regionFunctionObject.C
@@ -39,7 +39,7 @@ SourceFiles
 #ifndef functionObjects_regionFunctionObject_H
 #define functionObjects_regionFunctionObject_H
 
-#include "functionObject.H"
+#include "stateFunctionObject.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -53,21 +53,18 @@ namespace functionObjects
 {
 
 /*---------------------------------------------------------------------------*\
-                     Class regionFunctionObject Declaration
+                    Class regionFunctionObject Declaration
 \*---------------------------------------------------------------------------*/
 
 class regionFunctionObject
 :
-    public functionObject
+    public stateFunctionObject
 {
 
 protected:
 
     // Protected member data
 
-        //- Reference to the Time
-        const Time& time_;
-
         //- Reference to the region objectRegistry
         const objectRegistry& obr_;
 
@@ -86,7 +83,7 @@ protected:
         template<class ObjectType>
         bool store
         (
-            word& fieldName,
+            const word& fieldName,
             const tmp<ObjectType>& tfield,
             bool cacheable = false
         );

src/OpenFOAM/db/functionObjects/regionFunctionObject/regionFunctionObjectTemplates.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -51,7 +51,7 @@ const ObjectType& Foam::functionObjects::regionFunctionObject::lookupObject
 template<class ObjectType>
 bool Foam::functionObjects::regionFunctionObject::store
 (
-    word& fieldName,
+    const word& fieldName,
     const tmp<ObjectType>& tfield,
     bool cacheable
 )
@@ -68,16 +68,9 @@ bool Foam::functionObjects::regionFunctionObject::store
         return false;
     }
 
-    if
+    if (fieldName.size() && foundObject<ObjectType>(fieldName))
-    (
-        fieldName.size()
-     && obr_.foundObject<ObjectType>(fieldName)
-    )
     {
-        const ObjectType& field =
+        const ObjectType& field = lookupObject<ObjectType>(fieldName);
-        (
-            obr_.lookupObject<ObjectType>(fieldName)
-        );
 
         // If there is a result field already registered assign to the new
         // result field otherwise transfer ownership of the new result field to
@@ -97,10 +90,6 @@ bool Foam::functionObjects::regionFunctionObject::store
         {
             tfield.ref().rename(fieldName);
         }
-        else
-        {
-            fieldName = tfield().name();
-        }
 
         obr_.objectRegistry::store(tfield.ptr());
     }

src/OpenFOAM/db/functionObjects/stateFunctionObject/stateFunctionObject.C

@@ -23,79 +23,71 @@ License
 
 \*---------------------------------------------------------------------------*/
 
-#include "functionObjectState.H"
+#include "stateFunctionObject.H"
 #include "Time.H"
 
-const Foam::word Foam::functionObjectState::resultsName_ = "results";
+const Foam::word Foam::functionObjects::stateFunctionObject::resultsName_ =
+    "results";
 
 // * * * * * * * * * * * * Protected Member Functions  * * * * * * * * * * * //
 
-const Foam::IOdictionary& Foam::functionObjectState::stateDict() const
+const Foam::IOdictionary&
+Foam::functionObjects::stateFunctionObject::stateDict() const
 {
-    return obr_.time().functionObjects().stateDict();
+    return time_.functionObjects().stateDict();
 }
 
 
-Foam::IOdictionary& Foam::functionObjectState::stateDict()
+Foam::IOdictionary& Foam::functionObjects::stateFunctionObject::stateDict()
 {
-    return const_cast<IOdictionary&>(obr_.time().functionObjects().stateDict());
+    return const_cast<IOdictionary&>(time_.functionObjects().stateDict());
 }
 
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::functionObjectState::functionObjectState
+Foam::functionObjects::stateFunctionObject::stateFunctionObject
 (
-    const objectRegistry& obr,
+    const word& name,
-    const word& name
+    const Time& runTime
 )
 :
-    obr_(obr),
+    functionObject(name),
-    name_(name),
+    time_(runTime)
-    active_(true)
 {}
 
 
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
-Foam::functionObjectState::~functionObjectState()
+Foam::functionObjects::stateFunctionObject::~stateFunctionObject()
 {}
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-const Foam::word& Foam::functionObjectState::name() const
+Foam::dictionary& Foam::functionObjects::stateFunctionObject::propertyDict()
-{
-    return name_;
-}
-
-
-bool Foam::functionObjectState::active() const
-{
-    return active_;
-}
-
-
-Foam::dictionary& Foam::functionObjectState::propertyDict()
 {
     IOdictionary& stateDict = this->stateDict();
 
-    if (!stateDict.found(name_))
+    if (!stateDict.found(name()))
     {
-        stateDict.add(name_, dictionary());
+        stateDict.add(name(), dictionary());
     }
 
-    return stateDict.subDict(name_);
+    return stateDict.subDict(name());
 }
 
 
-bool Foam::functionObjectState::foundProperty(const word& entryName) const
+bool Foam::functionObjects::stateFunctionObject::foundProperty
+(
+    const word& entryName
+) const
 {
     const IOdictionary& stateDict = this->stateDict();
 
-    if (stateDict.found(name_))
+    if (stateDict.found(name()))
     {
-        const dictionary& baseDict = stateDict.subDict(name_);
+        const dictionary& baseDict = stateDict.subDict(name());
         return baseDict.found(entryName);
     }
 
@@ -103,13 +95,16 @@ bool Foam::functionObjectState::foundProperty(const word& entryName) const
 }
 
 
-Foam::word Foam::functionObjectState::resultType(const word& entryName) const
+Foam::word Foam::functionObjects::stateFunctionObject::resultType
+(
+    const word& entryName
+) const
 {
-    return objectResultType(name_, entryName);
+    return objectResultType(name(), entryName);
 }
 
 
-Foam::word Foam::functionObjectState::objectResultType
+Foam::word Foam::functionObjects::stateFunctionObject::objectResultType
 (
     const word& objectName,
     const word& entryName
@@ -142,13 +137,15 @@ Foam::word Foam::functionObjectState::objectResultType
 }
 
 
-Foam::List<Foam::word> Foam::functionObjectState::objectResultEntries() const
+Foam::List<Foam::word>
+Foam::functionObjects::stateFunctionObject::objectResultEntries() const
 {
-    return objectResultEntries(name_);
+    return objectResultEntries(name());
 }
 
 
-Foam::List<Foam::word> Foam::functionObjectState::objectResultEntries
+Foam::List<Foam::word> Foam::functionObjects::stateFunctionObject::
+objectResultEntries
 (
     const word& objectName
 ) const

src/OpenFOAM/db/functionObjects/stateFunctionObject/stateFunctionObject.H

@@ -29,60 +29,67 @@ Description
     information (data required for smooth restart behaviour) and results
     to/from the state dictionary
 
-See Also
+    Note: cannot access the state dictionary until after construction of the
+    function objects, since the owner container functionObjectList is owned
+    by time, and time owns the state dictionary.  I.e. need to wait for time
+    to be fully consttucted.
+
+See also
     Foam::functionObject
 
 SourceFiles
-    functionObjectState.C
+    stateFunctionObject.C
+    stateFunctionObjectTemplates.C
 
 \*---------------------------------------------------------------------------*/
 
-#ifndef functionObjectState_H
+#ifndef functionObjects_stateFunctionObject_H
-#define functionObjectState_H
+#define functionObjects_stateFunctionObject_H
 
-#include "objectRegistry.H"
+#include "functionObject.H"
-#include "IOdictionary.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
 {
 
+class IOdictionary;
+
+namespace functionObjects
+{
+
 /*---------------------------------------------------------------------------*\
-                     Class functionObjectState Declaration
+                     Class stateFunctionObject Declaration
 \*---------------------------------------------------------------------------*/
 
-class functionObjectState
+class stateFunctionObject
+:
+    public functionObject
 {
+
 private:
 
-    // Private data
+    // Private member data
 
         //- Name of the results dictionary
         static const word resultsName_;
 
-        //- Reference to the database
-        const objectRegistry& obr_;
-
 
     // Private Member Functions
 
         //- Disallow default bitwise copy construct
-        functionObjectState(const functionObjectState&);
+        stateFunctionObject(const stateFunctionObject&) = delete;
 
         //- Disallow default bitwise assignment
-        void operator=(const functionObjectState&);
+        void operator=(const stateFunctionObject&) = delete;
 
 
 protected:
 
-    // Protected data
+    // Protected Member Data
 
-        //- Name of model
+        //- Reference to the time database
-        const word name_;
+        const Time& time_;
-
-        //- Flag to indicate whether the object is active
-        bool active_;
 
 
     // Protacted Member Functions
@@ -100,29 +107,18 @@ public:
     // Constructors
 
         //- Construct from components
-        functionObjectState(const objectRegistry& obr, const word& name);
+        stateFunctionObject(const word& name, const Time& runTime);
 
 
     //- Destructor
-    virtual ~functionObjectState();
+    ~stateFunctionObject();
 
 
     // Member Functions
 
-        //- Return the name
-        const word& name() const;
-
-        //- Return the active flag
-        bool active() const;
-
         //- Return access to the property dictionary
         dictionary& propertyDict();
 
-        //- Set the active status by querying objectRegistry type
-        //  returns new active status
-        template<class Type>
-        bool setActive();
-
 
         // Properties
 
@@ -238,12 +234,13 @@ public:
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+} // End namespace functionObjects
 } // End namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 #ifdef NoRepository
-    #include "functionObjectStateTemplates.C"
+    #include "stateFunctionObjectTemplates.C"
 #endif
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

src/OpenFOAM/db/functionObjects/stateFunctionObject/stateFunctionObjectTemplates.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -23,28 +23,12 @@ License
 
 \*---------------------------------------------------------------------------*/
 
+#include "IOdictionary.H"
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 template<class Type>
-bool Foam::functionObjectState::setActive()
+Type Foam::functionObjects::stateFunctionObject::getProperty
-{
-    active_ = true;
-
-    if (!isA<Type>(obr_))
-    {
-        WarningInFunction
-            << "No " << Type::typeName << " available, deactivating " << name_
-            << endl;
-
-        active_ = false;
-    }
-
-    return active_;
-}
-
-
-template<class Type>
-Type Foam::functionObjectState::getProperty
 (
     const word& entryName,
     const Type& defaultValue
@@ -57,29 +41,29 @@ Type Foam::functionObjectState::getProperty
 
 
 template<class Type>
-void Foam::functionObjectState::getProperty
+void Foam::functionObjects::stateFunctionObject::getProperty
 (
     const word& entryName,
     Type& value
 ) const
 {
-    getObjectProperty(name_, entryName, value);
+    getObjectProperty(name(), entryName, value);
 }
 
 
 template<class Type>
-void Foam::functionObjectState::setProperty
+void Foam::functionObjects::stateFunctionObject::setProperty
 (
     const word& entryName,
     const Type& value
 )
 {
-    setObjectProperty(name_, entryName, value);
+    setObjectProperty(name(), entryName, value);
 }
 
 
 template<class Type>
-Type Foam::functionObjectState::getObjectProperty
+Type Foam::functionObjects::stateFunctionObject::getObjectProperty
 (
     const word& objectName,
     const word& entryName,
@@ -93,7 +77,7 @@ Type Foam::functionObjectState::getObjectProperty
 
 
 template<class Type>
-void Foam::functionObjectState::getObjectProperty
+void Foam::functionObjects::stateFunctionObject::getObjectProperty
 (
     const word& objectName,
     const word& entryName,
@@ -121,7 +105,7 @@ void Foam::functionObjectState::getObjectProperty
 
 
 template<class Type>
-void Foam::functionObjectState::setObjectProperty
+void Foam::functionObjects::stateFunctionObject::setObjectProperty
 (
     const word& objectName,
     const word& entryName,
@@ -141,18 +125,18 @@ void Foam::functionObjectState::setObjectProperty
 
 
 template<class Type>
-void Foam::functionObjectState::setResult
+void Foam::functionObjects::stateFunctionObject::setResult
 (
     const word& entryName,
     const Type& value
 )
 {
-    setObjectResult(name_, entryName, value);
+    setObjectResult(name(), entryName, value);
 }
 
 
 template<class Type>
-void Foam::functionObjectState::setObjectResult
+void Foam::functionObjects::stateFunctionObject::setObjectResult
 (
     const word& objectName,
     const word& entryName,
@@ -170,7 +154,7 @@ void Foam::functionObjectState::setObjectResult
 
     if (!resultsDict.found(objectName))
     {
-        resultsDict.add(name_, dictionary());
+        resultsDict.add(name(), dictionary());
     }
 
     dictionary& objectDict = resultsDict.subDict(objectName);
@@ -189,18 +173,18 @@ void Foam::functionObjectState::setObjectResult
 
 
 template<class Type>
-Type Foam::functionObjectState::getResult
+Type Foam::functionObjects::stateFunctionObject::getResult
 (
     const word& entryName,
     const Type& defaultValue
 ) const
 {
-    return getObjectResult(name_, entryName, defaultValue);
+    return getObjectResult(name(), entryName, defaultValue);
 }
 
 
 template<class Type>
-Type Foam::functionObjectState::getObjectResult
+Type Foam::functionObjects::stateFunctionObject::getObjectResult
 (
     const word& objectName,
     const word& entryName,
@@ -214,7 +198,7 @@ Type Foam::functionObjectState::getObjectResult
 
 
 template<class Type>
-void Foam::functionObjectState::getObjectResult
+void Foam::functionObjects::stateFunctionObject::getObjectResult
 (
     const word& objectName,
     const word& entryName,

src/OpenFOAM/db/functionObjects/timeControl/timeControl.H

@@ -60,6 +60,7 @@ public:
         ocAdjustableRunTime,  //!< Adjust time step for execution
         ocRunTime,            //!< run time for execution
         ocClockTime,          //!< clock time for execution
+        ocCpuTime,            //!< CPU time for execution
         ocOnEnd,              //!< on end of run
         ocNone                //!< no execution
     };

src/OpenFOAM/db/functionObjects/writeFile/writeFile.C

@@ -93,7 +93,7 @@ Foam::autoPtr<Foam::OFstream> Foam::functionObjects::writeFile::createFile
     if (Pstream::master() && writeToFile_)
     {
         const word startTimeName =
-            obr_.time().timeName(obr_.time().startTime().value());
+            fileObr_.time().timeName(fileObr_.time().startTime().value());
 
         fileName outputDir(baseFileDir()/prefix_/startTimeName);
 
@@ -105,7 +105,7 @@ Foam::autoPtr<Foam::OFstream> Foam::functionObjects::writeFile::createFile
         IFstream is(outputDir/(fName + ".dat"));
         if (is.good())
         {
-            fName = fName + "_" + obr_.time().timeName();
+            fName = fName + "_" + fileObr_.time().timeName();
         }
 
         osPtr.set(new OFstream(outputDir/(fName + ".dat")));

src/OpenFOAM/db/functionObjects/writeFile/writeFile.H

@@ -40,6 +40,7 @@ SourceFiles
 #define functionObjects_writeFile_H
 
 #include "objectRegistry.H"
+#include "OFstream.H"
 #include "IOmanip.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -129,7 +130,8 @@ public:
             const word& prefix
         );
 
-        //- Construct from components and read options from dictionary
+        //- Construct from objectRegistry and prefix, and read options
+        //  from dictionary
         writeFile
         (
             const objectRegistry& obr,
@@ -151,6 +153,12 @@ public:
         //- Return access to the file (if only 1)
         OFstream& file();
 
+        //- Flag to allow writing to file
+        bool writeToFile() const;
+
+        //- Return width of character stream output
+        label charWidth() const;
+
         //- Write a commented string to stream
         void writeCommented(Ostream& os, const string& str) const;
 
@@ -171,9 +179,6 @@ public:
             const string& property,
             const Type& value
         ) const;
-
-        //- Return width of character stream output
-        label charWidth() const;
 };
 
 

src/OpenFOAM/fields/ReadFields/ReadFields.C

@@ -84,149 +84,4 @@ Foam::wordList Foam::fieldNames
 }
 
 
-}
-
-
-template<class GeoFieldType>
-void Foam::readFields
-(
-    const typename GeoFieldType::Mesh& mesh,
-    const IOobjectList& objects,
-    const HashSet<word>& selectedFields,
-    LIFOStack<regIOobject*>& storedObjects
-)
-{
-    IOobjectList fields(objects.lookupClass(GeoFieldType::typeName));
-    if (!fields.size()) return;
-
-    bool firstField = true;
-
-    forAllConstIter(IOobjectList, fields, fieldIter)
-    {
-        const IOobject& io = *fieldIter();
-        const word& fieldName = io.name();
-
-        if (selectedFields.found(fieldName))
-        {
-            if (firstField)
-            {
-                Info<< "    " << GeoFieldType::typeName << "s:";
-                firstField = false;
-            }
-
-            Info<< " " << fieldName;
-
-            GeoFieldType* fieldPtr = new GeoFieldType
-            (
-                IOobject
-                (
-                    fieldName,
-                    io.instance(),
-                    io.local(),
-                    io.db(),
-                    IOobject::MUST_READ,
-                    IOobject::NO_WRITE
-                ),
-                mesh
-            );
-            fieldPtr->store();
-            storedObjects.push(fieldPtr);
-        }
-    }
-
-    if (!firstField)
-    {
-        Info<< endl;
-    }
-}
-
-
-template<class UniformFieldType>
-void Foam::readUniformFields
-(
-    const IOobjectList& objects,
-    const HashSet<word>& selectedFields,
-    LIFOStack<regIOobject*>& storedObjects,
-    const bool syncPar
-)
-{
-    // Search list of objects for wanted type
-    IOobjectList fields(objects.lookupClass(UniformFieldType::typeName));
-    if (!fields.size()) return;
-
-    wordList masterNames(fields.names());
-
-    if (syncPar && Pstream::parRun())
-    {
-        // Check that I have the same fields as the master
-        const wordList localNames(masterNames);
-        Pstream::scatter(masterNames);
-
-        HashSet<word> localNamesSet(localNames);
-
-        forAll(masterNames, i)
-        {
-            const word& masterFld = masterNames[i];
-
-            HashSet<word>::iterator iter = localNamesSet.find(masterFld);
-
-            if (iter == localNamesSet.end())
-            {
-                FatalErrorInFunction
-                    << "Fields not synchronised across processors." << endl
-                    << "Master has fields " << masterNames
-                    << "  processor " << Pstream::myProcNo()
-                    << " has fields " << localNames << exit(FatalError);
-            }
-            else
-            {
-                localNamesSet.erase(iter);
-            }
-        }
-
-        forAllConstIter(HashSet<word>, localNamesSet, iter)
-        {
-            FatalErrorInFunction
-                << "Fields not synchronised across processors." << endl
-                << "Master has fields " << masterNames
-                << "  processor " << Pstream::myProcNo()
-                << " has fields " << localNames << exit(FatalError);
-        }
-    }
-
-    bool firstField = true;
-
-    forAll(masterNames, i)
-    {
-        const IOobject& io = *fields[masterNames[i]];
-        const word& fieldName = io.name();
-
-        if (selectedFields.found(fieldName))
-        {
-            if (firstField)
-            {
-                Info<< "    " << UniformFieldType::typeName << "s:";
-                firstField = false;
-            }
-
-            Info<< " " << fieldName;
-
-            UniformFieldType* fieldPtr = new UniformFieldType
-            (
-                IOobject
-                (
-                    fieldName,
-                    io.instance(),
-                    io.local(),
-                    io.db(),
-                    IOobject::MUST_READ,
-                    IOobject::NO_WRITE
-                )
-            );
-            fieldPtr->store();
-            storedObjects.push(fieldPtr);
-        }
-    }
-
-    Info<< endl;
 // ************************************************************************* //

src/OpenFOAM/fields/ReadFields/ReadFieldsTemplates.C

@@ -311,4 +311,149 @@ void Foam::ReadFields
 }
 
 
+template<class GeoFieldType>
+void Foam::readFields
+(
+    const typename GeoFieldType::Mesh& mesh,
+    const IOobjectList& objects,
+    const HashSet<word>& selectedFields,
+    LIFOStack<regIOobject*>& storedObjects
+)
+{
+    IOobjectList fields(objects.lookupClass(GeoFieldType::typeName));
+    if (!fields.size()) return;
+
+    bool firstField = true;
+
+    forAllConstIter(IOobjectList, fields, fieldIter)
+    {
+        const IOobject& io = *fieldIter();
+        const word& fieldName = io.name();
+
+        if (selectedFields.found(fieldName))
+        {
+            if (firstField)
+            {
+                Info<< "    " << GeoFieldType::typeName << "s:";
+                firstField = false;
+            }
+
+            Info<< " " << fieldName;
+
+            GeoFieldType* fieldPtr = new GeoFieldType
+            (
+                IOobject
+                (
+                    fieldName,
+                    io.instance(),
+                    io.local(),
+                    io.db(),
+                    IOobject::MUST_READ,
+                    IOobject::NO_WRITE
+                ),
+                mesh
+            );
+            fieldPtr->store();
+            storedObjects.push(fieldPtr);
+        }
+    }
+
+    if (!firstField)
+    {
+        Info<< endl;
+    }
+}
+
+
+template<class UniformFieldType>
+void Foam::readUniformFields
+(
+    const IOobjectList& objects,
+    const HashSet<word>& selectedFields,
+    LIFOStack<regIOobject*>& storedObjects,
+    const bool syncPar
+)
+{
+    // Search list of objects for wanted type
+    IOobjectList fields(objects.lookupClass(UniformFieldType::typeName));
+    if (!fields.size()) return;
+
+    wordList masterNames(fields.names());
+
+    if (syncPar && Pstream::parRun())
+    {
+        // Check that I have the same fields as the master
+        const wordList localNames(masterNames);
+        Pstream::scatter(masterNames);
+
+        HashSet<word> localNamesSet(localNames);
+
+        forAll(masterNames, i)
+        {
+            const word& masterFld = masterNames[i];
+
+            HashSet<word>::iterator iter = localNamesSet.find(masterFld);
+
+            if (iter == localNamesSet.end())
+            {
+                FatalErrorInFunction
+                    << "Fields not synchronised across processors." << endl
+                    << "Master has fields " << masterNames
+                    << "  processor " << Pstream::myProcNo()
+                    << " has fields " << localNames << exit(FatalError);
+            }
+            else
+            {
+                localNamesSet.erase(iter);
+            }
+        }
+
+        forAllConstIter(HashSet<word>, localNamesSet, iter)
+        {
+            FatalErrorInFunction
+                << "Fields not synchronised across processors." << endl
+                << "Master has fields " << masterNames
+                << "  processor " << Pstream::myProcNo()
+                << " has fields " << localNames << exit(FatalError);
+        }
+    }
+
+    bool firstField = true;
+
+    forAll(masterNames, i)
+    {
+        const IOobject& io = *fields[masterNames[i]];
+        const word& fieldName = io.name();
+
+        if (selectedFields.found(fieldName))
+        {
+            if (firstField)
+            {
+                Info<< "    " << UniformFieldType::typeName << "s:";
+                firstField = false;
+            }
+
+            Info<< " " << fieldName;
+
+            UniformFieldType* fieldPtr = new UniformFieldType
+            (
+                IOobject
+                (
+                    fieldName,
+                    io.instance(),
+                    io.local(),
+                    io.db(),
+                    IOobject::MUST_READ,
+                    IOobject::NO_WRITE
+                )
+            );
+            fieldPtr->store();
+            storedObjects.push(fieldPtr);
+        }
+    }
+
+    Info<< endl;
+}
+
+
 // ************************************************************************* //

src/OpenFOAM/meshes/polyMesh/mapPolyMesh/mapDistribute/mapDistributeTemplates.C

@@ -32,7 +32,7 @@ License
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
-// In case of no transform: copy elements
+template<class T>
 void Foam::mapDistribute::applyDummyTransforms(List<T>& field) const
 {
     forAll(transformElements_, trafoI)

src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C

@@ -1120,9 +1120,9 @@ bool Foam::polyBoundaryMesh::writeData(Ostream& os) const
 
     forAll(patches, patchi)
     {
-        os  << indent << patches[patchi].name() << nl
+        os.beginBlock(patches[patchi].name()) << nl;
         os  << patches[patchi];
-            << incrIndent << patches[patchi] << decrIndent
+        os.endBlock() << endl;
     }
 
     os  << decrIndent << token::END_LIST;

src/OpenFOAM/meshes/polyMesh/polyMeshUpdate.C

@@ -91,6 +91,7 @@ void Foam::polyMesh::updateMesh(const mapPolyMesh& mpm)
                     newMotionPoints[newPointi] = points_[newPointi];
                 }
             }
+        }
         else
         {
             const labelList& pointMap = mpm.pointMap();
@@ -103,7 +104,7 @@ void Foam::polyMesh::updateMesh(const mapPolyMesh& mpm)
                 {
                     if (revPointMap[oldPointi] == newPointi) // master point
                     {
-                        newMotionPoints[newPoint] = oldMotionPoints[oldPointi];
+                        newMotionPoints[newPointi] = oldMotionPoints[oldPointi];
                     }
                     else
                     {

src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.C

@@ -126,8 +126,8 @@ Foam::polyPatch::polyPatch
     ),
     start_(start),
     boundaryMesh_(bm),
-    faceCellsPtr_(NULL),
+    faceCellsPtr_(nullptr),
-    mePtr_(NULL)
+    mePtr_(nullptr)
 {}
 
 

src/TurbulenceModels/compressible/CompressibleTurbulenceModel/CompressibleTurbulenceModel.H

@@ -45,7 +45,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-               Class CompressibleTurbulenceModel Declaration
+                 Class CompressibleTurbulenceModel Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class TransportModel>

src/TurbulenceModels/compressible/turbulentFluidThermoModels/derivedFvPatchFields/externalWallHeatFluxTemperature/externalWallHeatFluxTemperatureFvPatchScalarField.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.
@@ -147,8 +147,8 @@ externalWallHeatFluxTemperatureFvPatchScalarField
                     << "\n number of layers for thicknessLayers and "
                     << "kappaLayers must be the same"
                     << "\n for patch " << p.name()
-                    << " of field " << dimensionedInternalField().name()
+                    << " of field " << internalField().name()
-                    << " in file " << dimensionedInternalField().objectPath()
+                    << " in file " << internalField().objectPath()
                     << exit(FatalIOError);
             }
         }
@@ -331,7 +331,7 @@ void Foam::externalWallHeatFluxTemperatureFvPatchScalarField::updateCoeffs()
 
         Info<< patch().boundaryMesh().mesh().name() << ':'
             << patch().name() << ':'
-            << this->internalField().name() << " :"
+            << internalField().name() << " :"
             << " heat transfer rate:" << Q
             << " wall temperature "
             << " min:" << gMin(*this)

src/TurbulenceModels/compressible/turbulentFluidThermoModels/derivedFvPatchFields/externalWallHeatFluxTemperature/externalWallHeatFluxTemperatureFvPatchScalarField.H

@@ -117,8 +117,8 @@ public:
         //- Operation mode enumeration
         enum operationMode
         {
-            fixedHeatFlux,
+            fixedHeatFlux,              //< Fixed heat flux
-            fixedHeatTransferCoeff,
+            fixedHeatTransferCoeff,     //< Fixed heat transfer coefficient
             unknown
         };
 

src/TurbulenceModels/compressible/turbulentFluidThermoModels/derivedFvPatchFields/fixedIncidentRadiation/fixedIncidentRadiationFvPatchScalarField.C

@@ -114,8 +114,8 @@ fixedIncidentRadiationFvPatchScalarField
     QrIncident_(ptf.QrIncident_)
 {}
 
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 void Foam::radiation::fixedIncidentRadiationFvPatchScalarField::autoMap
 (
@@ -159,15 +159,12 @@ void Foam::radiation::fixedIncidentRadiationFvPatchScalarField::updateCoeffs()
 
     scalarField emissivity
     (
-        radiation.absorptionEmission().e()().boundaryField()
+        radiation.absorptionEmission().e()().boundaryField()[patch().index()]
-        [
-            patch().index()
-        ]
     );
 
     gradient() =
-        emissivity*
+        emissivity
-        (
+       *(
             QrIncident_
           - physicoChemical::sigma.value()*pow4(*this)
         )/kappa(*this);
@@ -179,7 +176,7 @@ void Foam::radiation::fixedIncidentRadiationFvPatchScalarField::updateCoeffs()
         scalar Qr = gSum(kappa(*this)*gradient()*patch().magSf());
         Info<< patch().boundaryMesh().mesh().name() << ':'
             << patch().name() << ':'
-            << this->dimensionedInternalField().name() << " -> "
+            << this->internalField().name() << " -> "
             << " radiativeFlux:" << Qr
             << " walltemperature "
             << " min:" << gMin(*this)

src/TurbulenceModels/compressible/turbulentFluidThermoModels/derivedFvPatchFields/temperatureCoupledBase/temperatureCoupledBase.C

@@ -135,7 +135,7 @@ Foam::tmp<Foam::scalarField> Foam::temperatureCoupledBase::kappa
                 const basicThermo& thermo =
                     mesh.lookupObject<basicThermo>(basicThermo::dictName);
 
-                return thermo.kappa(patchI);
+                return thermo.kappa(patchi);
             }
             else
             {

src/TurbulenceModels/compressible/turbulentFluidThermoModels/turbulentFluidThermoModels.C

@@ -100,9 +100,6 @@ makeLESModel(dynamicKEqn);
 #include "dynamicLagrangian.H"
 makeLESModel(dynamicLagrangian);
 
-#include "kOmegaSSTDES.H"
-makeLESModel(kOmegaSSTDES);
-
 #include "SpalartAllmarasDES.H"
 makeLESModel(SpalartAllmarasDES);
 

src/TurbulenceModels/incompressible/turbulentTransportModels/turbulentTransportModels.C

@@ -96,9 +96,6 @@ makeLESModel(dynamicKEqn);
 #include "dynamicLagrangian.H"
 makeLESModel(dynamicLagrangian);
 
-#include "kOmegaSSTDES.H"
-makeLESModel(kOmegaSSTDES);
-
 #include "SpalartAllmarasDES.H"
 makeLESModel(SpalartAllmarasDES);
 

src/TurbulenceModels/turbulenceModels/Base/kOmegaSST/kOmegaSSTBase.C

@@ -128,6 +128,28 @@ void kOmegaSSTBase<BasicEddyViscosityModel>::correctNut()
 }
 
 
+template<class BasicEddyViscosityModel>
+tmp<volScalarField::Internal> kOmegaSSTBase<BasicEddyViscosityModel>::Pk
+(
+    const volScalarField::Internal& G
+) const
+{
+    return min(G, (c1_*betaStar_)*this->k_()*this->omega_());
+}
+
+
+template<class BasicEddyViscosityModel>
+tmp<volScalarField::Internal>
+kOmegaSSTBase<BasicEddyViscosityModel>::epsilonByk
+(
+    const volScalarField::Internal& F1,
+    const volScalarField::Internal& F2
+) const
+{
+    return betaStar_*omega_();
+}
+
+
 template<class BasicEddyViscosityModel>
 tmp<fvScalarMatrix> kOmegaSSTBase<BasicEddyViscosityModel>::kSource() const
 {
@@ -409,7 +431,7 @@ void kOmegaSSTBase<BasicEddyViscosityModel>::correct()
     tgradU.clear();
 
     // Update omega and G at the wall
-    omega_.boundaryField().updateCoeffs();
+    omega_.boundaryFieldRef().updateCoeffs();
 
     volScalarField CDkOmega
     (
@@ -449,7 +471,7 @@ void kOmegaSSTBase<BasicEddyViscosityModel>::correct()
 
         omegaEqn.ref().relax();
         fvOptions.constrain(omegaEqn.ref());
-        omegaEqn.ref().boundaryManipulate(omega_.boundaryField());
+        omegaEqn.ref().boundaryManipulate(omega_.boundaryFieldRef());
         solve(omegaEqn);
         fvOptions.correct(omega_);
         bound(omega_, this->omegaMin_);

src/TurbulenceModels/turbulenceModels/Base/kOmegaSST/kOmegaSSTBase.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -52,7 +52,7 @@ Description
     and the addition of the optional F3 term for rough walls from
     \verbatim
         Hellsten, A. (1998).
-        "Some Improvements in Menter’s k-omega-SST turbulence model"
+        "Some Improvements in Menter's k-omega-SST turbulence model"
         29th AIAA Fluid Dynamics Conference, AIAA-98-2554.
     \endverbatim
 
@@ -202,8 +202,24 @@ protected:
         virtual void correctNut(const volScalarField& S2);
 
         virtual void correctNut();
+
+        //- Return k production rate
+        virtual tmp<volScalarField::Internal> Pk
+        (
+            const volScalarField::Internal& G
+        ) const;
+
+        //- Return epsilon/k which for standard RAS is betaStar*omega
+        virtual tmp<volScalarField::Internal> epsilonByk
+        (
+            const volScalarField::Internal& F1,
+            const volScalarField::Internal& F2
+        ) const;
+
         virtual tmp<fvScalarMatrix> kSource() const;
+
         virtual tmp<fvScalarMatrix> omegaSource() const;
+
         virtual tmp<fvScalarMatrix> Qsas
         (
             const volScalarField& S2,

src/TurbulenceModels/turbulenceModels/DES/SpalartAllmarasIDDES/SpalartAllmarasIDDES.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  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -98,7 +98,7 @@ tmp<volScalarField> SpalartAllmarasIDDES<BasicTurbulenceModel>::rd
             scalar(10)
         )
     );
-    tr.ref().boundaryField() == 0.0;
+    tr.ref().boundaryFieldRef() == 0.0;
 
     return tr;
 }

src/TurbulenceModels/turbulenceModels/DES/kOmegaSSTDDES/kOmegaSSTDDES.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -56,7 +56,7 @@ tmp<volScalarField> kOmegaSSTDDES<BasicTurbulenceModel>::rd
             scalar(10)
         )
     );
-    tr.ref().boundaryField() == 0.0;
+    tr.ref().boundaryFieldRef() == 0.0;
 
     return tr;
 }

src/TurbulenceModels/turbulenceModels/DES/kOmegaSSTDES/kOmegaSSTDES.C

@@ -179,7 +179,7 @@ void kOmegaSSTDES<BasicTurbulenceModel>::correct()
     tgradU.clear();
 
     // Update omega and G at the wall
-    omega.boundaryField().updateCoeffs();
+    omega.boundaryFieldRef().updateCoeffs();
 
     volScalarField CDkOmega
     (
@@ -208,7 +208,7 @@ void kOmegaSSTDES<BasicTurbulenceModel>::correct()
 
         omegaEqn.ref().relax();
 
-        omegaEqn.ref().boundaryManipulate(omega.boundaryField());
+        omegaEqn.ref().boundaryManipulate(omega.boundaryFieldRef());
 
         solve(omegaEqn);
         bound(omega, this->omegaMin_);

src/TurbulenceModels/turbulenceModels/DES/kOmegaSSTIDDES/kOmegaSSTIDDES.C

@@ -98,7 +98,7 @@ tmp<volScalarField> kOmegaSSTIDDES<BasicTurbulenceModel>::rd
             scalar(10)
         )
     );
-    tr.ref().boundaryField() == 0.0;
+    tr.ref().boundaryFieldRef() == 0.0;
 
     return tr;
 }

src/TurbulenceModels/turbulenceModels/LES/kOmegaSSTDES/kOmegaSSTDES.C

@@ -1,156 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     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 3 of the License, or
-    (at your option) any later version.
-
-    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-    for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
-\*---------------------------------------------------------------------------*/
-
-#include "kOmegaSSTDES.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-namespace LESModels
-{
-
-// * * * * * * * * * * * * Protected Member Functions  * * * * * * * * * * * //
-
-template<class BasicTurbulenceModel>
-tmp<volScalarField::Internal> kOmegaSSTDES<BasicTurbulenceModel>::Lt() const
-{
-    return sqrt(this->k_())/(this->betaStar_*this->omega_());
-}
-
-
-template<class BasicTurbulenceModel>
-tmp<volScalarField::Internal> kOmegaSSTDES<BasicTurbulenceModel>::FDES
-(
-    const volScalarField::Internal& F1,
-    const volScalarField::Internal& F2
-) const
-{
-    switch (FSST_)
-    {
-        case 0:
-            return max(Lt()/(CDES_*this->delta()()), scalar(1));
-        case 1:
-            return max(Lt()*(1 - F1)/(CDES_*this->delta()()), scalar(1));
-        case 2:
-            return max(Lt()*(1 - F2)/(CDES_*this->delta()()), scalar(1));
-        default:
-            FatalErrorInFunction
-                << "Incorrect FSST = " << FSST_ << ", should be 0, 1 or 2"
-                << exit(FatalError);
-            return F1;
-    }
-}
-
-
-template<class BasicTurbulenceModel>
-tmp<volScalarField::Internal> kOmegaSSTDES<BasicTurbulenceModel>::epsilonByk
-(
-    const volScalarField::Internal& F1,
-    const volScalarField::Internal& F2
-) const
-{
-    return this->betaStar_*this->omega_()*FDES(F1, F2);
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-template<class BasicTurbulenceModel>
-kOmegaSSTDES<BasicTurbulenceModel>::kOmegaSSTDES
-(
-    const alphaField& alpha,
-    const rhoField& rho,
-    const volVectorField& U,
-    const surfaceScalarField& alphaRhoPhi,
-    const surfaceScalarField& phi,
-    const transportModel& transport,
-    const word& propertiesName,
-    const word& type
-)
-:
-    kOmegaSST
-    <
-        LESeddyViscosity<BasicTurbulenceModel>,
-        BasicTurbulenceModel
-    >
-    (
-        type,
-        alpha,
-        rho,
-        U,
-        alphaRhoPhi,
-        phi,
-        transport,
-        propertiesName
-    ),
-
-    CDES_
-    (
-        dimensioned<scalar>::lookupOrAddToDict
-        (
-            "CDES",
-            this->coeffDict_,
-            0.61
-        )
-    ),
-    FSST_(this->coeffDict_.lookupOrDefault("FSST", 2))
-{
-    if (type == typeName)
-    {
-        this->printCoeffs(type);
-    }
-}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-template<class BasicTurbulenceModel>
-bool kOmegaSSTDES<BasicTurbulenceModel>::read()
-{
-    if
-    (
-        kOmegaSST<LESeddyViscosity<BasicTurbulenceModel>, BasicTurbulenceModel>
-        ::read()
-    )
-    {
-        CDES_.readIfPresent(this->coeffDict());
-        this->coeffDict().readIfPresent("FSST", FSST_);
-
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace LESModels
-} // End namespace Foam
-
-// ************************************************************************* //

src/TurbulenceModels/turbulenceModels/LES/kOmegaSSTDES/kOmegaSSTDES.H

@@ -1,174 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     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 3 of the License, or
-    (at your option) any later version.
-
-    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-    for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
-Class
-    Foam::LESModels::kOmegaSST
-
-Description
-    Implementation of the k-omega-SST-DES turbulence model for
-    incompressible and compressible flows.
-
-    DES model described in:
-    \verbatim
-        Menter, F. R., Kuntz, M., and Langtry, R. (2003).
-        Ten Years of Industrial Experience with the SST Turbulence Model.
-        Turbulence, Heat and Mass Transfer 4, ed: K. Hanjalic, Y. Nagano,
-        & M. Tummers, Begell House, Inc., 625 - 632.
-    \endverbatim
-
-    Optional support for zonal filtering based on F1 or F2 is provided as
-    described in the paper.
-
-    For further details of the implementation of the base k-omega-SST model
-    see Foam::kOmegaSST.
-
-Group
-    grpLESTurbulence
-
-See also
-    Foam::kOmegaSST
-
-SourceFiles
-    kOmegaSST.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef kOmegaSSTDES_H
-#define kOmegaSSTDES_H
-
-#include "kOmegaSSTBase.H"
-#include "LESModel.H"
-#include "LESeddyViscosity.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-namespace LESModels
-{
-
-/*---------------------------------------------------------------------------*\
-                          Class kOmegaSST Declaration
-\*---------------------------------------------------------------------------*/
-
-template<class BasicTurbulenceModel>
-class kOmegaSSTDES
-:
-    public Foam::kOmegaSST
-    <
-        LESeddyViscosity<BasicTurbulenceModel>,
-        BasicTurbulenceModel
-    >
-{
-
-protected:
-
-    // Protected data
-
-        // Model constants
-
-            //- DES coefficient
-            dimensionedScalar CDES_;
-
-            //- Zonal filter choice
-            //
-            //  - 0: no filtering
-            //  - 1: (1 - F1)
-            //  - 2: (1 - F2)
-            direction FSST_;
-
-
-    // Protected Member Functions
-
-        //- Return the turbulent length-scale
-        tmp<volScalarField::Internal> Lt() const;
-
-        //- The DES dissipation-rate multiplier with options zonal filtering
-        //  based on either F1 or F2
-        virtual tmp<volScalarField::Internal> FDES
-        (
-            const volScalarField::Internal& F1,
-            const volScalarField::Internal& F2
-        ) const;
-
-        //- Return epsilon/k which for standard RAS is betaStar*omega
-        virtual tmp<volScalarField::Internal> epsilonByk
-        (
-            const volScalarField::Internal& F1,
-            const volScalarField::Internal& F2
-        ) const;
-
-
-public:
-
-    typedef typename BasicTurbulenceModel::alphaField alphaField;
-    typedef typename BasicTurbulenceModel::rhoField rhoField;
-    typedef typename BasicTurbulenceModel::transportModel transportModel;
-
-
-    //- Runtime type information
-    TypeName("kOmegaSSTDES");
-
-
-    // Constructors
-
-        //- Construct from components
-        kOmegaSSTDES
-        (
-            const alphaField& alpha,
-            const rhoField& rho,
-            const volVectorField& U,
-            const surfaceScalarField& alphaRhoPhi,
-            const surfaceScalarField& phi,
-            const transportModel& transport,
-            const word& propertiesName = turbulenceModel::propertiesName,
-            const word& type = typeName
-        );
-
-
-    //- Destructor
-    virtual ~kOmegaSSTDES()
-    {}
-
-
-    // Member Functions
-
-        //- Read model coefficients if they have changed
-        virtual bool read();
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace LESModels
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-#ifdef NoRepository
-    #include "kOmegaSSTDES.C"
-#endif
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-#endif
-
-// ************************************************************************* //

src/TurbulenceModels/turbulenceModels/linearViscousStress/linearViscousStress.H

@@ -44,7 +44,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class linearViscousStress Declaration
+                     Class linearViscousStress Declaration
 \*---------------------------------------------------------------------------*/
 
 template<class BasicTurbulenceModel>

src/combustionModels/diffusionMulticomponent/diffusionMulticomponent.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2015 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2015-2016 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -36,40 +36,13 @@ void Foam::combustionModels::
 diffusionMulticomponent<CombThermoType, ThermoType>::init()
 {
     // Load default values
-    if (this->coeffs().found("Ci"))
+    this->coeffs().readIfPresent("Ci", Ci_);
-    {
+    this->coeffs().readIfPresent("YoxStream", YoxStream_);
-        this->coeffs().lookup("Ci") >> Ci_;
+    this->coeffs().readIfPresent("YfStream", YfStream_);
-    }
+    this->coeffs().readIfPresent("sigma", sigma_);
-
+    this->coeffs().readIfPresent("ftCorr", ftCorr_);
-    if (this->coeffs().found("YoxStream"))
+    this->coeffs().readIfPresent("alpha", alpha_);
-    {
+    this->coeffs().readIfPresent("laminarIgn", laminarIgn_);
-        this->coeffs().lookup("YoxStream") >> YoxStream_;
-    }
-
-    if (this->coeffs().found("YfStream"))
-    {
-        this->coeffs().lookup("YfStream") >> YfStream_;
-    }
-
-    if (this->coeffs().found("sigma"))
-    {
-        this->coeffs().lookup("sigma") >> sigma_;
-    }
-
-    if (this->coeffs().found("ftCorr"))
-    {
-        this->coeffs().lookup("ftCorr") >> ftCorr_;
-    }
-
-    if (this->coeffs().found("alpha"))
-    {
-        alpha_ = readScalar(this->coeffs().lookup("alpha"));
-    }
-
-    if (this->coeffs().found("laminarIgn"))
-    {
-        this->coeffs().lookup("laminarIgn") >> laminarIgn_;
-    }
 
     typedef typename Reaction<ThermoType>::specieCoeffs specieCoeffs;
 
@@ -142,7 +115,6 @@ diffusionMulticomponent<CombThermoType, ThermoType>::init()
         const scalar fStoich = 1.0/(1.0 + stoicRatio_[k]);
 
         Info << "stoichiometric mixture fraction : " << fStoich << endl;
-
     }
 }
 
@@ -164,7 +136,7 @@ diffusionMulticomponent
     specieThermo_
     (
         dynamic_cast<const reactingMixture<ThermoType>&>
-            (this->thermo()).speciesData()
+           (this->thermo()).speciesData()
     ),
     RijPtr_(reactions_.size()),
     Ci_(reactions_.size(), 1.0),
@@ -218,7 +190,6 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
 
         for (label k=0; k < nReactions; k++)
         {
-
             RijlPtr.set
             (
                 k,
@@ -246,8 +217,7 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
 
             if (laminarIgn_)
             {
-                Rijl.dimensionedInternalField() =
+                Rijl.ref() = -this->chemistryPtr_->calculateRR(k, fuelIndex);
-                    -this->chemistryPtr_->calculateRR(k, fuelIndex);
             }
 
 
@@ -287,11 +257,9 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
             (
                 "ft" + name(k),
                 (
-                    s_[k]*Yfuel
+                    s_[k]*Yfuel - (Yox - YoxStream_[k])
-                  - (Yox - YoxStream_[k])
                 )
-                /
+               /(
-                (
                     s_[k]*YfStream_[k] + YoxStream_[k]
                 )
             );
@@ -318,15 +286,9 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
               * exp(-sqr(ft - fStoich)/(2*sqr(sigma)))
             );
 
-            const volScalarField topHatFilter
+            const volScalarField topHatFilter(pos(filter - 1e-3));
-            (
-                pos(filter - 1e-3)
-            );
 
-            const volScalarField prob
+            const volScalarField prob("prob" + name(k), preExp*filter);
-            (
-                "prob" + name(k), preExp*filter
-            );
 
             const volScalarField RijkDiff
             (
@@ -383,8 +345,7 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
                 const scalar stoichCoeff = lhs[l].stoichCoeff;
 
                 this->chemistryPtr_->RR(lIndex) +=
-                    -Rijk*stoichCoeff*specieThermo_[lIndex].W()
+                   -Rijk*stoichCoeff*specieThermo_[lIndex].W()/fuelStoic/MwFuel;
-                   /fuelStoic/MwFuel;
 
             }
 
@@ -396,8 +357,7 @@ diffusionMulticomponent<CombThermoType, ThermoType>::correct()
                 const scalar stoichCoeff = rhs[r].stoichCoeff;
 
                 this->chemistryPtr_->RR(rIndex) +=
-                    Rijk*stoichCoeff*specieThermo_[rIndex].W()
+                    Rijk*stoichCoeff*specieThermo_[rIndex].W()/fuelStoic/MwFuel;
-                   /fuelStoic/MwFuel;
             }
         }
     }

src/dynamicMesh/fvMeshAdder/fvMeshAdderTemplates.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.
@@ -280,11 +280,9 @@ void Foam::fvMeshAdder::MapVolFields
         ++fieldIter
     )
     {
-        if (debug)
+        DebugPout
-        {
+            << "MapVolFields : Storing old time for " << fieldIter()->name()
-            Pout<< "MapVolFields : Storing old time for " << fieldIter()->name()
+            << endl;
-                << endl;
-        }
 
         const_cast<GeometricField<Type, fvPatchField, volMesh>*>(fieldIter())
             ->storeOldTimes();
@@ -310,11 +308,9 @@ void Foam::fvMeshAdder::MapVolFields
             const GeometricField<Type, fvPatchField, volMesh>& fldToAdd =
                 *fieldsToAdd[fld.name()];
 
-            if (debug)
+            DebugPout
-            {
+                << "MapVolFields : mapping " << fld.name()
-                Pout<< "MapVolFields : mapping " << fld.name()
+                << " and " << fldToAdd.name() << endl;
-                    << " and " << fldToAdd.name() << endl;
-            }
 
             MapVolField<Type>(meshMap, fld, fldToAdd);
         }
@@ -597,11 +593,9 @@ void Foam::fvMeshAdder::MapSurfaceFields
         ++fieldIter
     )
     {
-        if (debug)
+        DebugPout
-        {
+            << "MapSurfaceFields : Storing old time for "
-            Pout<< "MapSurfaceFields : Storing old time for "
+            << fieldIter()->name() << endl;
-                << fieldIter()->name() << endl;
-        }
 
         const_cast<fldType*>(fieldIter())->storeOldTimes();
     }
@@ -621,11 +615,9 @@ void Foam::fvMeshAdder::MapSurfaceFields
         {
             const fldType& fldToAdd = *fieldsToAdd[fld.name()];
 
-            if (debug)
+            DebugPout
-            {
+                << "MapSurfaceFields : mapping " << fld.name()
-                Pout<< "MapSurfaceFields : mapping " << fld.name()
+                << " and " << fldToAdd.name() << endl;
-                    << " and " << fldToAdd.name() << endl;
-            }
 
             MapSurfaceField<Type>(meshMap, fld, fldToAdd);
         }
@@ -697,11 +689,9 @@ void Foam::fvMeshAdder::MapDimFields
         {
             const fldType& fldToAdd = *fieldsToAdd[fld.name()];
 
-            if (debug)
+            DebugPout
-            {
+                << "MapDimFields : mapping " << fld.name()
-                Pout<< "MapDimFields : mapping " << fld.name()
+                << " and " << fldToAdd.name() << endl;
-                    << " and " << fldToAdd.name() << endl;
-            }
 
             MapDimField<Type>(meshMap, fld, fldToAdd);
         }
@@ -716,80 +706,4 @@ void Foam::fvMeshAdder::MapDimFields
 }
 
 
-template<class Type>
-void Foam::fvMeshAdder::MapDimField
-(
-    const mapAddedPolyMesh& meshMap,
-
-    DimensionedField<Type, volMesh>& fld,
-    const DimensionedField<Type, volMesh>& fldToAdd
-)
-{
-    const fvMesh& mesh = fld.mesh();
-
-    // Store old field
-    Field<Type> oldField(fld);
-
-    fld.setSize(mesh.nCells());
-
-    fld.rmap(oldField, meshMap.oldCellMap());
-    fld.rmap(fldToAdd, meshMap.addedCellMap());
-}
-
-
-template<class Type>
-void Foam::fvMeshAdder::MapDimFields
-(
-    const mapAddedPolyMesh& meshMap,
-    const fvMesh& mesh,
-    const fvMesh& meshToAdd
-)
-{
-    typedef DimensionedField<Type, volMesh> fldType;
-
-    // Note: use strict flag on lookupClass to avoid picking up
-    //       volFields
-    HashTable<const fldType*> fields
-    (
-        mesh.objectRegistry::lookupClass<fldType>(true)
-    );
-
-    HashTable<const fldType*> fieldsToAdd
-    (
-        meshToAdd.objectRegistry::lookupClass<fldType>(true)
-    );
-
-    for
-    (
-        typename HashTable<const fldType*>::
-            iterator fieldIter = fields.begin();
-        fieldIter != fields.end();
-        ++fieldIter
-    )
-    {
-        fldType& fld = const_cast<fldType&>(*fieldIter());
-
-        if (fieldsToAdd.found(fld.name()))
-        {
-            const fldType& fldToAdd = *fieldsToAdd[fld.name()];
-
-            if (debug)
-            {
-                Pout<< "MapDimFields : mapping " << fld.name()
-                    << " and " << fldToAdd.name() << endl;
-            }
-
-            MapDimField<Type>(meshMap, fld, fldToAdd);
-        }
-        else
-        {
-            WarningIn("fvMeshAdder::MapDimFields(..)")
-                << "Not mapping field " << fld.name()
-                << " since not present on mesh to add"
-                << endl;
-        }
-    }
-}
-
-
 // ************************************************************************* //

src/dynamicMesh/fvMeshDistribute/fvMeshDistribute.C

@@ -189,13 +189,14 @@ Foam::labelList Foam::fvMeshDistribute::select
 }
 
 
-// Check all procs have same names and in exactly same order.
 void Foam::fvMeshDistribute::checkEqualWordList
 (
     const string& msg,
     const wordList& lst
 )
 {
+    // Check all procs have same names and in exactly same order.
+
     List<wordList> allNames(Pstream::nProcs());
     allNames[Pstream::myProcNo()] = lst;
     Pstream::gatherList(allNames);
@@ -235,7 +236,6 @@ Foam::wordList Foam::fvMeshDistribute::mergeWordList(const wordList& procNames)
 }
 
 
-// Print some info on mesh.
 void Foam::fvMeshDistribute::printMeshInfo(const fvMesh& mesh)
 {
     Pout<< "Primitives:" << nl
@@ -322,9 +322,10 @@ void Foam::fvMeshDistribute::printCoupleInfo
 }
 
 
-// Finds (non-empty) patch that exposed internal and proc faces can be put into.
 Foam::label Foam::fvMeshDistribute::findNonEmptyPatch() const
 {
+    // Finds (non-empty) patch that exposed internal and proc faces can be
+    // put into.
     const polyBoundaryMesh& patches = mesh_.boundaryMesh();
 
     label nonEmptyPatchi = -1;
@@ -412,18 +413,22 @@ Foam::tmp<Foam::surfaceScalarField> Foam::fvMeshDistribute::generateTestField
 
     const surfaceVectorField n(mesh.Sf()/mesh.magSf());
 
-    forAll(fld, faceI)
+    forAll(fld, facei)
     {
-        fld[faceI] = (n[faceI] & testNormal);
+        fld[facei] = (n[facei] & testNormal);
     }
-    forAll(fld.boundaryField(), patchI)
+
+    surfaceScalarField::Boundary& fluxBf = fld.boundaryFieldRef();
+    const surfaceVectorField::Boundary& nBf = n.boundaryField();
+
+    forAll(fluxBf, patchi)
     {
-        fvsPatchScalarField& fvp = fld.boundaryField()[patchI];
+        fvsPatchScalarField& fvp = fluxBf[patchi];
 
         scalarField newPfld(fvp.size());
         forAll(newPfld, i)
         {
-            newPfld[i] = (n.boundaryField()[patchI][i] & testNormal);
+            newPfld[i] = (nBf[patchi][i] & testNormal);
         }
         fvp == newPfld;
     }
@@ -441,41 +446,41 @@ void Foam::fvMeshDistribute::testField(const surfaceScalarField& fld)
 
     const surfaceVectorField n(mesh.Sf()/mesh.magSf());
 
-    forAll(fld, faceI)
+    forAll(fld, facei)
     {
-        scalar cos = (n[faceI] & testNormal);
+        scalar cos = (n[facei] & testNormal);
 
-        if (mag(cos-fld[faceI]) > 1e-6)
+        if (mag(cos - fld[facei]) > 1e-6)
         {
             //FatalErrorInFunction
             WarningInFunction
-                << "On internal face " << faceI << " at "
+                << "On internal face " << facei << " at "
-                << mesh.faceCentres()[faceI]
+                << mesh.faceCentres()[facei]
-                << " the field value is " << fld[faceI]
+                << " the field value is " << fld[facei]
                 << " whereas cos angle of " << testNormal
-                << " with mesh normal " << n[faceI]
+                << " with mesh normal " << n[facei]
                 << " is " << cos
                 //<< exit(FatalError);
                 << endl;
         }
     }
-    forAll(fld.boundaryField(), patchI)
+    forAll(fld.boundaryField(), patchi)
     {
-        const fvsPatchScalarField& fvp = fld.boundaryField()[patchI];
+        const fvsPatchScalarField& fvp = fld.boundaryField()[patchi];
-        const fvsPatchVectorField& np = n.boundaryField()[patchI];
+        const fvsPatchVectorField& np = n.boundaryField()[patchi];
 
         forAll(fvp, i)
         {
             scalar cos = (np[i] & testNormal);
 
-            if (mag(cos-fvp[i]) > 1e-6)
+            if (mag(cos - fvp[i]) > 1e-6)
             {
-                label faceI = fvp.patch().start()+i;
+                label facei = fvp.patch().start()+i;
                 //FatalErrorInFunction
                 WarningInFunction
-                    << "On face " << faceI
+                    << "On face " << facei
                     << " on patch " << fvp.patch().name()
-                    << " at " << mesh.faceCentres()[faceI]
+                    << " at " << mesh.faceCentres()[facei]
                     << " the field value is " << fvp[i]
                     << " whereas cos angle of " << testNormal
                     << " with mesh normal " << np[i]
@@ -488,13 +493,14 @@ void Foam::fvMeshDistribute::testField(const surfaceScalarField& fld)
 }
 
 
-// Delete all processor patches. Move any processor faces into the last
-// non-processor patch.
 Foam::autoPtr<Foam::mapPolyMesh> Foam::fvMeshDistribute::deleteProcPatches
 (
     const label destinationPatch
 )
 {
+    // Delete all processor patches. Move any processor faces into the last
+    // non-processor patch.
+
     // New patchID per boundary faces to be repatched. Is -1 (no change)
     // or new patchID
     labelList newPatchID(mesh_.nFaces() - mesh_.nInternalFaces(), -1);
@@ -535,23 +541,23 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::fvMeshDistribute::deleteProcPatches
     // Delete (now empty) processor patches.
     {
         labelList oldToNew(identity(mesh_.boundaryMesh().size()));
-        label newI = 0;
+        label newi = 0;
         // Non processor patches first
         forAll(mesh_.boundaryMesh(), patchi)
         {
             if (!isA<processorPolyPatch>(mesh_.boundaryMesh()[patchi]))
             {
-                oldToNew[patchi] = newI++;
+                oldToNew[patchi] = newi++;
             }
         }
-        label nNonProcPatches = newI;
+        label nNonProcPatches = newi;
 
         // Processor patches as last
         forAll(mesh_.boundaryMesh(), patchi)
         {
             if (isA<processorPolyPatch>(mesh_.boundaryMesh()[patchi]))
             {
-                oldToNew[patchi] = newI++;
+                oldToNew[patchi] = newi++;
             }
         }
         fvMeshTools::reorderPatches(mesh_, oldToNew, nNonProcPatches, false);
@@ -561,7 +567,6 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::fvMeshDistribute::deleteProcPatches
 }
 
 
-// Repatch the mesh.
 Foam::autoPtr<Foam::mapPolyMesh> Foam::fvMeshDistribute::repatch
 (
     const labelList& newPatchID,         // per boundary face -1 or new patchID
@@ -2521,7 +2526,7 @@ Foam::autoPtr<Foam::mapDistributePolyMesh> Foam::fvMeshDistribute::distribute
             const labelList& oldPatchMap = map().oldPatchMap();
 
             //Note: old mesh faces never flipped!
-            forAll(constructPatchMap, procI)
+            forAll(constructPatchMap, proci)
             {
                 if (proci != sendProc && constructPatchMap[proci].size())
                 {

src/dynamicMesh/motionSolver/velocityDisplacement/velocityDisplacementMotionSolver.C

@@ -48,10 +48,7 @@ namespace Foam
 Foam::wordList
 Foam::velocityDisplacementMotionSolver::pointDisplacementBoundaryTypes() const
 {
-    const pointVectorField::GeometricBoundaryField& pmUbf
+    const pointVectorField::Boundary& pmUbf(pointMotionU().boundaryField());
-    (
-        pointMotionU().boundaryField()
-    );
 
     wordList cmUbf = pmUbf.types();
 
@@ -93,7 +90,7 @@ Foam::velocityDisplacementMotionSolver::velocityDisplacementMotionSolver
         pointDisplacementBoundaryTypes()
     );
 
-    pointDisplacement.internalField() = mesh.points() - points0;
+    pointDisplacement.primitiveFieldRef() = mesh.points() - points0;
 
     displacementMotionSolverPtr_.set
     (
@@ -155,6 +152,8 @@ void Foam::velocityDisplacementMotionSolver::solve()
     // Update the velocity boundary conditions
     pointMotionU().correctBoundaryConditions();
 
+    pointVectorField::Boundary& dispBf = displacement.boundaryFieldRef();
+
     // Update the displacement boundary conditions
     forAll(pointMotionU().boundaryField(), patchI)
     {
@@ -163,7 +162,7 @@ void Foam::velocityDisplacementMotionSolver::solve()
             pointMotionU().boundaryField()[patchI]
         );
 
-        displacement.boundaryField()[patchI] ==
+        dispBf[patchI] ==
             patchField.patchInternalField()*deltaT
           + patchField.patchInternalField(displacementOld);
     }
@@ -172,8 +171,8 @@ void Foam::velocityDisplacementMotionSolver::solve()
     displacementMotionSolverPtr_->solve();
 
     // Update the velocity
-    pointMotionU().internalField() =
+    pointMotionU().primitiveFieldRef() =
-        (displacement.internalField() - displacementOld)/deltaT;
+        (displacement.primitiveField() - displacementOld)/deltaT;
 }
 
 

src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.C

@@ -50,11 +50,11 @@ namespace Foam
 Foam::label Foam::addPatchCellLayer::nbrFace
 (
     const labelListList& edgeFaces,
-    const label edgeI,
+    const label edgei,
     const label facei
 )
 {
-    const labelList& eFaces = edgeFaces[edgeI];
+    const labelList& eFaces = edgeFaces[edgei];
 
     if (eFaces.size() == 2)
     {
@@ -97,19 +97,19 @@ bool Foam::addPatchCellLayer::sameEdgeNeighbour
     const boolList& doneEdge,
     const label thisGlobalFacei,
     const label nbrGlobalFacei,
-    const label edgeI
+    const label edgei
 ) const
 {
-    const edge& e = pp.edges()[edgeI];
+    const edge& e = pp.edges()[edgei];
 
     return
-        !doneEdge[edgeI]                            // not yet handled
+        !doneEdge[edgei]                            // not yet handled
      && (
             addedPoints_[e[0]].size()               // is extruded
          || addedPoints_[e[1]].size()
         )
      && (
-            nbrFace(globalEdgeFaces, edgeI, thisGlobalFacei)
+            nbrFace(globalEdgeFaces, edgei, thisGlobalFacei)
          == nbrGlobalFacei  // is to same neighbour
         );
 }
@@ -135,12 +135,12 @@ Foam::labelPair Foam::addPatchCellLayer::getEdgeString
     // Get edge that hasn't been done yet but needs extrusion
     forAll(fEdges, fp)
     {
-        label edgeI = fEdges[fp];
+        label edgei = fEdges[fp];
-        const edge& e = pp.edges()[edgeI];
+        const edge& e = pp.edges()[edgei];
 
         if
         (
-            !doneEdge[edgeI]
+            !doneEdge[edgei]
          && ( addedPoints_[e[0]].size() || addedPoints_[e[1]].size() )
         )
         {
@@ -229,14 +229,14 @@ Foam::label Foam::addPatchCellLayer::addSideFace
     const labelListList& addedCells,    // per pp face the new extruded cell
     const face& newFace,
     const label newPatchID,
-    const label zoneI,
+    const label zonei,
     const bool edgeFlip,
-    const label inflateFaceI,
+    const label inflateFacei,
 
-    const label ownFaceI,               // pp face that provides owner
+    const label ownFacei,               // pp face that provides owner
-    const label nbrFaceI,
+    const label nbrFacei,
-    const label meshEdgeI,              // corresponding mesh edge
+    const label meshEdgei,              // corresponding mesh edge
-    const label layerI,                 // layer
+    const label layeri,                 // layer
     const label numEdgeFaces,           // number of layers for edge
     const labelList& meshFaces,         // precalculated edgeFaces
     polyTopoChange& meshMod
@@ -261,18 +261,18 @@ Foam::label Foam::addPatchCellLayer::addSideFace
         if (addedCells[ownFacei].size() < numEdgeFaces)
         {
             label offset = numEdgeFaces - addedCells[ownFacei].size();
-            if (layerI <= offset)
+            if (layeri <= offset)
             {
                 layerOwn = 0;
             }
             else
             {
-                layerOwn = layerI - offset;
+                layerOwn = layeri - offset;
             }
         }
         else
         {
-            layerOwn = layerI;
+            layerOwn = layeri;
         }
 
 
@@ -313,15 +313,15 @@ Foam::label Foam::addPatchCellLayer::addSideFace
             label offset =
                 addedCells[ownFacei].size() - addedCells[nbrFacei].size();
 
-            layerOwn = layerI;
+            layerOwn = layeri;
 
-            if (layerI <= offset)
+            if (layeri <= offset)
             {
                 layerNbr = 0;
             }
             else
             {
-                layerNbr = layerI - offset;
+                layerNbr = layeri - offset;
             }
         }
         else if (addedCells[nbrFacei].size() > addedCells[ownFacei].size())
@@ -329,22 +329,22 @@ Foam::label Foam::addPatchCellLayer::addSideFace
             label offset =
                 addedCells[nbrFacei].size() - addedCells[ownFacei].size();
 
-            layerNbr = layerI;
+            layerNbr = layeri;
 
-            if (layerI <= offset)
+            if (layeri <= offset)
             {
                 layerOwn = 0;
             }
             else
             {
-                layerOwn = layerI - offset;
+                layerOwn = layeri - offset;
             }
         }
         else
         {
             // Same number of layers on both sides.
-            layerNbr = layerI;
+            layerNbr = layeri;
-            layerOwn = layerI;
+            layerOwn = layeri;
         }
 
 
@@ -364,7 +364,7 @@ Foam::label Foam::addPatchCellLayer::addSideFace
         }
 
 
-        addedFaceI = meshMod.setAction
+        addedFacei = meshMod.setAction
         (
             polyAddFace
             (
@@ -422,13 +422,13 @@ void Foam::addPatchCellLayer::setFaceProps
     const label facei,
 
     label& patchi,
-    label& zoneI,
+    label& zonei,
     bool& zoneFlip
 )
 {
     patchi = mesh.boundaryMesh().whichPatch(facei);
     zonei = mesh.faceZones().whichZone(facei);
-    if (zoneI != -1)
+    if (zonei != -1)
     {
         label index = mesh.faceZones()[zonei].whichFace(facei);
         zoneFlip = mesh.faceZones()[zonei].flipMap()[index];
@@ -716,13 +716,13 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
     // processor patch or create interprocessor-patch if necessary.
     // Sets edgePatchID[edgeI] but none of the other quantities
 
-    forAll(globalEdgeFaces, edgeI)
+    forAll(globalEdgeFaces, edgei)
     {
-        const labelList& eGlobalFaces = globalEdgeFaces[edgeI];
+        const labelList& eGlobalFaces = globalEdgeFaces[edgei];
         if
         (
             eGlobalFaces.size() == 2
-         && pp.edgeFaces()[edgeI].size() == 1
+         && pp.edgeFaces()[edgei].size() == 1
         )
         {
             // Locally but not globally a boundary edge. Hence a coupled
@@ -746,11 +746,11 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
             {
                 if (findIndex(gd[Pstream::myProcNo()], otherProci) != -1)
                 {
-                    // There is already a processorPolyPatch to otherProcI.
+                    // There is already a processorPolyPatch to otherProci.
                     // Use it. Note that we can only index procPatchMap
                     // if the processor actually is a neighbour processor
                     // so that is why we first check.
-                    edgePatchID[edgeI] = gd.procPatchMap()[otherProci];
+                    edgePatchID[edgei] = gd.procPatchMap()[otherProci];
                 }
                 else
                 {
@@ -786,20 +786,20 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
         {
             UIndirectList<label> ppFaces(pp.addressing(), edgeFaces[edgei]);
 
-            label meshEdgeI = meshEdges[edgeI];
+            label meshEdgei = meshEdges[edgei];
             const labelList& meshFaces = mesh.edgeFaces
             (
-                meshEdgeI,
+                meshEdgei,
                 dynMeshEdgeFaces
             );
 
-            if (edgeFaces[edgeI].size() == 2)
+            if (edgeFaces[edgei].size() == 2)
             {
                 // Internal edge. Look at any face (internal or boundary) to
                 // determine extrusion properties. First one that has zone
                 // info wins
 
-                label dummyPatchI = -1;
+                label dummyPatchi = -1;
                 findZoneFace
                 (
                     true,               // useInternalFaces,
@@ -850,7 +850,7 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
     // Now hopefully every boundary edge has a edge patch. Check
     if (debug)
     {
-        forAll(edgeFaces, edgeI)
+        forAll(edgeFaces, edgei)
         {
             if (edgeFaces[edgei].size() == 1 && edgePatchID[edgei] == -1)
             {
@@ -882,32 +882,32 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
             label myFaceI = pp.addressing()[edgeFaces[edgei][0]];
 
             // Pick up any boundary face on this edge and use its properties
-            label meshEdgeI = meshEdges[edgeI];
+            label meshEdgei = meshEdges[edgei];
             const labelList& meshFaces = mesh.edgeFaces
             (
-                meshEdgeI,
+                meshEdgei,
                 dynMeshEdgeFaces
             );
 
             forAll(meshFaces, k)
             {
-                label faceI = meshFaces[k];
+                label facei = meshFaces[k];
 
-                if (faceI != myFaceI && !mesh.isInternalFace(faceI))
+                if (facei != myFaceI && !mesh.isInternalFace(facei))
                 {
-                    if (patches.whichPatch(faceI) == edgePatchID[edgeI])
+                    if (patches.whichPatch(facei) == edgePatchID[edgei])
                     {
                         setFaceProps
                         (
                             mesh,
                             pp,
-                            edgeI,
+                            edgei,
-                            faceI,
+                            facei,
 
-                            edgePatchID[edgeI],
+                            edgePatchID[edgei],
-                            edgeZoneID[edgeI],
+                            edgeZoneID[edgei],
-                            edgeFlip[edgeI],
+                            edgeFlip[edgei],
-                            inflateFaceID[edgeI]
+                            inflateFaceID[edgei]
                         );
                         break;
                     }
@@ -947,17 +947,17 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
         boolList cppEdgeFlip(cpp.nEdges(), false);
         forAll(coupledEdges, i)
         {
-            label cppEdgeI = coupledEdges[i];
+            label cppEdgei = coupledEdges[i];
-            label ppEdgeI = patchEdges[i];
+            label ppEdgei = patchEdges[i];
 
-            cppEdgeZoneID[cppEdgeI] = edgeZoneID[ppEdgeI];
+            cppEdgeZoneID[cppEdgei] = edgeZoneID[ppEdgei];
             if (sameEdgeOrientation[i])
             {
-                cppEdgeFlip[cppEdgeI] = edgeFlip[ppEdgeI];
+                cppEdgeFlip[cppEdgei] = edgeFlip[ppEdgei];
             }
             else
             {
-                cppEdgeFlip[cppEdgeI] = !edgeFlip[ppEdgeI];
+                cppEdgeFlip[cppEdgei] = !edgeFlip[ppEdgei];
             }
         }
 
@@ -989,17 +989,17 @@ void Foam::addPatchCellLayer::calcExtrudeInfo
         // Convert data on coupled edges to pp edges
         forAll(coupledEdges, i)
         {
-            label cppEdgeI = coupledEdges[i];
+            label cppEdgei = coupledEdges[i];
-            label ppEdgeI = patchEdges[i];
+            label ppEdgei = patchEdges[i];
 
-            edgeZoneID[ppEdgeI] = cppEdgeZoneID[cppEdgeI];
+            edgeZoneID[ppEdgei] = cppEdgeZoneID[cppEdgei];
             if (sameEdgeOrientation[i])
             {
-                edgeFlip[ppEdgeI] = cppEdgeFlip[cppEdgeI];
+                edgeFlip[ppEdgei] = cppEdgeFlip[cppEdgei];
             }
             else
             {
-                edgeFlip[ppEdgeI] = !cppEdgeFlip[cppEdgeI];
+                edgeFlip[ppEdgei] = !cppEdgeFlip[cppEdgei];
             }
         }
     }
@@ -1070,11 +1070,11 @@ void Foam::addPatchCellLayer::setRefinement
         }
     }
 
-    forAll(globalEdgeFaces, edgeI)
+    forAll(globalEdgeFaces, edgei)
     {
-        if (globalEdgeFaces[edgeI].size() > 2)
+        if (globalEdgeFaces[edgei].size() > 2)
         {
-            const edge& e = pp.edges()[edgeI];
+            const edge& e = pp.edges()[edgei];
 
             if (nPointLayers[e[0]] > 0 || nPointLayers[e[1]] > 0)
             {
@@ -1082,10 +1082,10 @@ void Foam::addPatchCellLayer::setRefinement
                     << "Trying to extrude edge "
                     << e.line(pp.localPoints())
                     << " which is non-manifold (has "
-                    << globalEdgeFaces[edgeI].size()
+                    << globalEdgeFaces[edgei].size()
                     << " local or coupled faces using it)"
                     << " of which "
-                    << pp.edgeFaces()[edgeI].size()
+                    << pp.edgeFaces()[edgei].size()
                     << " local"
                     << abort(FatalError);
             }
@@ -1207,15 +1207,15 @@ void Foam::addPatchCellLayer::setRefinement
         // sides decide the same.
         // ~~~~~~~~~~~~~~~~~~~~~~
 
-        for (label edgeI = pp.nInternalEdges(); edgeI < pp.nEdges(); edgeI++)
+        for (label edgei = pp.nInternalEdges(); edgei < pp.nEdges(); edgei++)
         {
-            const edge& e = pp.edges()[edgeI];
+            const edge& e = pp.edges()[edgei];
 
             if (nPointLayers[e[0]] > 0 || nPointLayers[e[1]] > 0)
             {
                 // Edge is to become a face
 
-                const labelList& eFaces = pp.edgeFaces()[edgeI];
+                const labelList& eFaces = pp.edgeFaces()[edgei];
 
                 // First check: pp should be single connected.
                 if (eFaces.size() != 1)
@@ -1230,10 +1230,10 @@ void Foam::addPatchCellLayer::setRefinement
 
                 label myFacei = pp.addressing()[eFaces[0]];
 
-                label meshEdgeI = meshEdges[edgeI];
+                label meshEdgei = meshEdges[edgei];
 
                 // Mesh faces using edge
-                const labelList& meshFaces = mesh_.edgeFaces(meshEdgeI, ef);
+                const labelList& meshFaces = mesh_.edgeFaces(meshEdgei, ef);
 
                 // Check that there is only one patchface using edge.
                 const polyBoundaryMesh& patches = mesh_.boundaryMesh();
@@ -1609,26 +1609,26 @@ void Foam::addPatchCellLayer::setRefinement
         // partial list synchronisation.
         labelList meshEdgeLayers(mesh_.nEdges(), -1);
 
-        forAll(meshEdges, edgeI)
+        forAll(meshEdges, edgei)
         {
-            const edge& e = edges[edgeI];
+            const edge& e = edges[edgei];
 
-            label meshEdgeI = meshEdges[edgeI];
+            label meshEdgei = meshEdges[edgei];
 
             if ((nPointLayers[e[0]] == 0) && (nPointLayers[e[1]] == 0))
             {
-                meshEdgeLayers[meshEdgeI] = 0;
+                meshEdgeLayers[meshEdgei] = 0;
             }
             else
             {
-                const labelList& eFaces = pp.edgeFaces()[edgeI];
+                const labelList& eFaces = pp.edgeFaces()[edgei];
 
                 forAll(eFaces, i)
                 {
-                    meshEdgeLayers[meshEdgeI] = max
+                    meshEdgeLayers[meshEdgei] = max
                     (
                         nFaceLayers[eFaces[i]],
-                        meshEdgeLayers[meshEdgeI]
+                        meshEdgeLayers[meshEdgei]
                     );
                 }
             }
@@ -1642,9 +1642,9 @@ void Foam::addPatchCellLayer::setRefinement
             label(0)            // initial value
         );
 
-        forAll(meshEdges, edgeI)
+        forAll(meshEdges, edgei)
         {
-            edgeLayers[edgeI] = meshEdgeLayers[meshEdges[edgeI]];
+            edgeLayers[edgei] = meshEdgeLayers[meshEdges[edgei]];
         }
     }
 
@@ -1718,11 +1718,11 @@ void Foam::addPatchCellLayer::setRefinement
                 // because we loop in incrementing order as well we will
                 // always have nbrFacei > patchFacei.
 
-                label startEdgeI = fEdges[startFp];
+                label startEdgei = fEdges[startFp];
 
-                label meshEdgeI = meshEdges[startEdgeI];
+                label meshEdgei = meshEdges[startEdgei];
 
-                label numEdgeSideFaces = edgeLayers[startEdgeI];
+                label numEdgeSideFaces = edgeLayers[startEdgei];
 
                 for (label i = 0; i < numEdgeSideFaces; i++)
                 {
@@ -1897,9 +1897,9 @@ void Foam::addPatchCellLayer::setRefinement
                                             ) << nl
                                         << "Layer:" << i
                                         << " out of:" << numEdgeSideFaces << nl
-                                        << "ExtrudeEdge:" << meshEdgeI
+                                        << "ExtrudeEdge:" << meshEdgei
                                         << " at:"
-                                        <<  mesh_.edges()[meshEdgeI].line
+                                        <<  mesh_.edges()[meshEdgei].line
                                             (
                                                 mesh_.points()
                                             ) << nl
@@ -1924,13 +1924,13 @@ void Foam::addPatchCellLayer::setRefinement
                         label nbrFacei = nbrFace
                         (
                             pp.edgeFaces(),
-                            startEdgeI,
+                            startEdgei,
                             patchFacei
                         );
 
                         const labelList& meshFaces = mesh_.edgeFaces
                         (
-                            meshEdgeI,
+                            meshEdgei,
                             ef
                         );
 
@@ -1938,9 +1938,9 @@ void Foam::addPatchCellLayer::setRefinement
                         // of face edges so face orientation will be opposite
                         // that of the patch edge
                         bool zoneFlip = false;
-                        if (edgeZoneID[startEdgeI] != -1)
+                        if (edgeZoneID[startEdgei] != -1)
                         {
-                            zoneFlip = !edgeFlip[startEdgeI];
+                            zoneFlip = !edgeFlip[startEdgei];
                         }
 
                         addSideFace
@@ -1949,14 +1949,14 @@ void Foam::addPatchCellLayer::setRefinement
                             addedCells,
 
                             newFace,                // vertices of new face
-                            edgePatchID[startEdgeI],// -1 or patch for face
+                            edgePatchID[startEdgei],// -1 or patch for face
-                            edgeZoneID[startEdgeI],
+                            edgeZoneID[startEdgei],
                             zoneFlip,
-                            inflateFaceID[startEdgeI],
+                            inflateFaceID[startEdgei],
 
-                            patchFaceI,
+                            patchFacei,
-                            nbrFaceI,
+                            nbrFacei,
-                            meshEdgeI,          // (mesh) edge to inflate
+                            meshEdgei,          // (mesh) edge to inflate
                             i,                  // layer
                             numEdgeSideFaces,   // num layers
                             meshFaces,          // edgeFaces

src/dynamicMesh/polyTopoChange/polyTopoChange/hexRef8/refinementHistory.C

@@ -557,7 +557,6 @@ void Foam::refinementHistory::apply
 Foam::refinementHistory::refinementHistory(const IOobject& io)
 :
     regIOobject(io),
-    refCount(),
     active_(false)
 {
     // Warn for MUST_READ_IF_MODIFIED
@@ -600,7 +599,6 @@ Foam::refinementHistory::refinementHistory
 )
 :
     regIOobject(io),
-    refCount(),
     active_(active),
     splitCells_(splitCells),
     freeSplitCells_(0),
@@ -642,7 +640,6 @@ Foam::refinementHistory::refinementHistory
 )
 :
     regIOobject(io),
-    refCount(),
     active_(false),
     freeSplitCells_(0)
 {
@@ -698,7 +695,6 @@ Foam::refinementHistory::refinementHistory
 )
 :
     regIOobject(io),
-    refCount(),
     active_(active),
     freeSplitCells_(0)
 {
@@ -750,7 +746,6 @@ Foam::refinementHistory::refinementHistory
 )
 :
     regIOobject(io),
-    refCount(),
     active_(rh.active_),
     splitCells_(rh.splitCells()),
     freeSplitCells_(rh.freeSplitCells()),
@@ -773,7 +768,6 @@ Foam::refinementHistory::refinementHistory
 )
 :
     regIOobject(io),
-    refCount(),
     active_(false)
 {
     if
@@ -886,7 +880,6 @@ Foam::refinementHistory::refinementHistory
 Foam::refinementHistory::refinementHistory(const IOobject& io, Istream& is)
 :
     regIOobject(io),
-    refCount(),
     splitCells_(is),
     freeSplitCells_(0),
     visibleCells_(is)

src/dynamicMesh/polyTopoChange/polyTopoChange/hexRef8/refinementHistory.H

@@ -71,7 +71,6 @@ SourceFiles
 #ifndef refinementHistory_H
 #define refinementHistory_H
 
-#include "UPtrList.H"
 #include "DynamicList.H"
 #include "labelList.H"
 #include "FixedList.H"
@@ -99,13 +98,12 @@ Ostream& operator<<(Ostream&, const refinementHistory&);
 
 
 /*---------------------------------------------------------------------------*\
-                           Class refinementHistory Declaration
+                      Class refinementHistory Declaration
 \*---------------------------------------------------------------------------*/
 
 class refinementHistory
 :
-    public regIOobject,
+    public regIOobject
-    public refCount
 {
 public:
 

src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C

@@ -481,9 +481,9 @@ void Foam::polyTopoChange::makeCells
         if (faceOwner_[facei] < 0)
         {
             pointField newPoints;
-            if (faceI < faces_.size())
+            if (facei < faces_.size())
             {
-                const face& f = faces_[faceI];
+                const face& f = faces_[facei];
                 newPoints.setSize(f.size(), vector::max);
                 forAll(f, fp)
                 {

src/finiteVolume/fields/fvPatchFields/derived/turbulentDFSEMInlet/turbulentDFSEMInletFvPatchVectorField.C

@@ -29,6 +29,7 @@ License
 #include "fvPatchFieldMapper.H"
 #include "momentOfInertia.H"
 #include "cartesianCS.H"
+#include "IFstream.H"
 #include "OFstream.H"
 #include "globalIndex.H"
 
@@ -106,20 +107,19 @@ void Foam::turbulentDFSEMInletFvPatchVectorField::writeLumleyCoeffs() const
     // Before interpolation/raw data
     if (interpolateR_)
     {
-        AverageIOField<symmTensor> Rexp
+        fileName valsFile
         (
-            IOobject
+            this->db().time().caseConstant()
-            (
+           /"boundaryData"
-                "R",
+           /this->patch().name()
-                this->db().time().caseConstant(),
+           /"0"
-                "boundaryData"/patch().name()/"0",
+           /"R"
-                this->db(),
-                IOobject::MUST_READ,
-                IOobject::AUTO_WRITE,
-                false
-            )
         );
 
+        IFstream is(valsFile);
+
+        Field<symmTensor> Rexp(is);
+
         OFstream os(db().time().path()/"lumley_input.out");
 
         os  << "# xi" << token::TAB << "eta" << endl;
@@ -507,7 +507,7 @@ void Foam::turbulentDFSEMInletFvPatchVectorField::initialiseEddies()
     {
         WarningInFunction
             << "Patch: " << patch().patch().name()
-            << " on field " << dimensionedInternalField().name()
+            << " on field " << internalField().name()
             << ": No eddies seeded - please check your set-up" << endl;
     }
 }

src/finiteVolume/fields/fvPatchFields/derived/turbulentDFSEMInlet/turbulentDFSEMInletFvPatchVectorFieldTemplates.C

@@ -23,9 +23,9 @@ License
 
 \*---------------------------------------------------------------------------*/
 
-#include "AverageIOField.H"
 #include "pointToPointPlanarInterpolation.H"
 #include "Time.H"
+#include "IFstream.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -70,25 +70,23 @@ Foam::turbulentDFSEMInletFvPatchVectorField::interpolateBoundaryData
 {
     const word& patchName = this->patch().name();
 
-    // Note: reading from the '0' directory only
+    fileName valsFile
-    IOobject io
     (
-        fieldName,
+        this->db().time().caseConstant()
-        this->db().time().caseConstant(),
+       /"boundaryData"
-        "boundaryData"/patchName/"0",
+       /patchName
-        this->db(),
+       /"0"
-        IOobject::MUST_READ,
+       /fieldName
-        IOobject::AUTO_WRITE,
-        false
     );
 
-    Info<< "Turbulent DFSEM patch " << this->patch().name()
+    IFstream is(valsFile);
+    Field<Type> vals(is);
+
+    Info<< "Turbulent DFSEM patch " << patchName
         << ": interpolating field " << fieldName
-        << " from " << io.path() << endl;
+        << " from " << valsFile << endl;
 
-    AverageIOField<Type> aFld(io);
+    return patchMapper().interpolate(vals);
-
-    return patchMapper().interpolate(aFld);
 }
 
 

src/finiteVolume/functionObjects/fvMeshFunctionObject/fvMeshFunctionObject.H

@@ -78,10 +78,10 @@ private:
     // Private Member Functions
 
         //- Disallow default bitwise copy construct
-        fvMeshFunctionObject(const fvMeshFunctionObject&);
+        fvMeshFunctionObject(const fvMeshFunctionObject&) = delete;
 
         //- Disallow default bitwise assignment
-        void operator=(const fvMeshFunctionObject&);
+        void operator=(const fvMeshFunctionObject&) = delete;
 
 
 public:

src/finiteVolume/functionObjects/volRegion/volRegion.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -58,7 +58,7 @@ void Foam::functionObjects::volRegion::writeFileHeader
 (
     const writeFile& wf,
     Ostream& file
-)
+) const
 {
     wf.writeCommented(file, "Region");
     file<< setw(1) << ':' << setw(1) << ' '

src/finiteVolume/functionObjects/volRegion/volRegion.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -85,7 +85,7 @@ namespace functionObjects
 {
 
 /*---------------------------------------------------------------------------*\
-                         Class volRegion Declaration
+                          Class volRegion Declaration
 \*---------------------------------------------------------------------------*/
 
 class volRegion
@@ -106,8 +106,8 @@ public:
         //- Region type enumeration
         enum regionTypes
         {
-            vrtCellZone,
+            vrtCellZone,    //< cell zone
-            vrtAll
+            vrtAll          //< all cells
         };
 
         //- Region type names
@@ -131,7 +131,7 @@ protected:
     // Protected Member Functions
 
         //- Output file header information
-        void writeFileHeader(const writeFile& wf, Ostream& file);
+        void writeFileHeader(const writeFile& wf, Ostream& file) const;
 
 
 public:
@@ -143,11 +143,7 @@ public:
     // Constructors
 
         //- Construct from fvMesh and dictionary
-        volRegion
+        volRegion(const fvMesh& mesh, const dictionary& dict);
-        (
-            const fvMesh& mesh,
-            const dictionary& dict
-        );
 
 
     //- Destructor

src/functionObjects/field/CourantNo/CourantNo.H

@@ -38,7 +38,7 @@ Usage
     CourantNo1
     {
         type        CourantNo;
-        functionObjectLibs ("libutilityFunctionObjects.so");
+        libs        ("libfieldFunctionObjects.so");
         ...
     }
     \endverbatim
@@ -113,8 +113,8 @@ public:
         CourantNo
         (
             const word& name,
-            const Time&,
+            const Time& runTime,
-            const dictionary&
+            const dictionary& dict
         );