Merge commit 'origin/master' into splitCyclic

Conflicts:
	applications/utilities/mesh/manipulation/createBaffles/createBaffles.C
	applications/utilities/postProcessing/patch/patchIntegrate/patchIntegrate.C
	src/OpenFOAM/meshes/pointMesh/pointPatches/constraint/cyclic/cyclicPointPatch.C
	src/OpenFOAM/meshes/pointMesh/pointPatches/constraint/processor/processorPointPatch.C
	src/dynamicMesh/motionSmoother/motionSmoother.C
	src/dynamicMesh/motionSmoother/motionSmoother.H
	src/dynamicMesh/motionSmoother/motionSmootherTemplates.C

applications/solvers/combustion/XiFoam/bEqn.H

@@ -134,7 +134,7 @@ if (ign.ignited())
             (sigmas*SuInf*(Su0 - SuInf) + sqr(SuMin)*sigmaExt)
            /(sqr(Su0 - SuInf) + sqr(SuMin));
 
-        solve
+        fvScalarMatrix SuEqn
         (
             fvm::ddt(rho, Su)
           + fvm::div(phi + phiXi, Su, "div(phiXi,Su)")
@@ -144,6 +144,9 @@ if (ign.ignited())
           - fvm::SuSp(rho*(sigmas + Rc), Su)
         );
 
+        SuEqn.relax();
+        SuEqn.solve();
+
         // Limit the maximum Su
         // ~~~~~~~~~~~~~~~~~~~~
         Su.min(SuMax);
@@ -196,7 +199,7 @@ if (ign.ignited())
 
         // Solve for the flame wrinkling
         // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-        solve
+        fvScalarMatrix XiEqn
         (
             fvm::ddt(rho, Xi)
           + fvm::div(phi + phiXi, Xi, "div(phiXi,Xi)")
@@ -215,6 +218,8 @@ if (ign.ignited())
             )
         );
 
+        XiEqn.relax();
+        XiEqn.solve();
 
         // Correct boundedness of Xi
         // ~~~~~~~~~~~~~~~~~~~~~~~~~

applications/solvers/combustion/dieselEngineFoam/YEqn.H

@@ -14,7 +14,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
     label inertIndex = -1;
     volScalarField Yt = 0.0*Y[0];
 
-    for (label i=0; i<Y.size(); i++)
+    forAll(Y, i)
     {
         if (Y[i].name() != inertSpecie)
         {

applications/solvers/combustion/dieselEngineFoam/rhoEqn.H

@@ -43,7 +43,7 @@ volScalarField Sevap
     dimensionedScalar("zero", dimensionSet(1, -3, -1, 0, 0), 0.0)
 );
 
-for (label i=0; i<Y.size(); i++)
+forAll(Y, i)
 {
     if (dieselSpray.isLiquidFuel()[i])
     {

applications/solvers/combustion/reactingFoam/YEqn.H

@@ -13,7 +13,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
     label inertIndex = -1;
     volScalarField Yt = 0.0*Y[0];
 
-    for (label i=0; i<Y.size(); i++)
+    forAll(Y, i)
     {
         if (Y[i].name() != inertSpecie)
         {

applications/solvers/combustion/rhoReactingFoam/YEqn.H

@@ -13,7 +13,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
     label inertIndex = -1;
     volScalarField Yt = 0.0*Y[0];
 
-    for (label i=0; i<Y.size(); i++)
+    forAll(Y, i)
     {
         if (Y[i].name() != inertSpecie)
         {

applications/solvers/electromagnetics/magneticFoam/createFields.H

@@ -63,8 +63,7 @@
                 << exit(FatalIOError);
         }
 
-        const labelList& faces =
+        const labelList& faces = mesh.faceZones()[magnetZonei];
-            mesh.faceZones()[magnetZonei];
 
         const scalar muri = magnets[i].mur();
         const scalar Mri = magnets[i].Mr().value();

applications/solvers/heatTransfer/chtMultiRegionFoam/Allwclean

@@ -0,0 +1,8 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+set -x
+
+wclean
+wclean chtMultiRegionSimpleFoam
+
+# ----------------------------------------------------------------- end-of-file

applications/solvers/heatTransfer/chtMultiRegionFoam/Allwmake

@@ -0,0 +1,8 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+set -x
+
+wmake
+wmake chtMultiRegionSimpleFoam
+
+# ----------------------------------------------------------------- end-of-file

applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/Make/files

@@ -0,0 +1,4 @@
+chtMultiRegionSimpleFoam.C
+
+EXE = $(FOAM_APPBIN)/chtMultiRegionSimpleFoam
+

applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/Make/options

@@ -1,5 +1,7 @@
 EXE_INC = \
     /* -DFULLDEBUG -O0 -g */ \
+    -I.. \
+    -I../derivedFvPatchFields \
     -Ifluid \
     -Isolid \
     -I$(LIB_SRC)/finiteVolume/lnInclude \

applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/solid/createSolidFields.H

@@ -1,7 +1,6 @@
     // Initialise solid field pointer lists
     PtrList<volScalarField> rhos(solidRegions.size());
     PtrList<volScalarField> cps(solidRegions.size());
-    PtrList<volScalarField> rhosCps(solidRegions.size());
     PtrList<volScalarField> Ks(solidRegions.size());
     PtrList<volScalarField> Ts(solidRegions.size());
 
@@ -47,12 +46,6 @@
             )
         );
 
-        rhosCps.set
-        (
-            i,
-            new volScalarField("rhosCps", rhos[i]*cps[i])
-        );
-
         Info<< "    Adding to Ks\n" << endl;
         Ks.set
         (

applications/solvers/heatTransfer/chtMultiRegionFoam/solid/createSolidFields.H

@@ -1,7 +1,6 @@
     // Initialise solid field pointer lists
     PtrList<volScalarField> rhos(solidRegions.size());
     PtrList<volScalarField> cps(solidRegions.size());
-    PtrList<volScalarField> rhosCps(solidRegions.size());
     PtrList<volScalarField> Ks(solidRegions.size());
     PtrList<volScalarField> Ts(solidRegions.size());
 
@@ -47,12 +46,6 @@
             )
         );
 
-        rhosCps.set
-        (
-            i,
-            new volScalarField("rhosCps", rhos[i]*cps[i])
-        );
-
         Info<< "    Adding to Ks\n" << endl;
         Ks.set
         (

applications/solvers/heatTransfer/chtMultiRegionFoam/solid/solidRegionDiffusionNo.H

@@ -8,7 +8,7 @@
             (
                 solidRegions[regionI],
                 runTime,
-                rhosCps[regionI],
+                rhos[regionI]*cps[regionI],
                 Ks[regionI]
             ),
             DiNum

applications/solvers/heatTransfer/chtMultiRegionSimpleFoam/Make/files

@@ -1,5 +0,0 @@
-derivedFvPatchFields/solidWallHeatFluxTemperature/solidWallHeatFluxTemperatureFvPatchScalarField.C
-chtMultiRegionSimpleFoam.C
-
-EXE = $(FOAM_APPBIN)/chtMultiRegionSimpleFoam
-

applications/solvers/heatTransfer/chtMultiRegionSimpleFoam/derivedFvPatchFields/solidWallHeatFluxTemperature/solidWallHeatFluxTemperatureFvPatchScalarField.C

@@ -1,168 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 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 "solidWallHeatFluxTemperatureFvPatchScalarField.H"
-#include "addToRunTimeSelectionTable.H"
-#include "fvPatchFieldMapper.H"
-#include "volFields.H"
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::solidWallHeatFluxTemperatureFvPatchScalarField::
-solidWallHeatFluxTemperatureFvPatchScalarField
-(
-    const fvPatch& p,
-    const DimensionedField<scalar, volMesh>& iF
-)
-:
-    fixedGradientFvPatchScalarField(p, iF),
-    q_(p.size(), 0.0),
-    KName_("undefined-K")
-{}
-
-
-Foam::solidWallHeatFluxTemperatureFvPatchScalarField::
-solidWallHeatFluxTemperatureFvPatchScalarField
-(
-    const solidWallHeatFluxTemperatureFvPatchScalarField& ptf,
-    const fvPatch& p,
-    const DimensionedField<scalar, volMesh>& iF,
-    const fvPatchFieldMapper& mapper
-)
-:
-    fixedGradientFvPatchScalarField(ptf, p, iF, mapper),
-    q_(ptf.q_, mapper),
-    KName_(ptf.KName_)
-{}
-
-
-Foam::solidWallHeatFluxTemperatureFvPatchScalarField::
-solidWallHeatFluxTemperatureFvPatchScalarField
-(
-    const fvPatch& p,
-    const DimensionedField<scalar, volMesh>& iF,
-    const dictionary& dict
-)
-:
-    fixedGradientFvPatchScalarField(p, iF, dict),
-    q_("q", dict, p.size()),
-    KName_(dict.lookup("K"))
-{}
-
-
-Foam::solidWallHeatFluxTemperatureFvPatchScalarField::
-solidWallHeatFluxTemperatureFvPatchScalarField
-(
-    const solidWallHeatFluxTemperatureFvPatchScalarField& tppsf
-)
-:
-    fixedGradientFvPatchScalarField(tppsf),
-    q_(tppsf.q_),
-    KName_(tppsf.KName_)
-{}
-
-
-Foam::solidWallHeatFluxTemperatureFvPatchScalarField::
-solidWallHeatFluxTemperatureFvPatchScalarField
-(
-    const solidWallHeatFluxTemperatureFvPatchScalarField& tppsf,
-    const DimensionedField<scalar, volMesh>& iF
-)
-:
-    fixedGradientFvPatchScalarField(tppsf, iF),
-    q_(tppsf.q_),
-    KName_(tppsf.KName_)
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void Foam::solidWallHeatFluxTemperatureFvPatchScalarField::autoMap
-(
-    const fvPatchFieldMapper& m
-)
-{
-    fixedGradientFvPatchScalarField::autoMap(m);
-    q_.autoMap(m);
-}
-
-
-void Foam::solidWallHeatFluxTemperatureFvPatchScalarField::rmap
-(
-    const fvPatchScalarField& ptf,
-    const labelList& addr
-)
-{
-    fixedGradientFvPatchScalarField::rmap(ptf, addr);
-
-    const solidWallHeatFluxTemperatureFvPatchScalarField& hfptf =
-        refCast<const solidWallHeatFluxTemperatureFvPatchScalarField>(ptf);
-
-    q_.rmap(hfptf.q_, addr);
-}
-
-
-void Foam::solidWallHeatFluxTemperatureFvPatchScalarField::updateCoeffs()
-{
-    if (updated())
-    {
-        return;
-    }
-
-    const scalarField& Kw = patch().lookupPatchField<volScalarField, scalar>
-    (
-        KName_
-    );
-
-    gradient() = q_/Kw;
-
-    fixedGradientFvPatchScalarField::updateCoeffs();
-}
-
-
-void Foam::solidWallHeatFluxTemperatureFvPatchScalarField::write
-(
-    Ostream& os
-) const
-{
-    fixedGradientFvPatchScalarField::write(os);
-    q_.writeEntry("q", os);
-    os.writeKeyword("K") << KName_ << token::END_STATEMENT << nl;
-    this->writeEntry("value", os);
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-    makePatchTypeField
-    (
-        fvPatchScalarField,
-        solidWallHeatFluxTemperatureFvPatchScalarField
-    );
-}
-
-// ************************************************************************* //

applications/solvers/heatTransfer/chtMultiRegionSimpleFoam/derivedFvPatchFields/solidWallHeatFluxTemperature/solidWallHeatFluxTemperatureFvPatchScalarField.H

@@ -1,180 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 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
-    solidWallHeatFluxTemperatureFvPatchScalarField
-
-Description
-    Heat flux boundary condition for temperature on solid region
-
-    Example usage:
-        myWallPatch
-        {
-            type            solidWallHeatFluxTemperature;
-            K               K;                 // Name of K field
-            q               uniform 1000;      // Heat flux / [W/m2]
-            value           300.0;             // Initial temperature / [K]
-        }
-
-
-SourceFiles
-    solidWallHeatFluxTemperatureFvPatchScalarField.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef solidWallHeatFluxTemperatureFvPatchScalarField_H
-#define solidWallHeatFluxTemperatureFvPatchScalarField_H
-
-#include "fixedGradientFvPatchFields.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-      Class solidWallHeatFluxTemperatureFvPatchScalarField Declaration
-\*---------------------------------------------------------------------------*/
-
-class solidWallHeatFluxTemperatureFvPatchScalarField
-:
-    public fixedGradientFvPatchScalarField
-{
-    // Private data
-
-        //- Heat flux / [W/m2]
-        scalarField q_;
-
-        //- Name of thermal conductivity field
-        word KName_;
-
-
-public:
-
-    //- Runtime type information
-    TypeName("solidWallHeatFluxTemperature");
-
-
-    // Constructors
-
-        //- Construct from patch and internal field
-        solidWallHeatFluxTemperatureFvPatchScalarField
-        (
-            const fvPatch&,
-            const DimensionedField<scalar, volMesh>&
-        );
-
-        //- Construct from patch, internal field and dictionary
-        solidWallHeatFluxTemperatureFvPatchScalarField
-        (
-            const fvPatch&,
-            const DimensionedField<scalar, volMesh>&,
-            const dictionary&
-        );
-
-        //- Construct by mapping given
-        // solidWallHeatFluxTemperatureFvPatchScalarField
-        // onto a new patch
-        solidWallHeatFluxTemperatureFvPatchScalarField
-        (
-            const solidWallHeatFluxTemperatureFvPatchScalarField&,
-            const fvPatch&,
-            const DimensionedField<scalar, volMesh>&,
-            const fvPatchFieldMapper&
-        );
-
-        //- Construct as copy
-        solidWallHeatFluxTemperatureFvPatchScalarField
-        (
-            const solidWallHeatFluxTemperatureFvPatchScalarField&
-        );
-
-        //- Construct and return a clone
-        virtual tmp<fvPatchScalarField> clone() const
-        {
-            return tmp<fvPatchScalarField>
-            (
-                new solidWallHeatFluxTemperatureFvPatchScalarField(*this)
-            );
-        }
-
-        //- Construct as copy setting internal field reference
-        solidWallHeatFluxTemperatureFvPatchScalarField
-        (
-            const solidWallHeatFluxTemperatureFvPatchScalarField&,
-            const DimensionedField<scalar, volMesh>&
-        );
-
-        //- Construct and return a clone setting internal field reference
-        virtual tmp<fvPatchScalarField> clone
-        (
-            const DimensionedField<scalar, volMesh>& iF
-        ) const
-        {
-            return tmp<fvPatchScalarField>
-            (
-                new solidWallHeatFluxTemperatureFvPatchScalarField(*this, iF)
-            );
-        }
-
-
-    // Member functions
-
-        // Evaluation functions
-
-            //- Update the coefficients associated with the patch field
-            virtual void updateCoeffs();
-
-
-        // Mapping functions
-
-            //- Map (and resize as needed) from self given a mapping object
-            virtual void autoMap
-            (
-                const fvPatchFieldMapper&
-            );
-
-            //- Reverse map the given fvPatchField onto this fvPatchField
-            virtual void rmap
-            (
-                const fvPatchScalarField&,
-                const labelList&
-            );
-
-
-        // I-O
-
-            //- Write
-            void write(Ostream&) const;
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //

applications/solvers/incompressible/adjointShapeOptimizationFoam/createFields.H

@@ -84,10 +84,8 @@
     dimensionedScalar lambda(laminarTransport.lookup("lambda"));
     dimensionedScalar alphaMax(laminarTransport.lookup("alphaMax"));
 
-    const labelList& inletCells =
+    const labelList& inletCells = mesh.boundary()["inlet"].faceCells();
-        mesh.boundary()[mesh.boundaryMesh().findPatchID("inlet")].faceCells();
+    //const labelList& outletCells = mesh.boundary()["outlet"].faceCells();
-    //const labelList& outletCells =
-    //    mesh.boundary()[mesh.boundaryMesh().findPatchID("outlet")].faceCells();
 
     volScalarField alpha
     (

applications/solvers/incompressible/boundaryFoam/makeGraphs.H

@@ -25,9 +25,9 @@ makeGraph(y, flowDirection & R & flowDirection, "Rff", gFormat);
 makeGraph(y, wallNormal & R & wallNormal, "Rww", gFormat);
 makeGraph(y, flowDirection & R & wallNormal, "Rfw", gFormat);
 
-makeGraph(y, sqrt(mag(R.component(tensor::XX))), "u", gFormat);
+makeGraph(y, sqrt(mag(R.component(symmTensor::XX))), "u", gFormat);
-makeGraph(y, sqrt(mag(R.component(tensor::YY))), "v", gFormat);
+makeGraph(y, sqrt(mag(R.component(symmTensor::YY))), "v", gFormat);
-makeGraph(y, sqrt(mag(R.component(tensor::ZZ))), "w", gFormat);
+makeGraph(y, sqrt(mag(R.component(symmTensor::ZZ))), "w", gFormat);
-makeGraph(y, R.component(tensor::XY), "uv", gFormat);
+makeGraph(y, R.component(symmTensor::XY), "uv", gFormat);
 
 makeGraph(y, mag(fvc::grad(U)), "gammaDot", gFormat);

applications/solvers/incompressible/pimpleDyMFoam/correctPhi.H

@@ -27,7 +27,7 @@
         zeroGradientFvPatchScalarField::typeName
     );
 
-    for (label i=0; i<p.boundaryField().size(); i++)
+    forAll(p.boundaryField(), i)
     {
         if (p.boundaryField()[i].fixesValue())
         {

applications/solvers/incompressible/pimpleDyMFoam/pimpleDyMFoam.C

@@ -150,9 +150,9 @@ int main(int argc, char *argv[])
                 U -= rAU*fvc::grad(p);
                 U.correctBoundaryConditions();
             }
-        }
 
             turbulence->correct();
+        }
 
         runTime.write();
 

applications/solvers/lagrangian/incompressibleUncoupledKinematicParcelFoam/incompressibleUncoupledKinematicParcelFoam.C

@@ -41,7 +41,12 @@ Description
 
 int main(int argc, char *argv[])
 {
-    argList::addOption("cloudName", "cloud name");
+    argList::addOption
+    (
+        "cloudName",
+        "name",
+        "specify alternative cloud name. default is 'kinematicCloud'"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"

applications/solvers/lagrangian/reactingParcelFilmFoam/YEqn.H

@@ -14,7 +14,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
     label inertIndex = -1;
     volScalarField Yt = 0.0*Y[0];
 
-    for (label i=0; i<Y.size(); i++)
+    forAll(Y, i)
     {
         if (Y[i].name() != inertSpecie)
         {

applications/solvers/lagrangian/uncoupledKinematicParcelFoam/uncoupledKinematicParcelFoam.C

@@ -41,7 +41,12 @@ Description
 
 int main(int argc, char *argv[])
 {
-    argList::addOption("cloudName", "cloud name");
+    argList::addOption
+    (
+        "cloudName",
+        "name",
+        "specify alternative cloud name. default is 'kinematicCloud'"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"

applications/solvers/multiphase/bubbleFoam/createPhia.H

@@ -36,7 +36,7 @@
             calculatedFvPatchScalarField::typeName
         );
 
-        for (label i=0; i<Ua.boundaryField().size(); i++)
+        forAll(Ua.boundaryField(), i)
         {
             if (isA<fixedValueFvPatchVectorField>(Ua.boundaryField()[i]))
             {

applications/solvers/multiphase/bubbleFoam/createPhib.H

@@ -36,7 +36,7 @@
             calculatedFvPatchScalarField::typeName
         );
 
-        for (label i=0; i<Ub.boundaryField().size(); i++)
+        forAll(Ub.boundaryField(), i)
         {
             if (isA<fixedValueFvPatchVectorField>(Ub.boundaryField()[i]))
             {

applications/solvers/multiphase/compressibleInterDyMFoam/createFields.H

@@ -135,7 +135,7 @@
         zeroGradientFvPatchScalarField::typeName
     );
 
-    for (label i=0; i<p.boundaryField().size(); i++)
+    forAll(p.boundaryField(), i)
     {
         if (p.boundaryField()[i].fixesValue())
         {

applications/solvers/multiphase/interDyMFoam/createFields.H

@@ -98,7 +98,7 @@
         zeroGradientFvPatchScalarField::typeName
     );
 
-    for (label i=0; i<p.boundaryField().size(); i++)
+    forAll(p.boundaryField(), i)
     {
         if (p.boundaryField()[i].fixesValue())
         {

applications/solvers/multiphase/interFoam/correctPhi.H

@@ -7,7 +7,7 @@
         zeroGradientFvPatchScalarField::typeName
     );
 
-    for (label i=0; i<p.boundaryField().size(); i++)
+    forAll(p.boundaryField(), i)
     {
         if (p.boundaryField()[i].fixesValue())
         {

applications/solvers/multiphase/interPhaseChangeFoam/correctPhi.H

@@ -7,7 +7,7 @@
         zeroGradientFvPatchScalarField::typeName
     );
 
-    for (label i=0; i<p.boundaryField().size(); i++)
+    forAll(p.boundaryField(), i)
     {
         if (p.boundaryField()[i].fixesValue())
         {

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

@@ -106,7 +106,7 @@ Foam::phaseModel::phaseModel
             calculatedFvPatchScalarField::typeName
         );
 
-        for (label i=0; i<U_.boundaryField().size(); i++)
+        forAll(U_.boundaryField(), i)
         {
             if (isA<fixedValueFvPatchVectorField>(U_.boundaryField()[i]))
             {

applications/test/FixedList/FixedListTest.C

@@ -43,7 +43,6 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    argList::validArgs.clear();
     argList args(argc, argv);
 
     FixedList<label, 4> list;

applications/test/ODETest/ODETest.C

@@ -104,7 +104,6 @@ public:
 
 int main(int argc, char *argv[])
 {
-    argList::validArgs.clear();
     argList::validArgs.append("ODESolver");
     argList args(argc, argv);
 

applications/test/prefixOSstream/prefixOSstreamTest.C

@@ -45,7 +45,6 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    argList::validArgs.clear();
     argList args(argc, argv);
 
     //Pout.prefix() = '[' + name(Pstream::myProcNo()) + "] ";

applications/test/primitivePatch/testPrimitivePatch.C

@@ -220,10 +220,7 @@ int main(int argc, char *argv[])
 #   include "createPolyMesh.H"
 
     const word patchName = args[1];
-
+    const polyPatch& patch = mesh.boundaryMesh()[patchName];
-    label patchI = mesh.boundaryMesh().findPatchID(patchName);
-
-    const polyPatch& patch = mesh.boundaryMesh()[patchI];
 
     Info<< "Patch:" << patch.name() << endl;
 

applications/test/readCHEMKINIII/readCHEMKINIII.C

@@ -35,7 +35,6 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    argList::validArgs.clear();
     argList::validArgs.append("CHEMKINIIIFile");
     argList::addOption("thermo", "fileName");
     argList args(argc, argv);

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

@@ -38,7 +38,7 @@ Description
 
     E.g. to allow all faces on same patch to be merged:
 
-        combinePatchFaces .. cavity 180 -concaveAngle 90
+        combinePatchFaces 180 -concaveAngle 90
 
 \*---------------------------------------------------------------------------*/
 
@@ -428,15 +428,18 @@ int main(int argc, char *argv[])
 {
 #   include "addOverwriteOption.H"
 
-    argList::validArgs.append("feature angle [0..180]");
+    argList::validArgs.append("featureAngle [0..180]");
     argList::addOption
     (
         "concaveAngle",
-        "[0..180]",
+        "degrees",
-        "specify concave angle [0..180] degrees (default: 30.0 degrees)"
+        "specify concave angle [0..180] (default: 30 degrees)"
+    );
+    argList::addBoolOption
+    (
+        "snapMesh",
+        "use system/snapMeshDict"
     );
-
-    argList::addBoolOption("snapMesh");
 
 #   include "setRootCase.H"
 #   include "createTime.H"

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

@@ -51,7 +51,13 @@ int main(int argc, char *argv[])
     argList::validArgs.append("patchName");
     argList::validArgs.append("edgeWeight");
 
-    argList::addOption("useSet", "cellSet");
+    argList::addOption
+    (
+        "useSet",
+        "name",
+        "restrict cells to refine based on specified cellSet name"
+    );
+
 
 #   include "setRootCase.H"
 #   include "createTime.H"

applications/utilities/mesh/advanced/refinementLevel/refinementLevel.C

@@ -96,7 +96,11 @@ bool limitRefinementLevel
 
 int main(int argc, char *argv[])
 {
-    argList::addBoolOption("readLevel");
+    argList::addBoolOption
+    (
+        "readLevel",
+        "read level from refinementLevel file"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"
@@ -109,7 +113,7 @@ int main(int argc, char *argv[])
         << " to allow for some truncation error."
         << nl << endl;
 
-    bool readLevel = args.optionFound("readLevel");
+    const bool readLevel = args.optionFound("readLevel");
 
     const scalarField& vols = mesh.cellVolumes();
 

applications/utilities/mesh/advanced/splitCells/splitCells.C

@@ -517,12 +517,30 @@ void collectCuts
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "split cells with flat faces"
+    );
     #include "addOverwriteOption.H"
     argList::noParallel();
-    argList::addOption("set", "cellSet name");
+    argList::validArgs.append("edgeAngle [0..360]");
-    argList::addBoolOption("geometry");
+
-    argList::addOption("tol", "edge snap tolerance");
+    argList::addOption
-    argList::validArgs.append("edge angle [0..360]");
+    (
+        "set",
+        "name",
+        "split cells from specified cellSet only"
+    );
+    argList::addBoolOption
+    (
+        "geometry",
+        "use geometric cut for hexes as well"
+    );
+    argList::addOption
+    (
+        "tol",
+        "scalar", "edge snap tolerance (default 0.2)"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"
@@ -538,7 +556,7 @@ int main(int argc, char *argv[])
     const bool geometry  = args.optionFound("geometry");
     const bool overwrite = args.optionFound("overwrite");
 
-    scalar edgeTol = args.optionLookupOrDefault("tol", 0.2);
+    const scalar edgeTol = args.optionLookupOrDefault("tol", 0.2);
 
     Info<< "Trying to split cells with internal angles > feature angle\n" << nl
         << "featureAngle      : " << featureAngle << nl

applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L

@@ -235,7 +235,12 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("ANSYS input file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
 
     argList args(argc, argv);
 
@@ -244,8 +249,7 @@ int main(int argc, char *argv[])
         FatalError.exit();
     }
 
-    scalar scaleFactor = 1.0;
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
-    args.optionReadIfPresent("scale", scaleFactor);
 
 #   include "createTime.H"
 

applications/utilities/mesh/conversion/cfx4ToFoam/cfx4ToFoam.C

@@ -49,7 +49,12 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("CFX geom file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
 
     argList args(argc, argv);
 
@@ -58,8 +63,7 @@ int main(int argc, char *argv[])
          FatalError.exit();
     }
 
-    scalar scaleFactor = 1.0;
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
-    args.optionReadIfPresent("scale", scaleFactor);
 
 #   include "createTime.H"
 

applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L

@@ -761,10 +761,30 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("Fluent mesh file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
-    argList::addOption("ignoreCellGroups", "cell group names");
+    (
-    argList::addOption("ignoreFaceGroups", "face group names");
+        "scale",
-    argList::addBoolOption("cubit");
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
+    argList::addOption
+    (
+        "ignoreCellGroups",
+        "names",
+        "specify cell groups to ignore"
+    );
+    argList::addOption
+    (
+        "ignoreFaceGroups",
+        "names",
+        "specify face groups to ignore"
+    );
+
+    argList::addBoolOption
+    (
+        "cubit",
+        "special parsing of (incorrect) cubit files"
+    );
 
     argList args(argc, argv);
 

applications/utilities/mesh/conversion/fluentMeshToFoam/README.txt

@@ -20,8 +20,7 @@ Notes for fluentMeshToFoam with zone preservation
     with the cellZones(), faceZones() and pointZones() member functions
 
     - Example (Members from polyMesh.H and ZoneMesh.H):
-    label thisCellZoneID = mesh.cellZones().findZoneID("thisZoneName");
+    const labelList& thisCellZone = mesh.cellZones()["thisZoneName"];
-    const labelList& thisCellZone = mesh.cellZones()[thisCellZoneID];
 
     - Zone integrity is preserved during mesh modification and decompomposition.
 

applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L

@@ -866,9 +866,22 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("Fluent mesh file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
-    argList::addBoolOption("writeSets");
+    (
-    argList::addBoolOption("writeZones");
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
+    argList::addBoolOption
+    (
+        "writeSets",
+        "write cell zones and patches as sets"
+    );
+    argList::addBoolOption
+    (
+        "writeZones",
+        "write cell zones as zones"
+    );
 
     argList args(argc, argv);
 
@@ -877,8 +890,7 @@ int main(int argc, char *argv[])
         FatalError.exit();
     }
 
-    scalar scaleFactor = 1.0;
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
-    args.optionReadIfPresent("scale", scaleFactor);
 
     const bool writeSets  = args.optionFound("writeSets");
     const bool writeZones = args.optionFound("writeZones");

applications/utilities/mesh/conversion/foamToStarMesh/foamToStarMesh.C

@@ -69,7 +69,7 @@ int main(int argc, char *argv[])
     (
         "scale",
         "factor",
-        "specify geometry scaling factor - default is 1000 ([m] to [mm])"
+        "geometry scaling factor - default is 1000 ([m] to [mm])"
     );
     argList::addBoolOption
     (

applications/utilities/mesh/conversion/foamToSurface/foamToSurface.C

@@ -61,8 +61,8 @@ int main(int argc, char *argv[])
     argList::addOption
     (
         "scale",
-        "scale",
+        "factor",
-        "specify geometry scaling factor"
+        "geometry scaling factor - default is 1"
     );
     argList::addBoolOption
     (

applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L

@@ -628,7 +628,12 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("GAMBIT file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
 
     argList args(argc, argv);
 
@@ -637,8 +642,7 @@ int main(int argc, char *argv[])
          FatalError.exit();
     }
 
-    scalar scaleFactor = 1.0;
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
-    args.optionReadIfPresent("scale", scaleFactor);
 
 #   include "createTime.H"
 

applications/utilities/mesh/conversion/gmshToFoam/gmshToFoam.C

@@ -716,7 +716,11 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append(".msh file");
-    argList::addBoolOption("keepOrientation");
+    argList::addBoolOption
+    (
+        "keepOrientation",
+        "retain raw orientation for prisms/hexs"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"

applications/utilities/mesh/conversion/kivaToFoam/kivaToFoam.C

@@ -46,7 +46,7 @@ Description
 
 using namespace Foam;
 
-// Supported KIVA versions
+//- Supported KIVA versions
 enum kivaVersions
 {
     kiva3,
@@ -59,37 +59,51 @@ enum kivaVersions
 int main(int argc, char *argv[])
 {
     argList::noParallel();
-    argList::addOption("file", "fileName");
+    argList::addOption
-    argList::addOption("version", "[kiva3|kiva3v]");
+    (
-    argList::addOption("zHeadMin", "scalar");
+        "file",
+        "name",
+        "specify alternative input file name - default is otape17"
+    );
+    argList::addOption
+    (
+        "version",
+        "version",
+        "specify kiva version [kiva3|kiva3v] - default is '3v'"
+    );
+    argList::addOption
+    (
+        "zHeadMin",
+        "scalar",
+        "minimum z-height for transferring liner faces to cylinder-head"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"
 
-    fileName kivaFileName("otape17");
+    const fileName kivaFileName =
-    args.optionReadIfPresent("file", kivaFileName);
+        args.optionLookupOrDefault<fileName>("file", "otape17");
 
     kivaVersions kivaVersion = kiva3v;
     if (args.optionFound("version"))
     {
-        const word kivaVersionName = args["version"];
+        const word versionName = args["version"];
 
-        if (kivaVersionName == "kiva3")
+        if (versionName == "kiva3")
         {
             kivaVersion = kiva3;
         }
-        else if (kivaVersionName == "kiva3v")
+        else if (versionName == "kiva3v")
         {
             kivaVersion = kiva3v;
         }
         else
         {
             FatalErrorIn("main(int argc, char *argv[])")
-                << "KIVA file version " << kivaVersionName << " not supported"
+                << "KIVA file version " << versionName << " not supported"
                 << exit(FatalError);
 
             args.printUsage();
-
             FatalError.exit(1);
         }
     }

applications/utilities/mesh/conversion/kivaToFoam/readKivaGrid.H

@@ -315,7 +315,7 @@ for (label i=0; i<nPoints; i++)
     }
 }
 
-// Tranfer liner faces that are above the minimum cylinder-head z height
+// Transfer liner faces that are above the minimum cylinder-head z height
 // into the cylinder-head region
 if
 (

applications/utilities/mesh/conversion/mshToFoam/mshToFoam.C

@@ -56,7 +56,11 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append(".msh file");
-    argList::addBoolOption("hex");
+    argList::addBoolOption
+    (
+        "hex",
+        "treat input as containing hex instead of tet cells"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -69,11 +73,11 @@ int main(int argc, char *argv[])
 
     if (readHex)
     {
-        Info<< "Trying to read " << nCells << " hexes." << endl << endl;
+        Info<< "Trying to read " << nCells << " hexes." << nl << endl;
     }
     else
     {
-        Info<< "Trying to read " << nCells << " tets." << endl << endl;
+        Info<< "Trying to read " << nCells << " tets." << nl << endl;
     }
 
     cellShapeList cells(nCells);

applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C

@@ -57,10 +57,28 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("PLOT3D geom file");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
-    argList::addBoolOption("noBlank");
+    (
-    argList::addBoolOption("singleBlock");
+        "scale",
-    argList::addOption("2D", "thickness");
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
+    argList::addBoolOption
+    (
+        "noBlank",
+        "skip blank items"
+    );
+    argList::addBoolOption
+    (
+        "singleBlock",
+        "input is a single block"
+    );
+    argList::addOption
+    (
+        "2D",
+        "thickness",
+        "use when converting a 2-D geometry"
+    );
 
     argList args(argc, argv);
 
@@ -69,8 +87,7 @@ int main(int argc, char *argv[])
          FatalError.exit();
     }
 
-    scalar scaleFactor = 1.0;
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
-    args.optionReadIfPresent("scale", scaleFactor);
 
     bool readBlank = !args.optionFound("noBlank");
     bool singleBlock = args.optionFound("singleBlock");

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

@@ -356,7 +356,7 @@ int main(int argc, char *argv[])
     argList::noParallel();
     timeSelector::addOptions(true, false);
 
-    argList::validArgs.append("feature angle[0-180]");
+    argList::validArgs.append("featureAngle [0-180]");
     argList::addBoolOption
     (
         "splitAllFaces",

applications/utilities/mesh/conversion/sammToFoam/sammToFoam.C

@@ -40,7 +40,12 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("SAMM mesh file prefix");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
 
     argList args(argc, argv);
 
@@ -49,7 +54,7 @@ int main(int argc, char *argv[])
         FatalError.exit();
     }
 
-    scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
 
 #   include "createTime.H"
 

applications/utilities/mesh/conversion/star3ToFoam/star3ToFoam.C

@@ -40,7 +40,12 @@ int main(int argc, char *argv[])
 {
     argList::noParallel();
     argList::validArgs.append("STAR mesh file prefix");
-    argList::addOption("scale", "scale factor");
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
 
     argList args(argc, argv);
 
@@ -49,7 +54,7 @@ int main(int argc, char *argv[])
         FatalError.exit();
     }
 
-    scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
+    const scalar scaleFactor = args.optionLookupOrDefault("scale", 1.0);
 
 #   include "createTime.H"
 

applications/utilities/mesh/conversion/star4ToFoam/star4ToFoam.C

@@ -69,7 +69,7 @@ int main(int argc, char *argv[])
     argList::addOption
     (
         "scale",
-        "scale",
+        "factor",
         "geometry scaling factor - default is 0.001 ([mm] to [m])"
     );
     argList::addBoolOption

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

@@ -97,7 +97,11 @@ label findFace(const primitiveMesh& mesh, const face& f)
 int main(int argc, char *argv[])
 {
     argList::validArgs.append("file prefix");
-    argList::addBoolOption("noFaceFile");
+    argList::addBoolOption
+    (
+        "noFaceFile",
+        "skip reading .face file for boundary information"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"

applications/utilities/mesh/conversion/writeMeshObj/writeMeshObj.C

@@ -371,27 +371,65 @@ void writePointCells
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "for mesh debugging: write mesh as separate OBJ files"
+    );
+
     timeSelector::addOptions();
-    argList::addBoolOption("patchFaces");
+    argList::addBoolOption
-    argList::addBoolOption("patchEdges");
+    (
-    argList::addOption("cell", "cellI");
+        "patchFaces",
-    argList::addOption("face", "faceI");
+        "write patch faces edges"
-    argList::addOption("point", "pointI");
+    );
-    argList::addOption("cellSet", "setName");
+    argList::addBoolOption
-    argList::addOption("faceSet", "setName");
+    (
+        "patchEdges",
+        "write patch boundary edges"
+    );
+    argList::addOption
+    (
+        "cell",
+        "int",
+        "write points for the specified cell"
+    );
+    argList::addOption
+    (
+        "face",
+        "int",
+        "write specified face"
+    );
+    argList::addOption
+    (
+        "point",
+        "int",
+        "write specified point"
+    );
+    argList::addOption
+    (
+        "cellSet",
+        "name",
+        "write points for specified cellSet"
+    );
+    argList::addOption
+    (
+        "faceSet",
+        "name",
+        "write points for specified faceSet"
+    );
     #include "addRegionOption.H"
 
     #include "setRootCase.H"
     #include "createTime.H"
     runTime.functionObjects().off();
 
-    bool patchFaces = args.optionFound("patchFaces");
+    const bool patchFaces = args.optionFound("patchFaces");
-    bool patchEdges = args.optionFound("patchEdges");
+    const bool patchEdges = args.optionFound("patchEdges");
-    bool doCell     = args.optionFound("cell");
+    const bool doCell     = args.optionFound("cell");
-    bool doPoint    = args.optionFound("point");
+    const bool doPoint    = args.optionFound("point");
-    bool doFace     = args.optionFound("face");
+    const bool doFace     = args.optionFound("face");
-    bool doCellSet  = args.optionFound("cellSet");
+    const bool doCellSet  = args.optionFound("cellSet");
-    bool doFaceSet  = args.optionFound("faceSet");
+    const bool doFaceSet  = args.optionFound("faceSet");
 
 
     Info<< "Writing mesh objects as .obj files such that the object"
@@ -465,7 +503,6 @@ int main(int argc, char *argv[])
                     << endl;
 
                 writePoints(mesh, cells.toc(), runTime.timeName());
-
             }
             if (doFaceSet)
             {

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

@@ -42,7 +42,7 @@ Usage
     Specify an alternative mesh region.
 
     @param -dict \<filename\> \n
-    Specify an alternative dictionary for the block mesh description.
+    Specify alternative dictionary for the block mesh description.
 
 \*---------------------------------------------------------------------------*/
 
@@ -80,7 +80,7 @@ int main(int argc, char *argv[])
     (
         "dict",
         "file",
-        "specify an alternative dictionary for the blockMesh description"
+        "specify alternative dictionary for the blockMesh description"
     );
 
 #   include "addRegionOption.H"

applications/utilities/mesh/generation/blockMesh/mergePatchPairs.H

@@ -27,10 +27,7 @@
                 // Master patch
                 const word masterPatchName(mergePatchPairs[pairI].first());
                 const polyPatch& masterPatch =
-                    mesh.boundaryMesh()
+                    mesh.boundaryMesh()[masterPatchName];
-                    [
-                        mesh.boundaryMesh().findPatchID(masterPatchName)
-                    ];
 
                 labelList isf(masterPatch.size());
 
@@ -51,10 +48,7 @@
                 // Slave patch
                 const word slavePatchName(mergePatchPairs[pairI].second());
                 const polyPatch& slavePatch =
-                    mesh.boundaryMesh()
+                    mesh.boundaryMesh()[slavePatchName];
-                    [
-                        mesh.boundaryMesh().findPatchID(slavePatchName)
-                    ];
 
                 labelList osf(slavePatch.size());
 

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

@@ -123,7 +123,7 @@ void createDummyFvMeshFiles(const polyMesh& mesh, const word& regionName)
 
 label findPatchID(const polyBoundaryMesh& patches, const word& name)
 {
-    label patchID = patches.findPatchID(name);
+    const label patchID = patches.findPatchID(name);
 
     if (patchID == -1)
     {

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

@@ -632,7 +632,7 @@ int main(int argc, char *argv[])
     argList::validArgs.append("thickness");
 
     #include "addRegionOption.H"
-    argList::validOptions.insert("overwrite", "");
+    #include "addOverwriteOption.H"
     #include "setRootCase.H"
     #include "createTime.H"
     #include "createNamedMesh.H"
@@ -849,8 +849,7 @@ int main(int argc, char *argv[])
     nExtrudeFaces = 0;
     forAll(zoneNames, i)
     {
-        label zoneI = faceZones.findZoneID(zoneNames[i]);
+        const faceZone& fz = faceZones[zoneNames[i]];
-        const faceZone& fz = faceZones[zoneI];
         forAll(fz, j)
         {
             extrudeTopPatchID[nExtrudeFaces] = interRegionTopPatch[i];

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -143,11 +143,19 @@ castellatedMeshControls
                 }
             }
 
-            // Optional angle to detect small-large cell situation perpendicular
+            //- Optional angle to detect small-large cell situation
-            // to the surface. Is the angle of face w.r.t the local surface
+            //  perpendicular to the surface. Is the angle of face w.r.t.
-            // normal. Use on flat(ish) surfaces only. Otherwise
+            //  the local surface normal. Use on flat(ish) surfaces only.
-            // leave out or set to negative number.
+            //  Otherwise leave out or set to negative number.
             //perpendicularAngle 10;
+
+
+            //- Optional faceZone and (for closed surface) cellZone with
+            //  how to select the cells that are in the cellZone
+            //  (inside / outside / specified insidePoint)
+	    //faceZone sphere;
+            //cellZone sphere;
+            //cellZoneInside inside;  //outside/insidePoint
         }
     }
 

applications/utilities/mesh/manipulation/cellSet/Make/files

@@ -1,4 +0,0 @@
-cellSet.C
-
-EXE = $(FOAM_APPBIN)/cellSet
-

applications/utilities/mesh/manipulation/cellSet/cellSet.C

@@ -1,196 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 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/>.
-
-Description
-    Selects a cell set through a dictionary.
-
-\*---------------------------------------------------------------------------*/
-
-#include "argList.H"
-#include "Time.H"
-#include "polyMesh.H"
-#include "topoSetSource.H"
-#include "cellSet.H"
-
-using namespace Foam;
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Main program:
-
-int main(int argc, char *argv[])
-{
-#   include "setRootCase.H"
-#   include "createTime.H"
-#   include "createPolyMesh.H"
-
-    Info<< "Reading cellSetDict\n" << endl;
-
-    IOdictionary cellSetDict
-    (
-        IOobject
-        (
-            "cellSetDict",
-            runTime.system(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::NO_WRITE
-        )
-    );
-
-
-    const word setName(cellSetDict.lookup("name"));
-    const word actionName(cellSetDict.lookup("action"));
-
-    topoSetSource::setAction action = topoSetSource::toAction(actionName);
-
-
-    // Create topoSetSources
-    PtrList<topoSetSource> topoSetSources
-    (
-        cellSetDict.lookup("topoSetSources"),
-        topoSetSource::iNew(mesh)
-    );
-
-
-    // Load set to work
-    autoPtr<topoSet> currentSetPtr(NULL);
-    IOobject::readOption r;
-
-    if ((action == topoSetSource::NEW) || (action == topoSetSource::CLEAR))
-    {
-        r = IOobject::NO_READ;
-
-        currentSetPtr.reset
-        (
-            new cellSet
-            (
-                mesh,
-                setName,
-                mesh.nCells()/10+1  // Reasonable size estimate.
-            )
-        );
-    }
-    else
-    {
-        r = IOobject::MUST_READ;
-
-        currentSetPtr.reset
-        (
-            new cellSet
-            (
-                mesh,
-                setName,
-                r
-            )
-        );
-    }
-
-    topoSet& currentSet = currentSetPtr();
-
-    Info<< "Set:" << currentSet.name()
-        << "  Size:" << currentSet.size()
-        << "  Action:" << actionName
-        << endl;
-
-    if ((r == IOobject::MUST_READ) && (action != topoSetSource::LIST))
-    {
-        // currentSet has been read so can make copy.
-        //backup(mesh, setName, currentSet, setName + "_old");
-    }
-
-    if (action == topoSetSource::CLEAR)
-    {
-        // Already handled above by not reading
-    }
-    else if (action == topoSetSource::INVERT)
-    {
-        currentSet.invert(currentSet.maxSize(mesh));
-    }
-    else if (action == topoSetSource::LIST)
-    {
-        currentSet.writeDebug(Info, mesh, 100);
-        Info<< endl;
-    }
-    else if (action == topoSetSource::SUBSET)
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            // Backup current set.
-            autoPtr<topoSet> oldSet
-            (
-                topoSet::New
-                (
-                    currentSet.type(),
-                    mesh,
-                    currentSet.name() + "_old2",
-                    currentSet
-                )
-            );
-
-            currentSet.clear();
-
-            topoSetSources[topoSetSourceI].applyToSet
-            (
-                topoSetSource::NEW,
-                currentSet
-            );
-
-            // Combine new value of currentSet with old one.
-            currentSet.subset(oldSet);
-        }
-    }
-    else
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            topoSetSources[topoSetSourceI].applyToSet(action, currentSet);
-        }
-    }
-
-
-    if (action != topoSetSource::LIST)
-    {
-        // Set has changed.
-
-        // Sync across coupled patches.
-        currentSet.sync(mesh);
-
-        Info<< "Writing " << currentSet.name()
-            << " (size " << currentSet.size() << ") to "
-            << currentSet.instance()/currentSet.local()
-               /currentSet.name()
-            << endl << endl;
-
-        currentSet.write();
-    }
-
-    Info<< "\nEnd\n" << endl;
-
-    return 0;
-}
-
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/cellSet/cellSetDict

@@ -1,149 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
-|   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      cellSetDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Name of set to operate on
-name c0;
-
-// One of clear/new/invert/add/delete|subset/list
-action new;
-
-// Actions to apply to cellSet. These are all the topoSetSource's ending
-// in ..ToCell (see the meshTools library).
-
-topoSetSources
-(
-    // Select by explicitly providing cell labels
-    labelToCell
-    {
-        value (12 13 56);   // labels of cells
-    }
-
-    // Copy elements from cellSet
-    cellToCell
-    {
-        set c1;
-    }
-
-    // Cells in cell zone
-    zoneToCell
-    {
-        name ".*Zone";      // Name of cellZone, regular expressions allowed
-    }
-
-    // Cells on master or slave side of faceZone
-    faceZoneToCell
-    {
-        name ".*Zone";      // Name of faceZone, regular expressions allowed
-        option master;      // master/slave
-    }
-
-    // Select based on faceSet
-    faceToCell
-    {
-        set f0;             // Name of faceSet
-
-        //option neighbour; // cell with neighbour in faceSet
-        //option owner;     //  ,,       owner
-        option any;         // cell with any face in faceSet
-        //option all;       // cell with all faces in faceSet
-    }
-
-    // Select based on pointSet
-    pointToCell
-    {
-        set p0;
-        option any;         // cell with any point in pointSet
-        //option all;       // cell with all points in pointSet
-    }
-
-    // Select based on cellShape
-    shapeToCell
-    {
-        type hex;           // hex/wedge/prism/pyr/tet/tetWedge/splitHex
-    }
-
-    // Cells with cell centre within box
-    boxToCell
-    {
-       box   (0 0 0) (1 1 1);
-    }
-
-    // Cells with cell centre within box
-    // Is skewed, rotated box. Given as origin and three spanning vectors.
-    rotatedBoxToCell
-    {
-       origin   (0.2 0.2 -10);
-       i        (0.2 0.2 0);
-       j        (-0.2 0.2 0);
-       k        (10 10 10);
-    }
-
-    // Cells with centre within cylinder
-    cylinderToCell
-    {
-       p1       (0.2 0.2 -10); // start point on cylinder axis
-       p2       (0.2 0.2 0);   // end point on cylinder axis
-       radius   5.0;
-    }
-
-    // Cells with centre within sphere
-    sphereToCell
-    {
-       centre   (0.2 0.2 -10);
-       radius   5.0;
-    }
-
-    // Cells with cellCentre nearest to coordinates
-    nearestToCell
-    {
-       points ((0 0 0) (1 1 1)(2 2 2));
-    }
-
-    // Select based on surface
-    surfaceToCell
-    {
-        file            "www.avl.com-geometry.stl";
-        outsidePoints   ((-99 -99 -59));    // definition of outside
-        includeCut      false;              // cells cut by surface
-        includeInside   false;              // cells not on outside of surf
-        includeOutside  false;              // cells on outside of surf
-        nearDistance    -1;                 // cells with centre near surf
-                                            // (set to -1 if not used)
-        curvature       0.9;                // cells within nearDistance
-                                            // and near surf curvature
-                                            // (set to -100 if not used)
-    }
-
-    // values of field within certain range
-    fieldToCell
-    {
-        fieldName   U;      // Note: uses mag(U) since volVectorField
-        min         0.1;
-        max         0.5;
-    }
-
-    // Mesh region (non-face connected part of (subset of)mesh)
-    regionToCell
-    {
-        set         c0;         // name of cellSet giving mesh subset
-        insidePoint (1 2 3);    // point inside region to select
-    }
-
-);
-
-
-// ************************************************************************* //

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

@@ -48,9 +48,21 @@ int main(int argc, char *argv[])
 {
     timeSelector::addOptions();
 #   include "addRegionOption.H"
-    argList::addBoolOption("noTopology");
+    argList::addBoolOption
-    argList::addBoolOption("allGeometry");
+    (
-    argList::addBoolOption("allTopology");
+        "noTopology",
+        "skip checking the mesh topology"
+    );
+    argList::addBoolOption
+    (
+        "allGeometry",
+        "include bounding box checks"
+    );
+    argList::addBoolOption
+    (
+        "allTopology",
+        "include extra topology checks"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"

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

@@ -107,7 +107,7 @@ void modifyOrAddFace
 
 label findPatchID(const polyMesh& mesh, const word& name)
 {
-    label patchI = mesh.boundaryMesh().findPatchID(name);
+    const label patchI = mesh.boundaryMesh().findPatchID(name);
 
     if (patchI == -1)
     {
@@ -124,6 +124,12 @@ label findPatchID(const polyMesh& mesh, const word& name)
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "Makes internal faces into boundary faces.\n"
+        "Does not duplicate points, unlike mergeOrSplitBaffles."
+    );
+
     #include "addOverwriteOption.H"
     #include "addRegionOption.H"
 
@@ -136,10 +142,23 @@ int main(int argc, char *argv[])
     );
     argList::addBoolOption("internalFacesOnly");
 
+    argList::addOption
+    (
+        "additionalPatches",
+        "(patch2 .. patchN)",
+        "specify additional patches for creating baffles"
+    );
+    argList::addBoolOption
+    (
+        "internalFacesOnly",
+        "do not convert boundary faces"
+    );
+
     #include "setRootCase.H"
     #include "createTime.H"
     runTime.functionObjects().off();
     #include "createNamedMesh.H"
+
     const word oldInstance = mesh.pointsInstance();
 
     const polyBoundaryMesh& patches = mesh.boundaryMesh();

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

@@ -672,17 +672,17 @@ int main(int argc, char *argv[])
     {
         const dictionary& dict = patchSources[addedI];
 
-        word patchName(dict.lookup("name"));
+        const word patchName(dict.lookup("name"));
-
         label destPatchI = patches.findPatchID(patchName);
 
         if (destPatchI == -1)
         {
-            FatalErrorIn(args.executable()) << "patch " << patchName
+            FatalErrorIn(args.executable())
-                << " not added. Problem." << abort(FatalError);
+                << "patch " << patchName << " not added. Problem."
+                << abort(FatalError);
         }
 
-        word sourceType(dict.lookup("constructFrom"));
+        const word sourceType(dict.lookup("constructFrom"));
 
         if (sourceType == "patches")
         {
@@ -710,7 +710,7 @@ int main(int argc, char *argv[])
         }
         else if (sourceType == "set")
         {
-            word setName(dict.lookup("set"));
+            const word setName(dict.lookup("set"));
 
             faceSet faces(mesh, setName);
 

applications/utilities/mesh/manipulation/faceSet/Make/files

@@ -1,4 +0,0 @@
-faceSet.C
-
-EXE = $(FOAM_APPBIN)/faceSet
-

applications/utilities/mesh/manipulation/faceSet/Make/options

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

applications/utilities/mesh/manipulation/faceSet/faceSet.C

@@ -1,196 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 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/>.
-
-Description
-    Selects a face set through a dictionary.
-
-\*---------------------------------------------------------------------------*/
-
-#include "argList.H"
-#include "Time.H"
-#include "polyMesh.H"
-#include "topoSetSource.H"
-#include "faceSet.H"
-
-using namespace Foam;
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Main program:
-
-int main(int argc, char *argv[])
-{
-#   include "setRootCase.H"
-#   include "createTime.H"
-#   include "createPolyMesh.H"
-
-    Info<< "Reading faceSetDict\n" << endl;
-
-    IOdictionary faceSetDict
-    (
-        IOobject
-        (
-            "faceSetDict",
-            runTime.system(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::NO_WRITE
-        )
-    );
-
-
-    const word setName(faceSetDict.lookup("name"));
-    const word actionName(faceSetDict.lookup("action"));
-
-    topoSetSource::setAction action = topoSetSource::toAction(actionName);
-
-
-    // Create topoSetSources
-    PtrList<topoSetSource> topoSetSources
-    (
-        faceSetDict.lookup("topoSetSources"),
-        topoSetSource::iNew(mesh)
-    );
-
-
-    // Load set to work
-    autoPtr<topoSet> currentSetPtr(NULL);
-    IOobject::readOption r;
-
-    if ((action == topoSetSource::NEW) || (action == topoSetSource::CLEAR))
-    {
-        r = IOobject::NO_READ;
-
-        currentSetPtr.reset
-        (
-            new faceSet
-            (
-                mesh,
-                setName,
-                mesh.nFaces()/10+1  // Reasonable size estimate.
-            )
-        );
-    }
-    else
-    {
-        r = IOobject::MUST_READ;
-
-        currentSetPtr.reset
-        (
-            new faceSet
-            (
-                mesh,
-                setName,
-                r
-            )
-        );
-    }
-
-    topoSet& currentSet = currentSetPtr();
-
-    Info<< "Set:" << currentSet.name()
-        << "  Size:" << currentSet.size()
-        << "  Action:" << actionName
-        << endl;
-
-    if ((r == IOobject::MUST_READ) && (action != topoSetSource::LIST))
-    {
-        // currentSet has been read so can make copy.
-        //backup(mesh, setName, currentSet, setName + "_old");
-    }
-
-    if (action == topoSetSource::CLEAR)
-    {
-        // Already handled above by not reading
-    }
-    else if (action == topoSetSource::INVERT)
-    {
-        currentSet.invert(currentSet.maxSize(mesh));
-    }
-    else if (action == topoSetSource::LIST)
-    {
-        currentSet.writeDebug(Info, mesh, 100);
-        Info<< endl;
-    }
-    else if (action == topoSetSource::SUBSET)
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            // Backup current set.
-            autoPtr<topoSet> oldSet
-            (
-                topoSet::New
-                (
-                    currentSet.type(),
-                    mesh,
-                    currentSet.name() + "_old2",
-                    currentSet
-                )
-            );
-
-            currentSet.clear();
-
-            topoSetSources[topoSetSourceI].applyToSet
-            (
-                topoSetSource::NEW,
-                currentSet
-            );
-
-            // Combine new value of currentSet with old one.
-            currentSet.subset(oldSet);
-        }
-    }
-    else
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            topoSetSources[topoSetSourceI].applyToSet(action, currentSet);
-        }
-    }
-
-
-    if (action != topoSetSource::LIST)
-    {
-        // Set has changed.
-
-        // Sync across coupled patches.
-        currentSet.sync(mesh);
-
-        Info<< "Writing " << currentSet.name()
-            << " (size " << currentSet.size() << ") to "
-            << currentSet.instance()/currentSet.local()
-               /currentSet.name()
-            << endl << endl;
-
-        currentSet.write();
-    }
-
-    Info<< "\nEnd\n" << endl;
-
-    return 0;
-}
-
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/faceSet/faceSetDict

@@ -1,82 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
-|   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      faceSetDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Name of set to operate on
-name f0;
-
-// One of clear/new/invert/add/delete|subset/list
-action new;
-
-// Actions to apply to pointSet. These are all the topoSetSource's ending
-// in ..ToFace (see the meshTools library).
-topoSetSources
-(
-    // Copy elements from faceSet
-    faceToFace
-    {
-        set f1;
-    }
-
-    // Select based on cellSet
-    cellToFace
-    {
-        set c0;
-        option all;         // All faces of cells
-        //option both;      // Only faces whose owner&neighbour are in cellSet
-    }
-
-    // Select based on pointSet
-    pointToFace
-    {
-        set p0;
-        option any;         // Faces using any point in pointSet
-        //option all        // Faces with all points in pointSet
-    }
-
-    //  Select by explicitly providing face labels
-    labelToFace
-    {
-        value (12 13 56);   // labels of faces
-    }
-
-    // All faces of patch
-    patchToFace
-    {
-        name ".*Wall";      // Name of patch, regular expressions allowed
-    }
-
-    // All faces of faceZone
-    zoneToFace
-    {
-        name ".*Zone1";     // Name of faceZone, regular expressions allowed
-    }
-
-    // Faces with face centre within box
-    boxToFace
-    {
-        box  (0 0 0) (1 1 1);
-    }
-
-    // Faces with normal to within certain angle aligned with vector.
-    normalToFace
-    {
-        normal (0 0 1);     // Vector
-        cos     0.01;       // Tolerance (max cos of angle)
-    }
-);
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/mergeMeshes/createTimes.H

@@ -1,15 +1,22 @@
     Info<< nl << "Create Times" << endl;
 
+    const fileName masterCasePath = masterCase.path();
+    const fileName masterCaseName = masterCase.name();
+
     Time runTimeMaster
     (
         Time::controlDictName,
-        rootDirMaster,
+        masterCasePath,
-        caseDirMaster
+        masterCaseName
     );
 
+    const fileName addCasePath = addCase.path();
+    const fileName addCaseName = addCase.name();
+
     Time runTimeToAdd
     (
         Time::controlDictName,
-        rootDirToAdd,
+        addCasePath,
-        caseDirToAdd
+        addCaseName
     );
+

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

@@ -32,16 +32,74 @@ Description
 
 using namespace Foam;
 
+void getRootCase(fileName& casePath)
+{
+    casePath.clean();
+
+    if (casePath.empty() || casePath == ".")
+    {
+        // handle degenerate form and '.'
+        casePath = cwd();
+    }
+    else if (casePath[0] != '/' && casePath.name() == "..")
+    {
+        // avoid relative cases ending in '..' - makes for very ugly names
+        casePath = cwd()/casePath;
+        casePath.clean();
+    }
+}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 // Main program:
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "merge two meshes"
+    );
+
     argList::noParallel();
-#   include "setRoots.H"
+    argList::validArgs.append("masterCase");
+    argList::addOption
+    (
+        "masterRegion",
+        "name",
+        "specify alternative mesh region for the master mesh"
+    );
+
+    argList::validArgs.append("addCase");
+    argList::addOption
+    (
+        "addRegion",
+        "name",
+        "specify alternative mesh region for the additional mesh"
+    );
+
+    argList args(argc, argv);
+    if (!args.check())
+    {
+         FatalError.exit();
+    }
+
+    fileName masterCase = args[1];
+    word masterRegion = polyMesh::defaultRegion;
+    args.optionReadIfPresent("masterRegion", masterRegion);
+
+    fileName addCase = args[2];
+    word addRegion = polyMesh::defaultRegion;
+    args.optionReadIfPresent("addRegion", addRegion);
+
+    getRootCase(masterCase);
+    getRootCase(addCase);
+
+    Info<< "Master:      " << masterCase << "  region " << masterRegion << nl
+        << "mesh to add: " << addCase    << "  region " << addRegion << endl;
+
     #include "createTimes.H"
 
-    Info<< "Reading master mesh for time = " << runTimeMaster.timeName() << endl;
+    Info<< "Reading master mesh for time = " << runTimeMaster.timeName() << nl;
 
     Info<< "Create mesh\n" << endl;
     mergePolyMesh masterMesh
@@ -55,7 +113,7 @@ int main(int argc, char *argv[])
     );
 
 
-    Info<< "Reading mesh to add for time = " << runTimeToAdd.timeName() << endl;
+    Info<< "Reading mesh to add for time = " << runTimeToAdd.timeName() << nl;
 
     Info<< "Create mesh\n" << endl;
     polyMesh meshToAdd

applications/utilities/mesh/manipulation/mergeMeshes/setRoots.H

@@ -1,32 +0,0 @@
-    argList::validArgs.clear();
-
-    argList::validArgs.append("master root");
-    argList::validArgs.append("master case");
-    argList::addOption("masterRegion", "name");
-
-    argList::validArgs.append("root to add");
-    argList::validArgs.append("case to add");
-    argList::addOption("addRegion", "name");
-
-    argList args(argc, argv);
-
-    if (!args.check())
-    {
-         FatalError.exit();
-    }
-
-    fileName rootDirMaster = args[1];
-    fileName caseDirMaster = args[2];
-    word masterRegion = polyMesh::defaultRegion;
-    args.optionReadIfPresent("masterRegion", masterRegion);
-
-    fileName rootDirToAdd = args[3];
-    fileName caseDirToAdd = args[4];
-    word addRegion = polyMesh::defaultRegion;
-    args.optionReadIfPresent("addRegion", addRegion);
-
-    Info<< "Master:      " << rootDirMaster << " " << caseDirMaster
-        << "  region " << masterRegion << nl
-        << "mesh to add: " << rootDirToAdd << " " << caseDirToAdd
-        << "  region " << addRegion << endl;
-

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

@@ -221,15 +221,30 @@ labelList findBaffles(const polyMesh& mesh, const labelList& boundaryFaces)
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "Detect faces that share points (baffles).\n"
+        "Merge them or duplicate the points."
+    );
+
     #include "addOverwriteOption.H"
     #include "addRegionOption.H"
-    argList::addBoolOption("split");
+    argList::addBoolOption
-    argList::addBoolOption("detectOnly");
+    (
+        "detectOnly",
+        "find baffles only, but do not merge or split them"
+    );
+    argList::addBoolOption
+    (
+        "split",
+        "topologically split duplicate surfaces"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"
     runTime.functionObjects().off();
     #include "createNamedMesh.H"
+
     const word oldInstance = mesh.pointsInstance();
 
     const bool split      = args.optionFound("split");
@@ -248,12 +263,10 @@ int main(int argc, char *argv[])
     if (detectOnly)
     {
         findBaffles(mesh, boundaryFaces);
-
         return 0;
     }
 
 
-
     // Read objects in time directory
     IOobjectList objects(mesh, runTime.timeName());
 

applications/utilities/mesh/manipulation/objToVTK/objToVTK.C

@@ -110,7 +110,6 @@ labelList parseVertices(const string& line)
 int main(int argc, char *argv[])
 {
     argList::noParallel();
-    argList::validArgs.clear();
     argList::validArgs.append("OBJ file");
     argList::validArgs.append("output VTK file");
     argList args(argc, argv);

applications/utilities/mesh/manipulation/pointSet/Make/files

@@ -1,4 +0,0 @@
-pointSet.C
-
-EXE = $(FOAM_APPBIN)/pointSet
-

applications/utilities/mesh/manipulation/pointSet/Make/options

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

applications/utilities/mesh/manipulation/pointSet/pointSet.C

@@ -1,196 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 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/>.
-
-Description
-    Selects a point set through a dictionary.
-
-\*---------------------------------------------------------------------------*/
-
-#include "argList.H"
-#include "Time.H"
-#include "polyMesh.H"
-#include "topoSetSource.H"
-#include "pointSet.H"
-
-using namespace Foam;
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Main program:
-
-int main(int argc, char *argv[])
-{
-#   include "setRootCase.H"
-#   include "createTime.H"
-#   include "createPolyMesh.H"
-
-    Info<< "Reading pointSetDict\n" << endl;
-
-    IOdictionary pointSetDict
-    (
-        IOobject
-        (
-            "pointSetDict",
-            runTime.system(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::NO_WRITE
-        )
-    );
-
-
-    const word setName(pointSetDict.lookup("name"));
-    const word actionName(pointSetDict.lookup("action"));
-
-    topoSetSource::setAction action = topoSetSource::toAction(actionName);
-
-
-    // Create topoSetSources
-    PtrList<topoSetSource> topoSetSources
-    (
-        pointSetDict.lookup("topoSetSources"),
-        topoSetSource::iNew(mesh)
-    );
-
-
-    // Load set to work
-    autoPtr<topoSet> currentSetPtr(NULL);
-    IOobject::readOption r;
-
-    if ((action == topoSetSource::NEW) || (action == topoSetSource::CLEAR))
-    {
-        r = IOobject::NO_READ;
-
-        currentSetPtr.reset
-        (
-            new pointSet
-            (
-                mesh,
-                setName,
-                mesh.nPoints()/10+1  // Reasonable size estimate.
-            )
-        );
-    }
-    else
-    {
-        r = IOobject::MUST_READ;
-
-        currentSetPtr.reset
-        (
-            new pointSet
-            (
-                mesh,
-                setName,
-                r
-            )
-        );
-    }
-
-    topoSet& currentSet = currentSetPtr();
-
-    Info<< "Set:" << currentSet.name()
-        << "  Size:" << currentSet.size()
-        << "  Action:" << actionName
-        << endl;
-
-    if ((r == IOobject::MUST_READ) && (action != topoSetSource::LIST))
-    {
-        // currentSet has been read so can make copy.
-        //backup(mesh, setName, currentSet, setName + "_old");
-    }
-
-    if (action == topoSetSource::CLEAR)
-    {
-        // Already handled above by not reading
-    }
-    else if (action == topoSetSource::INVERT)
-    {
-        currentSet.invert(currentSet.maxSize(mesh));
-    }
-    else if (action == topoSetSource::LIST)
-    {
-        currentSet.writeDebug(Info, mesh, 100);
-        Info<< endl;
-    }
-    else if (action == topoSetSource::SUBSET)
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            // Backup current set.
-            autoPtr<topoSet> oldSet
-            (
-                topoSet::New
-                (
-                    currentSet.type(),
-                    mesh,
-                    currentSet.name() + "_old2",
-                    currentSet
-                )
-            );
-
-            currentSet.clear();
-
-            topoSetSources[topoSetSourceI].applyToSet
-            (
-                topoSetSource::NEW,
-                currentSet
-            );
-
-            // Combine new value of currentSet with old one.
-            currentSet.subset(oldSet);
-        }
-    }
-    else
-    {
-        // Apply topoSetSources to it to handle new/add/delete
-        forAll(topoSetSources, topoSetSourceI)
-        {
-            topoSetSources[topoSetSourceI].applyToSet(action, currentSet);
-        }
-    }
-
-
-    if (action != topoSetSource::LIST)
-    {
-        // Set has changed.
-
-        // Sync across coupled patches.
-        currentSet.sync(mesh);
-
-        Info<< "Writing " << currentSet.name()
-            << " (size " << currentSet.size() << ") to "
-            << currentSet.instance()/currentSet.local()
-               /currentSet.name()
-            << endl << endl;
-
-        currentSet.write();
-    }
-
-    Info<< "\nEnd\n" << endl;
-
-    return 0;
-}
-
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/pointSet/pointSetDict

@@ -1,84 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
-|   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      pointSetDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Name of set to operate on
-name p0;
-
-// One of clear/new/invert/add/delete|subset/list
-action new;
-
-// Actions to apply to pointSet. These are all the topoSetSource's ending
-// in ..ToPoint (see the meshTools library).
-topoSetSources
-(
-    // Copy elements from pointSet
-    pointToPoint
-    {
-        set p1;
-    }
-
-    // Select based on cellSet
-    cellToPoint
-    {
-        set c0;
-        option all;         // all points of cell
-    }
-
-    // Select based on faceSet
-    faceToPoint
-    {
-        set f0;             // name of faceSet
-        option all;         // all points of face
-    }
-
-    // Select by explicitly providing point labels
-    labelToPoint
-    {
-        value (12 13 56);   // labels of points
-    }
-
-    // All points in pointzone
-    zoneToPoint
-    {
-        name ".*Zone";      // name of pointZone, regular expressions allowed
-    }
-
-    // Points nearest to coordinates
-    nearestToPoint
-    {
-       points ((0 0 0) (1 1 1));
-    }
-
-    // Points with coordinate within box
-    boxToPoint
-    {
-       box   (0 0 0) (1 1 1);
-    }
-
-    // Select based on surface
-    surfaceToPoint
-    {
-        file            "www.avl.com-geometry.stl";
-        nearDistance    0.1;    // points near to surface
-        includeInside   false;  // points on inside of surface
-                                // (requires closed surface with consistent
-                                //  normals)
-        includeOutside  false;  //   ,,    outside  ,,
-    }
-);
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/refineMesh/refineMesh.C

@@ -290,8 +290,17 @@ label twoDNess(const polyMesh& mesh)
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "refine cells in multiple directions"
+    );
+
     #include "addOverwriteOption.H"
-    argList::addBoolOption("dict");
+    argList::addBoolOption
+    (
+        "dict",
+        "refine according to system/refineMeshDict"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"
@@ -301,7 +310,6 @@ int main(int argc, char *argv[])
 
     printEdgeStats(mesh);
 
-
     //
     // Read/construct control dictionary
     //