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

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/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/incompressible/adjointShapeOptimizationFoam/createFields.H

@@ -1,4 +1,4 @@
-    Info << "Reading field p\n" << endl;
+    Info<< "Reading field p\n" << endl;
     volScalarField p
     (
         IOobject
@@ -12,7 +12,7 @@
         mesh
     );
 
-    Info << "Reading field U\n" << endl;
+    Info<< "Reading field U\n" << endl;
     volVectorField U
     (
         IOobject
@@ -34,7 +34,7 @@
     setRefCell(p, mesh.solutionDict().subDict("SIMPLE"), pRefCell, pRefValue);
 
 
-    Info << "Reading field pa\n" << endl;
+    Info<< "Reading field pa\n" << endl;
     volScalarField pa
     (
         IOobject
@@ -48,7 +48,7 @@
         mesh
     );
 
-    Info << "Reading field Ua\n" << endl;
+    Info<< "Reading field Ua\n" << endl;
     volVectorField Ua
     (
         IOobject
@@ -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/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/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/settlingFoam/pmhEqn.H

@@ -17,7 +17,7 @@ phi =
 surfaceScalarField phiU("phiU", phi);
 phi -= ghf*fvc::snGrad(rho)*rUAf*mesh.magSf();
 
-for(int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
+for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
 {
     fvScalarMatrix pmhEqn
     (

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
 
 \*---------------------------------------------------------------------------*/
 
@@ -429,15 +429,18 @@ 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

@@ -46,12 +46,18 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    #include "addOverwriteOption.H"
     argList::noParallel();
     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

@@ -96,11 +96,15 @@ bool limitRefinementLevel
 
 int main(int argc, char *argv[])
 {
-    argList::addBoolOption("readLevel");
+    argList::addBoolOption
+    (
+        "readLevel",
+        "read level from refinementLevel file"
+    );
 
-#   include "setRootCase.H"
+    #include "setRootCase.H"
-#   include "createTime.H"
+    #include "createTime.H"
-#   include "createPolyMesh.H"
+    #include "createPolyMesh.H"
 
     Info<< "Dividing cells into bins depending on cell volume.\nThis will"
         << " correspond to refinement levels for a mesh with only 2x2x2"
@@ -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

@@ -517,17 +517,35 @@ void collectCuts
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    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::validArgs.append("edge angle [0..360]");
 
-#   include "setRootCase.H"
+    argList::addOption
-#   include "createTime.H"
+    (
+        "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"
     runTime.functionObjects().off();
-#   include "createPolyMesh.H"
+    #include "createPolyMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     const scalar featureAngle = args.argRead<scalar>(1);
@@ -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");
@@ -1554,7 +1566,7 @@ int main(int argc, char *argv[])
     // interior boundaries are handled via faceSets
     // cell zones will only be written if there is more than one
 
-    if (writeZones && cellGroupZoneID.size()>1)
+    if (writeZones && cellGroupZoneID.size() > 1)
     {
         Info<< "Adding Zones" << endl;
         List<pointZone*> pz(0);

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[])
 {
-    timeSelector::addOptions();
+    argList::addNote
-    argList::addBoolOption("patchFaces");
+    (
-    argList::addBoolOption("patchEdges");
+        "for mesh debugging: write mesh as separate OBJ files"
-    argList::addOption("cell", "cellI");
+    );
-    argList::addOption("face", "faceI");
-    argList::addOption("point", "pointI");
-    argList::addOption("cellSet", "setName");
-    argList::addOption("faceSet", "setName");
-#   include "addRegionOption.H"
 
-#   include "setRootCase.H"
+    timeSelector::addOptions();
-#   include "createTime.H"
+    argList::addBoolOption
+    (
+        "patchFaces",
+        "write patch faces edges"
+    );
+    argList::addBoolOption
+    (
+        "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"
@@ -401,7 +439,7 @@ int main(int argc, char *argv[])
 
     instantList timeDirs = timeSelector::select0(runTime, args);
 
-#   include "createNamedPolyMesh.H"
+    #include "createNamedPolyMesh.H"
 
     forAll(timeDirs, timeI)
     {
@@ -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)
     {
@@ -124,18 +124,35 @@ label findPatchID(const polyMesh& mesh, const word& name)
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    argList::addNote
-#   include "addRegionOption.H"
+    (
+        "Makes internal faces into boundary faces.\n"
+        "Does not duplicate points, unlike mergeOrSplitBaffles."
+    );
+
+    #include "addOverwriteOption.H"
+    #include "addRegionOption.H"
 
     argList::validArgs.append("faceZone");
     argList::validArgs.append("patch");
-    argList::addOption("additionalPatches", "(patch2 .. patchN)");
-    argList::addBoolOption("internalFacesOnly");
 
-#   include "setRootCase.H"
+    argList::addOption
-#   include "createTime.H"
+    (
+        "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"
+    #include "createNamedMesh.H"
+
     const word oldInstance = mesh.pointsInstance();
 
     const polyBoundaryMesh& patches = mesh.boundaryMesh();

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

@@ -681,17 +681,17 @@ 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")
         {
@@ -719,7 +719,7 @@ 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::noParallel();
+    argList::addNote
-#   include "setRoots.H"
+    (
-#   include "createTimes.H"
+        "merge two meshes"
+    );
 
-    Info<< "Reading master mesh for time = " << runTimeMaster.timeName() << endl;
+    argList::noParallel();
+    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() << 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[])
 {
-#   include "addOverwriteOption.H"
+    argList::addNote
-#   include "addRegionOption.H"
+    (
-    argList::addBoolOption("split");
+        "Detect faces that share points (baffles).\n"
-    argList::addBoolOption("detectOnly");
+        "Merge them or duplicate the points."
+    );
 
-#   include "setRootCase.H"
+    #include "addOverwriteOption.H"
-#   include "createTime.H"
+    #include "addRegionOption.H"
+    argList::addBoolOption
+    (
+        "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"
+    #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

@@ -290,18 +290,26 @@ label twoDNess(const polyMesh& mesh)
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    argList::addNote
-    argList::addBoolOption("dict");
+    (
+        "refine cells in multiple directions"
+    );
 
-#   include "setRootCase.H"
+    #include "addOverwriteOption.H"
-#   include "createTime.H"
+    argList::addBoolOption
+    (
+        "dict",
+        "refine according to system/refineMeshDict"
+    );
+
+    #include "setRootCase.H"
+    #include "createTime.H"
     runTime.functionObjects().off();
-#   include "createPolyMesh.H"
+    #include "createPolyMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     printEdgeStats(mesh);
 
-
     //
     // Read/construct control dictionary
     //

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

@@ -363,9 +363,21 @@ autoPtr<mapPolyMesh> reorderMesh
 
 int main(int argc, char *argv[])
 {
-    argList::addBoolOption("blockOrder");
+    argList::addBoolOption
-    argList::addBoolOption("orderPoints");
+    (
-    argList::addBoolOption("writeMaps");
+        "blockOrder",
+        "order cells into regions (using decomposition)"
+    );
+    argList::addBoolOption
+    (
+        "orderPoints",
+        "order points into internal and boundary points"
+    );
+    argList::addBoolOption
+    (
+        "writeMaps",
+        "write cellMap, faceMap, pointMap in polyMesh/"
+    );
 
 #   include "addOverwriteOption.H"
 #   include "addTimeOptions.H"

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

@@ -439,6 +439,7 @@ bool doCommand
     const word& actionName,
     const bool writeVTKFile,
     const bool writeCurrentTime,
+    const bool noSync,
     Istream& is
 )
 {
@@ -581,7 +582,7 @@ bool doCommand
                 // Set will have been modified.
 
                 // Synchronize for coupled patches.
-                currentSet.sync(mesh);
+                if (!noSync) currentSet.sync(mesh);
 
                 // Write
                 if (writeVTKFile)
@@ -828,7 +829,17 @@ int main(int argc, char *argv[])
 #   include "addRegionOption.H"
     argList::addBoolOption("noVTK", "do not write VTK files");
     argList::addBoolOption("loop", "execute batch commands for all timesteps");
-    argList::addOption("batch", "file");
+    argList::addOption
+    (
+        "batch",
+        "file",
+        "process in batch mode, using input from specified file"
+    );
+    argList::addBoolOption
+    (
+        "noSync",
+        "do not synchronise selection across coupled patches"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -837,6 +848,7 @@ int main(int argc, char *argv[])
     const bool writeVTK = !args.optionFound("noVTK");
     const bool loop = args.optionFound("loop");
     const bool batch = args.optionFound("batch");
+    const bool noSync = args.optionFound("noSync");
 
     if (loop && !batch)
     {
@@ -1004,6 +1016,7 @@ int main(int argc, char *argv[])
                     actionName,
                     writeVTK,
                     loop,   // if in looping mode dump sets to time directory
+                    noSync,
                     is
                 );
 

applications/utilities/mesh/manipulation/setsToZones/setsToZones.C

@@ -57,14 +57,23 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
-    argList::addBoolOption("noFlipMap");
+    argList::addNote
+    (
+        "add point/face/cell Zones from similar named point/face/cell Sets"
+    );
 
-#   include "addRegionOption.H"
+    argList::addBoolOption
-#   include "addTimeOptions.H"
+    (
-#   include "setRootCase.H"
+        "noFlipMap",
-#   include "createTime.H"
+        "ignore orientation of faceSet"
+    );
 
-    bool noFlipMap = args.optionFound("noFlipMap");
+    #include "addRegionOption.H"
+    #include "addTimeOptions.H"
+    #include "setRootCase.H"
+    #include "createTime.H"
+
+    const bool noFlipMap = args.optionFound("noFlipMap");
 
     // Get times list
     instantList Times = runTime.times();
@@ -73,11 +82,11 @@ int main(int argc, char *argv[])
     label endTime = Times.size();
 
     // check -time and -latestTime options
-#   include "checkTimeOption.H"
+    #include "checkTimeOption.H"
 
     runTime.setTime(Times[startTime], startTime);
 
-#   include "createNamedPolyMesh.H"
+    #include "createNamedPolyMesh.H"
 
     // Search for list of objects for the time of the mesh
     word setsInstance = runTime.findInstance
@@ -153,9 +162,19 @@ int main(int argc, char *argv[])
         DynamicList<label> addressing(set.size());
         DynamicList<bool> flipMap(set.size());
 
-        if (!noFlipMap)
+        if (noFlipMap)
         {
-            word setName(set.name() + "SlaveCells");
+            // No flip map.
+            forAll(faceLabels, i)
+            {
+                label faceI = faceLabels[i];
+                addressing.append(faceI);
+                flipMap.append(false);
+            }
+        }
+        else
+        {
+            const word setName(set.name() + "SlaveCells");
 
             Info<< "Trying to load cellSet " << setName
                 << " to find out the slave side of the zone." << nl
@@ -226,16 +245,6 @@ int main(int argc, char *argv[])
                 flipMap.append(flip);
             }
         }
-        else
-        {
-            // No flip map.
-            forAll(faceLabels, i)
-            {
-                label faceI = faceLabels[i];
-                addressing.append(faceI);
-                flipMap.append(false);
-            }
-        }
 
         label zoneID = mesh.faceZones().findZoneID(set.name());
         if (zoneID == -1)

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

@@ -85,12 +85,12 @@ label findEdge(const primitiveMesh& mesh, const label v0, const label v1)
 // Checks whether patch present
 void checkPatch(const polyBoundaryMesh& bMesh, const word& name)
 {
-    label patchI = bMesh.findPatchID(name);
+    const label patchI = bMesh.findPatchID(name);
 
     if (patchI == -1)
     {
         FatalErrorIn("checkPatch(const polyBoundaryMesh&, const word&)")
-            << "Cannot find patch " << name << endl
+            << "Cannot find patch " << name << nl
             << "It should be present but of zero size" << endl
             << "Valid patches are " << bMesh.names()
             << exit(FatalError);

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

@@ -1473,26 +1473,68 @@ void writeCellToRegion(const fvMesh& mesh, const labelList& cellRegion)
 }
 
 
-
 // Main program:
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    argList::addNote
-    argList::addBoolOption("cellZones");
+    (
-    argList::addBoolOption("cellZonesOnly");
+        "splits mesh into multiple regions (detected by walking across faces)"
-    argList::addOption("cellZonesFileOnly", "cellZonesName");
+    );
-    argList::addOption("blockedFaces", "faceSet");
+    #include "addOverwriteOption.H"
-    argList::addBoolOption("makeCellZones");
+    argList::addBoolOption
-    argList::addBoolOption("largestOnly");
+    (
-    argList::addOption("insidePoint", "point");
+        "cellZones",
-    argList::addBoolOption("detectOnly");
+        "additionally split cellZones off into separate regions"
-    argList::addBoolOption("sloppyCellZones");
+    );
+    argList::addBoolOption
+    (
+        "cellZonesOnly",
+        "use cellZones only to split mesh into regions; do not use walking"
+    );
+    argList::addOption
+    (
+        "cellZonesFileOnly",
+        "file",
+        "like -cellZonesOnly, but use specified file"
+    );
+    argList::addOption
+    (
+        "blockedFaces",
+        "faceSet",
+        "specify additional region boundaries that walking does not cross"
+    );
+    argList::addBoolOption
+    (
+        "makeCellZones",
+        "place cells into cellZones instead of splitting mesh"
+    );
+    argList::addBoolOption
+    (
+        "largestOnly",
+        "only write largest region"
+    );
+    argList::addOption
+    (
+        "insidePoint",
+        "point",
+        "only write region containing point"
+    );
+    argList::addBoolOption
+    (
+        "detectOnly",
+        "do not write mesh"
+    );
+    argList::addBoolOption
+    (
+        "sloppyCellZones",
+        "try to match heuristically regions to existing cell zones"
+    );
 
-#   include "setRootCase.H"
+    #include "setRootCase.H"
-#   include "createTime.H"
+    #include "createTime.H"
     runTime.functionObjects().off();
-#   include "createMesh.H"
+    #include "createMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     word blockedFacesName;
@@ -1514,10 +1556,7 @@ int main(int argc, char *argv[])
     if
     (
         (useCellZonesOnly || useCellZonesFile)
-     && (
+     && (useCellZones || blockedFacesName.size())
-            blockedFacesName != word::null
-         || useCellZones
-        )
     )
     {
         FatalErrorIn(args.executable())
@@ -1529,7 +1568,6 @@ int main(int argc, char *argv[])
     }
 
 
-
     if (insidePoint && largestOnly)
     {
         FatalErrorIn(args.executable())
@@ -1719,7 +1757,6 @@ int main(int argc, char *argv[])
     writeCellToRegion(mesh, cellRegion);
 
 
-
     // Sizes per region
     // ~~~~~~~~~~~~~~~~
 

applications/utilities/mesh/manipulation/stitchMesh/stitchMesh.C

@@ -40,6 +40,7 @@ Description
     Comparable to running a meshModifier of the form
     (if masterPatch is called "M" and slavePatch "S"):
 
+    @verbatim
     couple
     {
         type                    slidingInterface;
@@ -51,6 +52,7 @@ Description
         slavePatchName          S;
         typeOfMatch             partial or integral
     }
+    @endverbatim
 
 
 \*---------------------------------------------------------------------------*/
@@ -168,7 +170,7 @@ label addCellZone(const polyMesh& mesh, const word& name)
 // Checks whether patch present
 void checkPatch(const polyBoundaryMesh& bMesh, const word& name)
 {
-    label patchI = bMesh.findPatchID(name);
+    const label patchI = bMesh.findPatchID(name);
 
     if (patchI == -1)
     {
@@ -192,22 +194,41 @@ void checkPatch(const polyBoundaryMesh& bMesh, const word& name)
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "merge the faces on the specified patches (if geometrically possible)\n"
+        "so the faces become internal"
+    );
+
     argList::noParallel();
-#   include "addOverwriteOption.H"
+    #include "addOverwriteOption.H"
-#   include "addRegionOption.H"
+    #include "addRegionOption.H"
 
     argList::validArgs.append("masterPatch");
     argList::validArgs.append("slavePatch");
 
-    argList::addBoolOption("partial");
+    argList::addBoolOption
-    argList::addBoolOption("perfect");
+    (
+        "partial",
+        "couple partially overlapping patches"
+    );
+    argList::addBoolOption
+    (
+        "perfect",
+        "couple perfectly aligned patches"
+    );
+    argList::addOption
+    (
+        "toleranceDict",
+        "file",
+        "dictionary file with tolerances"
+    );
 
-    argList::addOption("toleranceDict", "file with tolerances");
+    #include "setRootCase.H"
-
+    #include "createTime.H"
-#   include "setRootCase.H"
-#   include "createTime.H"
     runTime.functionObjects().off();
-#   include "createNamedMesh.H"
+    #include "createNamedMesh.H"
+
     const word oldInstance = mesh.pointsInstance();
 
     const word masterPatchName = args[1];
@@ -220,7 +241,7 @@ int main(int argc, char *argv[])
     if (partialCover && perfectCover)
     {
         FatalErrorIn(args.executable())
-            << "Cannot both supply partial and perfect." << endl
+            << "Cannot supply both partial and perfect." << endl
             << "Use perfect match option if the patches perfectly align"
             << " (both vertex positions and face centres)" << endl
             << exit(FatalError);
@@ -291,11 +312,7 @@ int main(int argc, char *argv[])
     // Create and add face zones and mesh modifiers
 
     // Master patch
-    const polyPatch& masterPatch =
+    const polyPatch& masterPatch = mesh.boundaryMesh()[masterPatchName];
-        mesh.boundaryMesh()
-        [
-            mesh.boundaryMesh().findPatchID(masterPatchName)
-        ];
 
     // Make list of masterPatch faces
     labelList isf(masterPatch.size());
@@ -352,11 +369,7 @@ int main(int argc, char *argv[])
         );
 
         // Slave patch
-        const polyPatch& slavePatch =
+        const polyPatch& slavePatch = mesh.boundaryMesh()[slavePatchName];
-            mesh.boundaryMesh()
-            [
-                mesh.boundaryMesh().findPatchID(slavePatchName)
-            ];
 
         labelList osf(slavePatch.size());
 

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

@@ -150,14 +150,25 @@ void subsetPointFields
 
 int main(int argc, char *argv[])
 {
-#   include "addOverwriteOption.H"
+    argList::addNote
-    argList::validArgs.append("set");
+    (
-    argList::addOption("patch", "patch name");
+        "select a mesh subset based on a cellSet"
+    );
 
-#   include "setRootCase.H"
+    #include "addOverwriteOption.H"
-#   include "createTime.H"
+    argList::validArgs.append("cellSet");
+    argList::addOption
+    (
+        "patch",
+        "name",
+        "add exposed internal faces to specified patch instead of to "
+        "'oldInternalFaces'"
+    );
+    #include "setRootCase.H"
+    #include "createTime.H"
     runTime.functionObjects().off();
-#   include "createMesh.H"
+    #include "createMesh.H"
+
     const word oldInstance = mesh.pointsInstance();
 
     const word setName = args[1];
@@ -190,7 +201,7 @@ int main(int argc, char *argv[])
     else
     {
         Info<< "Adding exposed internal faces to a patch called"
-            << " \"oldInternalFaces\" (created if nessecary)" << endl
+            << " \"oldInternalFaces\" (created if necessary)" << endl
             << endl;
     }
 

applications/utilities/mesh/manipulation/topoSet/Make/files

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

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

@@ -0,0 +1,233 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    Operates on cellSets/faceSets/pointSets through a dictionary.
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "Time.H"
+#include "polyMesh.H"
+#include "topoSetSource.H"
+#include "cellSet.H"
+#include "faceSet.H"
+#include "pointSet.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::addOption
+    (
+        "dict",
+        "file",
+        "specify an alternative dictionary for the topoSet dictionary"
+    );
+#   include "addRegionOption.H"
+    argList::addBoolOption
+    (
+        "noSync",
+        "do not synchronise selection across coupled patches"
+    );
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createNamedPolyMesh.H"
+
+    const bool noSync = args.optionFound("noSync");
+
+    const word dictName("topoSetDict");
+
+    fileName dictPath = dictName;
+    if (args.optionFound("dict"))
+    {
+        dictPath = args["dict"];
+        if (isDir(dictPath))
+        {
+            dictPath = dictPath / dictName;
+        }
+    }
+
+    Info<< "Reading " << dictName << "\n" << endl;
+
+    IOdictionary topoSetDict
+    (
+        (
+            args.optionFound("dict")
+          ? IOobject
+            (
+                dictPath,
+                mesh,
+                IOobject::MUST_READ,
+                IOobject::NO_WRITE
+            )
+          : IOobject
+            (
+                dictName,
+                runTime.system(),
+                mesh,
+                IOobject::MUST_READ,
+                IOobject::NO_WRITE
+            )
+        ) 
+    );
+
+
+    // Read set construct info from dictionary
+    PtrList<dictionary> patchSources(topoSetDict.lookup("actions"));
+
+    forAll(patchSources, i)
+    {
+        const dictionary& dict = patchSources[i];
+
+        const word setName(dict.lookup("name"));
+        const word actionName(dict.lookup("action"));
+        const word setType(dict.lookup("type"));
+
+
+        topoSetSource::setAction action = topoSetSource::toAction(actionName);
+
+        autoPtr<topoSet> currentSet;
+        if
+        (
+            (action == topoSetSource::NEW)
+         || (action == topoSetSource::CLEAR)
+        )
+        {
+            currentSet = topoSet::New(setType, mesh, setName, 10000);
+            Info<< "Created set " << setName << endl;
+        }
+        else if (action == topoSetSource::REMOVE)
+        {
+            //?
+        }
+        else
+        {
+            currentSet = topoSet::New
+            (
+                setType,
+                mesh,
+                setName,
+                IOobject::MUST_READ
+            );
+            Info<< "Read set " << setName << " with size "
+                << currentSet().size() << endl;
+        }
+
+
+
+        // Handle special actions (clear, invert) locally, rest through sources.
+        switch (action)
+        {
+            case topoSetSource::NEW:
+            case topoSetSource::ADD:
+            case topoSetSource::DELETE:
+            {
+                Info<< "    Applying source " << word(dict.lookup("source"))
+                    << endl;
+                autoPtr<topoSetSource> source = topoSetSource::New
+                (
+                    dict.lookup("source"),
+                    mesh,
+                    dict.subDict("sourceInfo")
+                );
+
+                source().applyToSet(action, currentSet());
+                // Synchronize for coupled patches.
+                if (!noSync) currentSet().sync(mesh);
+                currentSet().write();
+            }
+            break;
+
+            case topoSetSource::SUBSET:
+            {
+                Info<< "    Applying source " << word(dict.lookup("source"))
+                    << endl;
+                autoPtr<topoSetSource> source = topoSetSource::New
+                (
+                    dict.lookup("source"),
+                    mesh,
+                    dict.subDict("sourceInfo")
+                );
+
+                // Backup current set.
+                autoPtr<topoSet> oldSet
+                (
+                    topoSet::New
+                    (
+                        setType,
+                        mesh,
+                        currentSet().name() + "_old2",
+                        currentSet()
+                    )
+                );
+
+                currentSet().clear();
+                source().applyToSet(topoSetSource::NEW, currentSet());
+
+                // Combine new value of currentSet with old one.
+                currentSet().subset(oldSet());
+                // Synchronize for coupled patches.
+                if (!noSync) currentSet().sync(mesh);
+                currentSet().write();
+            }
+            break;
+
+            case topoSetSource::CLEAR:
+                Info<< "    Clearing set" << endl;
+                currentSet().clear();
+                currentSet().write();
+            break;
+
+            case topoSetSource::INVERT:
+                Info<< "    Inverting set" << endl;
+                currentSet().invert(currentSet().maxSize(mesh));
+                currentSet().write();
+            break;
+
+            default:
+                WarningIn(args.executable())
+                    << "Unhandled action " << action << endl;
+            break;
+        }
+
+        if (currentSet.valid())
+        {
+            Info<< "    Set " << currentSet().name()
+                << " now size " << currentSet().size()
+                << endl;
+        }
+    }
+
+    Info<< "\nEnd\n" << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/mesh/manipulation/topoSet/topoSetDict

@@ -0,0 +1,363 @@
+/*--------------------------------*- 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      topoSetDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// List of actions. Each action is a dictionary with e.g.
+//     // name of set
+//     name    c0;
+//
+//     // type: pointSet/faceSet/cellSet/faceZoneSet/cellZoneSet
+//     type    cellSet;
+//
+//     // action to perform on set. Two types:
+//     // - require no source : clear/invert
+//     // - require source    : new/add/delete/subset
+//     action  new;
+//
+// The source entry varies according to the type of set:
+//
+// cellSet
+// ~~~~~~~
+//
+//    // Select by explicitly providing cell labels
+//    source labelToCell;
+//    {
+//        value (12 13 56);   // labels of cells
+//    }
+//
+//    // Copy elements from cellSet
+//    source cellToCell;
+//    {
+//        set c1;
+//    }
+//
+//    // Cells in cell zone
+//    source zoneToCell;
+//    {
+//        name ".*Zone";      // Name of cellZone, regular expressions allowed
+//    }
+//
+//    // Cells on master or slave side of faceZone
+//    source faceZoneToCell;
+//    {
+//        name ".*Zone";      // Name of faceZone, regular expressions allowed
+//        option master;      // master/slave
+//    }
+//
+//    // Select based on faceSet
+//    source 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
+//    source pointToCell;
+//    {
+//        set p0;
+//        option any;         // cell with any point in pointSet
+//        //option all;       // cell with all points in pointSet
+//    }
+//
+//    // Select based on cellShape
+//    source shapeToCell;
+//    {
+//        type hex;           // hex/wedge/prism/pyr/tet/tetWedge/splitHex
+//    }
+//
+//    // Cells with cell centre within box
+//    source 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.
+//    source 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
+//    source 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
+//    source sphereToCell;
+//    {
+//       centre   (0.2 0.2 -10);
+//       radius   5.0;
+//    }
+//
+//    // Cells with cellCentre nearest to coordinates
+//    source nearestToCell;
+//    {
+//       points ((0 0 0) (1 1 1)(2 2 2));
+//    }
+//
+//    // Select based on surface
+//    source 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
+//    source 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)
+//    source regionToCell;
+//    {
+//        set         c0;         // name of cellSet giving mesh subset
+//        insidePoint (1 2 3);    // point inside region to select
+//    }
+//
+//
+//
+// faceSet
+// ~~~~~~~
+//
+//    // Copy elements from faceSet
+//    source faceToFace;
+//    {
+//        set f1;
+//    }
+//
+//    // Select based on cellSet
+//    source cellToFace;
+//    {
+//        set c0;
+//        option all;         // All faces of cells
+//        //option both;      // Only faces whose owner&neighbour are in cellSet
+//    }
+//
+//    // Select based on pointSet
+//    source 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
+//    source labelToFace;
+//    {
+//        value (12 13 56);   // labels of faces
+//    }
+//
+//    // All faces of patch
+//    source patchToFace;
+//    {
+//        name ".*Wall";      // Name of patch, regular expressions allowed
+//    }
+//
+//    // All faces of faceZone
+//    source zoneToFace;
+//    {
+//        name ".*Zone1";     // Name of faceZone, regular expressions allowed
+//    }
+//
+//    // Faces with face centre within box
+//    source boxToFace;
+//    {
+//        box  (0 0 0) (1 1 1);
+//    }
+//
+//    // Faces with normal to within certain angle aligned with vector.
+//    source normalToFace;
+//    {
+//        normal (0 0 1);     // Vector
+//        cos     0.01;       // Tolerance (max cos of angle)
+//    }
+//
+//
+//
+// pointSet
+// ~~~~~~~
+//
+//    // Copy elements from pointSet
+//    source pointToPoint;
+//    {
+//        set p1;
+//    }
+//
+//    // Select based on cellSet
+//    source cellToPoint;
+//    {
+//        set c0;
+//        option all;         // all points of cell
+//    }
+//
+//    // Select based on faceSet
+//    source faceToPoint;
+//    {
+//        set f0;             // name of faceSet
+//        option all;         // all points of face
+//    }
+//
+//    // Select by explicitly providing point labels
+//    source labelToPoint;
+//    {
+//        value (12 13 56);   // labels of points
+//    }
+//
+//    // All points in pointzone
+//    source zoneToPoint;
+//    {
+//        name ".*Zone";      // name of pointZone, regular expressions allowed
+//    }
+//
+//    // Points nearest to coordinates
+//    source nearestToPoint;
+//    {
+//       points ((0 0 0) (1 1 1));
+//    }
+//
+//    // Points with coordinate within box
+//    source boxToPoint;
+//    {
+//       box   (0 0 0) (1 1 1);
+//    }
+//
+//    // Select based on surface
+//    source 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  ,,
+//    }
+//
+//
+//
+//
+// cellZoneSet
+// ~~~~~~~~~~~
+// (mirrors operations on a cellSet into a cellZone)
+//
+//    // Select based on cellSet
+//    source setToCellZone;
+//    {
+//        set c0;           // name of cellSet
+//    }
+//
+//
+//
+// faceZoneSet
+// ~~~~~~~~~~~
+//    // Select based on faceSet without orientation
+//    source setToFaceZone;
+//    {
+//        set f0;           // name of faceSet
+//    }
+//
+//    // Select based on faceSet, using cellSet to determine orientation
+//    source setsToFaceZone;
+//    {
+//        faceSet f0;       // name of faceSet
+//        cellSet c0;       // name of cellSet of slave side
+//    }
+
+
+
+actions
+(
+    // Example:pick up internal faces on outside of cellSet
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    // Load initial cellSet
+    {
+        name    c0;
+        type    cellSet;
+        action  new;
+        source labelToCell;
+        sourceInfo
+        {
+            value (12 13 56);
+        }
+    }
+
+    // Get all faces in cellSet
+    {
+        name    f0;
+        type    faceSet;
+        action  new;
+        source  cellToFace;
+        sourceInfo
+        {
+            set     c0;
+            option  all;
+        }
+    }
+
+    // Determine inverse cellSet
+    {
+        name    c1;
+        type    cellSet;
+        action  new;
+        source  cellToCell;
+        sourceInfo
+        {
+            set c0;
+        }
+    }
+    {
+        name    c1;
+        type    cellSet;
+        action  invert;
+    }
+
+    // Keep in f0 all faces in c1
+    {
+        name    f0;
+        type    faceSet;
+        action  subset;
+        source  cellToFace;
+        sourceInfo
+        {
+            set     c1;
+            option  all;
+        }
+    }
+);
+
+// ************************************************************************* //

applications/utilities/mesh/manipulation/transformPoints/transformPoints.C

@@ -158,13 +158,13 @@ int main(int argc, char *argv[])
     (
         "rollPitchYaw",
         "vector",
-        "transform in terms of '( roll pitch yaw )' in degrees"
+        "transform in terms of '(roll pitch yaw)' in degrees"
     );
     argList::addOption
     (
         "yawPitchRoll",
         "vector",
-        "transform in terms of '( yaw pitch roll )' in degrees"
+        "transform in terms of '(yaw pitch roll)' in degrees"
     );
     argList::addBoolOption
     (

applications/utilities/miscellaneous/expandDictionary/expandDictionary.C

@@ -44,7 +44,6 @@ int main(int argc, char *argv[])
 {
     argList::noBanner();
     argList::noParallel();
-    argList::validArgs.clear();
     argList::validArgs.append("inputDict");
     argList args(argc, argv);
 

applications/utilities/miscellaneous/foamInfoExec/foamInfoExec.C

@@ -22,7 +22,7 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Description
-    Interrogates a case and prints information to screen
+    Interrogates a case and prints information to stdout
 
 \*---------------------------------------------------------------------------*/
 
@@ -38,15 +38,33 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "interrogates a case and prints information to stdout"
+    );
+
+    argList::noBanner();
     argList::noParallel();
-    argList::addBoolOption("times");
+    argList::addBoolOption("times", "list available times");
-    argList::addOption("dictionary", "dictionary name");
+    argList::addBoolOption
-    argList::addBoolOption("keywords");
+    (
-    argList::addOption("entry", "entry name");
+        "keywords",
+        "report keywords for the specified dictionary"
+    );
+    argList::addOption
+    (
+        "dict",
+        "file",
+        "specify a dictionary to interrogate"
+    );
+    argList::addOption
+    (
+        "entry",
+        "name",
+        "report the named entry for the specified dictionary"
+    );
 
-#   include "setRootCase.H"
+    #include "setRootCase.H"
-
-    Info<< endl;
 
     if (args.optionFound("times"))
     {
@@ -61,11 +79,11 @@ int main(int argc, char *argv[])
         }
     }
 
-    if (args.optionFound("dictionary"))
+    if (args.optionFound("dict"))
     {
-        fileName dictFileName
+        const fileName dictFileName
         (
-            args.rootPath()/args.caseName()/args["dictionary"]
+            args.rootPath()/args.caseName()/args["dict"]
         );
 
         IFstream dictFile(dictFileName);
@@ -74,14 +92,7 @@ int main(int argc, char *argv[])
         {
             dictionary dict(dictFile);
 
-            if (args.optionFound("keywords") && !args.optionFound("entry"))
+            if (args.optionFound("entry"))
-            {
-                forAllConstIter(dictionary, dict, iter)
-                {
-                    Info<< iter().keyword() << endl;
-                }
-            }
-            else if (args.optionFound("entry"))
             {
                 wordList entryNames
                 (
@@ -152,6 +163,13 @@ int main(int argc, char *argv[])
                     FatalError.exit(2);
                 }
             }
+            else if (args.optionFound("keywords"))
+            {
+                forAllConstIter(dictionary, dict, iter)
+                {
+                    Info<< iter().keyword() << endl;
+                }
+            }
             else
             {
                 Info<< dict;

applications/utilities/parallelProcessing/decomposePar/decomposePar.C

@@ -81,8 +81,13 @@ Usage
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "decompose a mesh and fields of a case for parallel execution"
+    );
+
     argList::noParallel();
-#   include "addRegionOption.H"
+    #include "addRegionOption.H"
     argList::addBoolOption
     (
         "cellDist",
@@ -110,12 +115,7 @@ int main(int argc, char *argv[])
         "only decompose geometry if the number of domains has changed"
     );
 
-    argList::addNote
+    #include "setRootCase.H"
-    (
-        "decompose a mesh and fields of a case for parallel execution"
-    );
-
-#   include "setRootCase.H"
 
     word regionName = fvMesh::defaultRegion;
     word regionDir = word::null;
@@ -132,7 +132,7 @@ int main(int argc, char *argv[])
     bool forceOverwrite          = args.optionFound("force");
     bool ifRequiredDecomposition = args.optionFound("ifRequired");
 
-#   include "createTime.H"
+    #include "createTime.H"
 
     Info<< "Time = " << runTime.timeName() << endl;
 

applications/utilities/parallelProcessing/decomposePar/domainDecompositionDistribute.C

@@ -55,7 +55,7 @@ void Foam::domainDecomposition::distributeCells()
 
         forAll(pNames, i)
         {
-            label patchI = patches.findPatchID(pNames[i]);
+            const label patchI = patches.findPatchID(pNames[i]);
 
             if (patchI == -1)
             {

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -279,6 +279,11 @@ autoPtr<mapPolyMesh> mergeSharedPoints
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "reconstruct a mesh using geometric information only"
+    );
+
     argList::noParallel();
     argList::addOption
     (
@@ -293,15 +298,10 @@ int main(int argc, char *argv[])
         "do (slower) geometric matching on all boundary faces"
     );
 
-    argList::addNote
+    #include "addTimeOptions.H"
-    (
+    #include "addRegionOption.H"
-        "reconstruct a mesh using geometric information only"
+    #include "setRootCase.H"
-    );
+    #include "createTime.H"
-
-#   include "addTimeOptions.H"
-#   include "addRegionOption.H"
-#   include "setRootCase.H"
-#   include "createTime.H"
 
     Info<< "This is an experimental tool which tries to merge"
         << " individual processor" << nl

applications/utilities/parallelProcessing/redistributeMeshPar/redistributeMeshPar.C

@@ -503,7 +503,13 @@ void compareFields
 int main(int argc, char *argv[])
 {
 #   include "addRegionOption.H"
-    argList::addOption("mergeTol", "relative merge distance");
+    argList::addOption
+    (
+        "mergeTol",
+        "scalar",
+        "specify the merge distance relative to the bounding box size "
+        "(default 1E-6)"
+    );
     // Create argList. This will check for non-existing processor dirs.
 #   include "setRootCase.H"
 

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

@@ -341,9 +341,9 @@ int main(int argc, char *argv[])
         {
             wordList fieldNames = objects.names(volFieldTypes[i]);
 
-            for (label j=0; j<fieldNames.size(); j++)
+            forAll(fieldNames, j)
             {
-                word fieldName = fieldNames[j];
+                const word& fieldName = fieldNames[j];
 
 #               include "checkData.H"
 

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

@@ -176,7 +176,11 @@ static void writeFaceData
 int main(int argc, char *argv[])
 {
     argList::noParallel();
-    argList::addBoolOption("noWall");
+    argList::addBoolOption
+    (
+        "noWall",
+        "skip setting wall information"
+    );
     timeSelector::addOptions(true, false);
 
 #   include "setRootCase.H"

applications/utilities/postProcessing/dataConversion/foamToGMV/gmvOutput.H

@@ -6,10 +6,10 @@ for (label i=0; i < nTypes; i++)
     {
         gmvFile << "variable" << nl;
     }
-    for (label j=0; j < fieldNames.size(); j++)
-    {
 
-        word fieldName = fieldNames[j];
+    forAll(fieldNames, j)
+    {
+        const word& fieldName = fieldNames[j];
 
         IOobject fieldObject
         (

applications/utilities/postProcessing/dataConversion/foamToGMV/gmvOutputHeader.H

@@ -20,7 +20,7 @@ for (label indx=0;indx<nPoints;indx++)
 }
 gmvFile << nl;
 gmvFile << "cells   " << cells.size() << nl;
-for (label indx=0;indx<cells.size();indx++)
+forAll(cells, indx)
 {
     label nNodes = cells[indx].size();
     if (nNodes == 8)

applications/utilities/postProcessing/dataConversion/foamToTecplot360/foamToTecplot360.C

@@ -31,7 +31,7 @@ Usage
 
     - foamToTecplot360 [OPTION]
 
-    @param -fields \<fields\>\n
+    @param -fields \<names\>\n
     Convert selected fields only. For example,
     @verbatim
          -fields '( p T U )'
@@ -163,30 +163,65 @@ labelList getSelectedPatches
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "Tecplot binary file format writer"
+    );
+
     timeSelector::addOptions();
+    #include "addRegionOption.H"
 
-#   include "addRegionOption.H"
+    argList::addOption
-
+    (
-    argList::addOption("fields", "fields");
+        "fields",
-    argList::addOption("cellSet", "cellSet name");
+        "names",
-    argList::addOption("faceSet", "faceSet name");
+        "convert selected fields only. eg, '(p T U)'"
-    argList::addBoolOption("nearCellValue");
+    );
-    argList::addBoolOption("noInternal");
+    argList::addOption
-    argList::addBoolOption("noPointValues");
+    (
+        "cellSet",
+        "name",
+        "restrict conversion to the specified cellSet"
+    );
+    argList::addOption
+    (
+        "faceSet",
+        "name",
+        "restrict conversion to the specified cellSet"
+    );
+    argList::addBoolOption
+    (
+        "nearCellValue",
+        "output cell value on patches instead of patch value itself"
+    );
+    argList::addBoolOption
+    (
+        "noInternal",
+        "do not generate file for mesh, only for patches"
+    );
+    argList::addBoolOption
+    (
+        "noPointValues",
+        "no pointFields"
+    );
     argList::addOption
     (
         "excludePatches",
         "patches (wildcards) to exclude"
     );
-    argList::addBoolOption("noFaceZones");
+    argList::addBoolOption
+    (
+        "noFaceZones",
+        "no faceZones"
+    );
 
-#   include "setRootCase.H"
+    #include "setRootCase.H"
-#   include "createTime.H"
+    #include "createTime.H"
 
-    bool doWriteInternal = !args.optionFound("noInternal");
+    const bool doWriteInternal = !args.optionFound("noInternal");
-    bool doFaceZones     = !args.optionFound("noFaceZones");
+    const bool doFaceZones     = !args.optionFound("noFaceZones");
-
+    const bool nearCellValue = args.optionFound("nearCellValue");
-    bool nearCellValue = args.optionFound("nearCellValue");
+    const bool noPointValues = args.optionFound("noPointValues");
 
     if (nearCellValue)
     {
@@ -195,8 +230,6 @@ int main(int argc, char *argv[])
             << nl << endl;
     }
 
-    bool noPointValues = args.optionFound("noPointValues");
-
     if (noPointValues)
     {
         WarningIn(args.executable())

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

@@ -40,7 +40,6 @@ Usage
 
     - foamToVTK [OPTION]
 
-
     @param -ascii \n
     Write VTK data in ASCII format instead of binary.
 
@@ -78,6 +77,9 @@ Usage
     @param -noLinks \n
     (in parallel) do not link processor files to master
 
+    @param poly \n
+    write polyhedral cells without tet/pyramid decomposition
+
     @param -allPatches \n
     Combine all patches into a single file
 
@@ -95,7 +97,7 @@ Usage
 
 Note
     mesh subset is handled by vtkMesh. Slight inconsistency in
-    interpolation: on the internal field it interpolates the whole volfield
+    interpolation: on the internal field it interpolates the whole volField
     to the whole-mesh pointField and then selects only those values it
     needs for the subMesh (using the fvMeshSubset cellMap(), pointMap()
     functions). For the patches however it uses the
@@ -226,13 +228,17 @@ labelList getSelectedPatches
 
 int main(int argc, char *argv[])
 {
+    argList::addNote
+    (
+        "legacy VTK file format writer"
+    );
     timeSelector::addOptions();
 
-#   include "addRegionOption.H"
+    #include "addRegionOption.H"
-
     argList::addOption
     (
-        "fields", "wordList",
+        "fields",
+        "wordList",
         "only convert the specified fields - eg '(p T U)'"
     );
     argList::addOption
@@ -241,25 +247,64 @@ int main(int argc, char *argv[])
         "name",
         "convert a mesh subset corresponding to the specified cellSet"
     );
-    argList::addOption("faceSet", "name");
+    argList::addOption
-    argList::addOption("pointSet", "name");
+    (
+        "faceSet",
+        "name",
+        "restrict conversion to the specified faceSet"
+    );
+    argList::addOption
+    (
+        "pointSet",
+        "name",
+        "restrict conversion to the specified pointSet"
+    );
     argList::addBoolOption
     (
         "ascii",
         "write in ASCII format instead of binary"
     );
-    argList::addBoolOption("surfaceFields");
+    argList::addBoolOption
-    argList::addBoolOption("nearCellValue");
+    (
-    argList::addBoolOption("noInternal");
+        "poly",
-    argList::addBoolOption("noPointValues");
+        "write polyhedral cells without tet/pyramid decomposition"
-    argList::addBoolOption("allPatches");
+    );
+    argList::addBoolOption
+    (
+        "surfaceFields",
+        "write surfaceScalarFields (e.g., phi)"
+    );
+    argList::addBoolOption
+    (
+        "nearCellValue",
+        "use cell value on patches instead of patch value itself"
+    );
+    argList::addBoolOption
+    (
+        "noInternal",
+        "do not generate file for mesh, only for patches"
+    );
+    argList::addBoolOption
+    (
+        "noPointValues",
+        "no pointFields"
+    );
+    argList::addBoolOption
+    (
+        "allPatches",
+        "combine all patches into a single file"
+    );
     argList::addOption
     (
         "excludePatches",
         "wordReList",
         "a list of patches to exclude - eg '( inlet \".*Wall\" )' "
     );
-    argList::addBoolOption("noFaceZones");
+    argList::addBoolOption
+    (
+        "noFaceZones",
+        "no faceZones"
+    );
     argList::addBoolOption
     (
         "noLinks",
@@ -271,8 +316,8 @@ int main(int argc, char *argv[])
         "use the time name instead of the time index when naming the files"
     );
 
-#   include "setRootCase.H"
+    #include "setRootCase.H"
-#   include "createTime.H"
+    #include "createTime.H"
 
     const bool doWriteInternal = !args.optionFound("noInternal");
     const bool doFaceZones     = !args.optionFound("noFaceZones");
@@ -280,6 +325,9 @@ int main(int argc, char *argv[])
     const bool binary          = !args.optionFound("ascii");
     const bool useTimeName     = args.optionFound("useTimeName");
 
+    // decomposition of polyhedral cells into tets/pyramids cells
+    vtkTopo::decomposePoly     = !args.optionFound("poly");
+
     if (binary && (sizeof(floatScalar) != 4 || sizeof(label) != 4))
     {
         FatalErrorIn(args.executable())
@@ -941,17 +989,17 @@ int main(int argc, char *argv[])
 
                 Info<< "    FaceZone  : " << patchFileName << endl;
 
-                std::ofstream str(patchFileName.c_str());
+                std::ofstream ostr(patchFileName.c_str());
 
-                writeFuns::writeHeader(str, binary, pp.name());
+                writeFuns::writeHeader(ostr, binary, pp.name());
-                str << "DATASET POLYDATA" << std::endl;
+                ostr<< "DATASET POLYDATA" << std::endl;
 
                 writePatchGeom
                 (
                     binary,
                     pp().localFaces(),
                     pp().localPoints(),
-                    str
+                    ostr
                 );
             }
         }

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

@@ -28,7 +28,6 @@ License
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-// Construct from components
 Foam::internalWriter::internalWriter
 (
     const vtkMesh& vMesh,
@@ -58,8 +57,7 @@ Foam::internalWriter::internalWriter
     const labelList& addPointCellLabels = topo.addPointCellLabels();
     const label nTotPoints = mesh.nPoints() + addPointCellLabels.size();
 
-    os_ << "POINTS " << nTotPoints
+    os_ << "POINTS " << nTotPoints << " float" << std::endl;
-        << " float" << std::endl;
 
     DynamicList<floatScalar> ptField(3*nTotPoints);
 
@@ -87,9 +85,7 @@ Foam::internalWriter::internalWriter
         nFaceVerts += vtkVertLabels[cellI].size() + 1;
     }
 
-    os_ << "CELLS " << vtkVertLabels.size() << ' ' << nFaceVerts
+    os_ << "CELLS " << vtkVertLabels.size() << ' ' << nFaceVerts << std::endl;
-        << std::endl;
-
 
     DynamicList<label> vertLabels(nFaceVerts);
 
@@ -104,7 +100,6 @@ Foam::internalWriter::internalWriter
     writeFuns::write(os_, binary_, vertLabels);
 
 
-
     const labelList& vtkCellTypes = topo.cellTypes();
 
     os_ << "CELL_TYPES " << vtkCellTypes.size() << std::endl;
@@ -128,8 +123,7 @@ void Foam::internalWriter::writeCellIDs()
     const labelList& superCells = topo.superCells();
 
     // Cell ids first
-    os_ << "cellID 1 " << vtkCellTypes.size() << " int"
+    os_ << "cellID 1 " << vtkCellTypes.size() << " int" << std::endl;
-        << std::endl;
 
     labelList cellId(vtkCellTypes.size());
     label labelI = 0;

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

@@ -30,7 +30,6 @@ License
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-// Construct from components
 Foam::lagrangianWriter::lagrangianWriter
 (
     const vtkMesh& vMesh,