Merge branch 'master' into molecularDynamics

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

@@ -28,7 +28,8 @@ Description
     Work in progress! Handles ascii multiblock (and optionally singleBlock)
     format.
     By default expects blanking. Use -noBlank if none.
-    Use -2D <thickness> if 2D.
+    Use -2D @a thickness if 2D.
+
     Niklas Nordin has experienced a problem with lefthandedness of the blocks.
     The code should detect this automatically - see hexBlock::readPoints but
     if this goes wrong just set the blockHandedness_ variable to 'right'

applications/utilities/mesh/generation/blockMesh/Make/files

@@ -26,6 +26,6 @@ blockPoints.C
 blockCells.C
 blockBoundary.C
 
-genBlockMesh.C
+blockMeshApp.C
 
 EXE = $(FOAM_APPBIN)/blockMesh

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

@@ -1,3 +1,4 @@
     argList::noParallel();
     argList::validOptions.insert("blockTopology", "");
+    argList::validOptions.insert("dict", "dictionary");
 #   include "addRegionOption.H"

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

@@ -77,11 +77,21 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Reading block mesh description dictionary" << endl;
 
+    word dictName("blockMeshDict");
+    fileName dictPath(runTime.constant()/polyMeshDir);
+
+    if (args.options().found("dict"))
+    {
+        fileName userDict(args.options()["dict"]);
+
+        dictName = userDict.name();
+        dictPath = userDict.path();
+    }
+
     IOobject meshDescriptionIOobject
     (
-        "blockMeshDict",
-        runTime.constant(),
-        polyMeshDir,
+        dictName,
+        dictPath,
         runTime,
         IOobject::MUST_READ,
         IOobject::NO_WRITE,
@@ -91,13 +101,14 @@ int main(int argc, char *argv[])
     if (!meshDescriptionIOobject.headerOk())
     {
         FatalErrorIn(args.executable())
-            << "Cannot open mesh description file " << nl
-            << runTime.constant()/polyMeshDir/"blockMeshDict" << nl
+            << "Cannot open mesh description file: " << nl
+            << dictPath/dictName << nl
             << exit(FatalError);
     }
 
     IOdictionary meshDescription(meshDescriptionIOobject);
 
+
     Info<< nl << "Creating block mesh" << endl;
 
     blockMesh blocks(meshDescription);

applications/utilities/miscellaneous/foamDebugSwitches/Make/options

@@ -1,10 +1,8 @@
 EXE_LIBS = \
-    -lautoMesh \
     -lbasicThermophysicalModels \
     -lchemistryModel \
     -lcombustionThermophysicalModels \
     -lcompressibleLESModels \
-    -lcompressibleRASModels \
     -ldecompositionMethods \
     -ldieselSpray \
     -ldynamicFvMesh \
@@ -17,6 +15,7 @@ EXE_LIBS = \
     -lfvMotionSolvers \
     -lincompressibleLESModels \
     -lincompressibleTransportModels \
+    -lcompressibleRASModels \
     -lincompressibleRASModels \
     -linterfaceProperties \
     -llagrangianIntermediate \
@@ -39,5 +38,5 @@ EXE_LIBS = \
     -lspecie \
     -lthermophysicalFunctions \
     -ltopoChangerFvMesh \
-    -ltriSurface
-
+    -ltriSurface \
+    -lautoMesh

applications/utilities/postProcessing/graphics/PV3FoamReader/PV3FoamReader/PV3FoamReader_SM.xml

@@ -90,52 +90,6 @@
             <BooleanDomain name="bool"/>
         </IntVectorProperty>
 
-<!-- Time step edit box -->
-<!-- OLESEN
-<IntVectorProperty
-            name="TimeStepRangeInfo"
-            command="GetTimeStepRange"
-            information_only="1">
-            <SimpleIntInformationHelper/>
-        </IntVectorProperty>
-        <IntVectorProperty
-            name="TimeStep"
-            command="SetTimeStep"
-            number_of_elements="1"
-            animateable="1"
-            default_values="0"
-            information_property="TimestepValues">
-            <IntRangeDomain
-                name="range">
-                <RequiredProperties>
-                    <Property name="TimeStepRangeInfo"
-                              function="Range"/>
-                </RequiredProperties>
-            </IntRangeDomain>
-        </IntVectorProperty>
--->
-
-<!-- Time step limits boxes -->
-<!--        <IntVectorProperty
-            name="TimeStepLimitsInfo"
-            command="GetTimeStepLimits"
-            information_only="1">
-            <SimpleIntInformationHelper/>
-        </IntVectorProperty>
-        <IntVectorProperty
-            name="TimeStepLimits"
-            command="SetTimeStepLimits"
-            number_of_elements="2"
-            default_values="2 5" >
-            <IntRangeDomain
-                name="range">
-                <RequiredProperties>
-                    <Property name="TimeStepLimitsInfo"
-                              function="Range"/>
-                </RequiredProperties>
-            </IntRangeDomain>
-        </IntVectorProperty>-->
-
 <!-- Available regions array -->
         <StringVectorProperty
             name="RegionArrayInfo"
@@ -233,7 +187,9 @@
         </StringVectorProperty>
 
 <!-- Available times array -->
-<!--        <StringVectorProperty
+<!-- PV3FOAM_TIMESELECTION must be defined when compiling vtkPV3Foam
+     might discard this in the future
+        <StringVectorProperty
             name="TimeArrayInfo"
             information_only="1">
             <ArraySelectionInformationHelper
@@ -255,6 +211,8 @@
                 </RequiredProperties>
             </ArraySelectionDomain>
         </StringVectorProperty>
+
+PV3FOAM_TIMESELECTION
 -->
 
     </SourceProxy>

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/Make/options

@@ -1,4 +1,5 @@
 EXE_INC = \
+    /* -DPV3FOAM_TIMESELECTION */ \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \

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

@@ -27,8 +27,6 @@ License
 #include "vtkPV3Foam.H"
 
 // Foam includes
-#include "argList.H"
-#include "JobInfo.H"
 #include "Time.H"
 #include "fvMesh.H"
 #include "IOobjectList.H"
@@ -176,11 +174,7 @@ void Foam::vtkPV3Foam::resetCounters()
 
 void Foam::vtkPV3Foam::initializeTime()
 {
-    if (debug)
-    {
-        Info<< "entered Foam::vtkPV3Foam::initializeTime" << endl;
-    }
-
+#ifdef PV3FOAM_TIMESELECTION
     Time& runTime = dbPtr_();
 
     // Get times list
@@ -206,6 +200,7 @@ void Foam::vtkPV3Foam::initializeTime()
             times[timeI].name().c_str()
         );
     }
+#endif /* PV3FOAM_TIMESELECTION */
 }
 
 
@@ -213,8 +208,8 @@ bool Foam::vtkPV3Foam::setTime(const double& requestedTime)
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::setTime("
-            << requestedTime << ")" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::setTime(" << requestedTime << ")"
+            << endl;
     }
 
     Time& runTime = dbPtr_();
@@ -249,12 +244,14 @@ bool Foam::vtkPV3Foam::setTime(const double& requestedTime)
         found = true;
     }
 
+    runTime.setTime(times[nearestIndex], nearestIndex);
+
     if (debug)
     {
-        Info<< "Selecting time " << times[nearestIndex].name() << endl;
+        Info<< "<end> Foam::vtkPV3Foam::setTime() - selected time "
+            << times[nearestIndex].name() << endl;
     }
 
-    runTime.setTime(times[nearestIndex], nearestIndex);
     return found;
 }
 
@@ -263,7 +260,7 @@ void Foam::vtkPV3Foam::updateSelectedRegions()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateSelectedRegions" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateSelectedRegions" << endl;
     }
 
     vtkDataArraySelection* arraySelection = reader_->GetRegionSelection();
@@ -281,10 +278,15 @@ void Foam::vtkPV3Foam::updateSelectedRegions()
 
         if (debug)
         {
-            Info<< "region " << regionId
-                << " = " << selectedRegions_[regionId] << endl;
+            Info<< "  region[" << regionId << "] = "
+                << selectedRegions_[regionId]
+                << " : " << arraySelection->GetArrayName(regionId) << endl;
         }
     }
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateSelectedRegions" << endl;
+    }
 }
 
 
@@ -294,13 +296,14 @@ Foam::stringList Foam::vtkPV3Foam::getSelectedArrayEntries
     const bool firstWord
 )
 {
-    if (debug)
-    {
-        Info<< "entered Foam::vtkPV3Foam::getSelectedArrayEntries" << endl;
-    }
-
     stringList selections(arraySelection->GetNumberOfArrays());
     label nElem = 0;
+
+    if (debug)
+    {
+        Info << "selections(";
+    }
+
     forAll (selections, elemI)
     {
         if (arraySelection->GetArraySetting(elemI))
@@ -316,16 +319,22 @@ Foam::stringList Foam::vtkPV3Foam::getSelectedArrayEntries
             {
                 selections[nElem] = arraySelection->GetArrayName(elemI);
             }
+
+            if (debug)
+            {
+                Info << " " << selections[nElem];
+            }
+
             ++nElem;
         }
     }
 
-    selections.setSize(nElem);
     if (debug)
     {
-        Info<< "Active array: " << selections << endl;
+        Info << " )" << endl;
     }
 
+    selections.setSize(nElem);
     return selections;
 }
 
@@ -337,14 +346,14 @@ Foam::stringList Foam::vtkPV3Foam::getSelectedArrayEntries
     const bool firstWord
 )
 {
-    if (debug)
-    {
-        Info<< "entered Foam::vtkPV3Foam::getSelectedArrayEntries" << endl;
-    }
-
     stringList selections(selector.size());
     label nElem = 0;
 
+    if (debug)
+    {
+        Info << "selections(";
+    }
+
     for
     (
         int regionId = selector.start();
@@ -366,16 +375,22 @@ Foam::stringList Foam::vtkPV3Foam::getSelectedArrayEntries
                 selections[nElem] = arraySelection->GetArrayName(regionId);
             }
 
+            if (debug)
+            {
+                Info << " " << selections[nElem];
+            }
+
             ++nElem;
         }
     }
 
-    selections.setSize(nElem);
     if (debug)
     {
-        Info<< "Active array: " << selections << endl;
+        Info << " )" << endl;
     }
 
+
+    selections.setSize(nElem);
     return selections;
 }
 
@@ -386,9 +401,9 @@ void Foam::vtkPV3Foam::setSelectedArrayEntries
     const stringList& selections
 )
 {
-    if (debug)
+    if (debug > 1)
     {
-        Info<< "entered Foam::vtkPV3Foam::setSelectedArrayEntries" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::setSelectedArrayEntries" << endl;
     }
     const label nEntries = arraySelection->GetNumberOfArrays();
 
@@ -398,7 +413,7 @@ void Foam::vtkPV3Foam::setSelectedArrayEntries
     // Loop through entries, setting values from selectedEntries
     forAll (selections, elemI)
     {
-        if (debug)
+        if (debug > 1)
         {
             Info<< "selections[" << elemI << "] = " << selections[elemI]
                 << endl;
@@ -410,7 +425,7 @@ void Foam::vtkPV3Foam::setSelectedArrayEntries
 
             if (arrayName == selections[elemI])
             {
-                if (debug)
+                if (debug > 1)
                 {
                     Info<< "enabling array: " << arrayName << " Index = "
                         << i
@@ -425,6 +440,10 @@ void Foam::vtkPV3Foam::setSelectedArrayEntries
             }
         }
     }
+    if (debug > 1)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::setSelectedArrayEntries" << endl;
+    }
 }
 
 
@@ -455,8 +474,7 @@ Foam::vtkPV3Foam::vtkPV3Foam
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::vtkPV3Foam with "
-            << FileName << endl;
+        Info<< "Foam::vtkPV3Foam::vtkPV3Foam - " << FileName << endl;
     }
 
     // avoid argList and get rootPath/caseName directly from the file
@@ -471,6 +489,22 @@ Foam::vtkPV3Foam::vtkPV3Foam
         fullCasePath = cwd();
     }
 
+    // Set the case as an environment variable - some BCs might use this
+    if (fullCasePath.name().find("processor", 0) == 0)
+    {
+        setEnv("FOAM_CASE", fullCasePath.path(), true);
+    }
+    else
+    {
+        setEnv("FOAM_CASE", fullCasePath, true);
+    }
+
+    if (debug)
+    {
+        Info<< "fullCasePath=" << fullCasePath << nl
+            << "FOAM_CASE=" << getEnv("FOAM_CASE") << endl;
+    }
+
     // Create time object
     dbPtr_.reset
     (
@@ -504,7 +538,7 @@ Foam::vtkPV3Foam::~vtkPV3Foam()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::~vtkPV3Foam" << endl;
+        Info<< "<end> Foam::vtkPV3Foam::~vtkPV3Foam" << endl;
     }
 
     if (meshPtr_)
@@ -521,7 +555,7 @@ void Foam::vtkPV3Foam::UpdateInformation()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::UpdateInformation" << nl
+        Info<< "<beg> Foam::vtkPV3Foam::UpdateInformation - "
             << "TimeStep = " << reader_->GetTimeStep() << endl;
     }
 
@@ -575,6 +609,12 @@ void Foam::vtkPV3Foam::UpdateInformation()
 
     // Update lagrangian field array
     updateInformationLagrangianFields();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::UpdateInformation" << endl;
+    }
+
 }
 
 
@@ -585,7 +625,7 @@ void Foam::vtkPV3Foam::Update
 {
     if (debug)
     {
-        cout<< "entered Foam::vtkPV3Foam::Update" << nl
+        cout<< "<beg> Foam::vtkPV3Foam::Update" << nl
             <<"Update\n";
         output->Print(cout);
 
@@ -596,7 +636,6 @@ void Foam::vtkPV3Foam::Update
     }
 
 
-
     // Set up region selection(s)
     updateSelectedRegions();
 
@@ -673,15 +712,16 @@ double* Foam::vtkPV3Foam::timeSteps(int& nTimeSteps)
     int nTimes = 0;
     double* ts = NULL;
 
-    vtkDataArraySelection* arraySelection = reader_->GetTimeSelection();
-
     if (dbPtr_.valid())
     {
         Time& runTime = dbPtr_();
 
         instantList times = runTime.times();
+
+#ifdef PV3FOAM_TIMESELECTION
         List<bool> selected = List<bool>(times.size(), false);
 
+        vtkDataArraySelection* arraySelection = reader_->GetTimeSelection();
         const label nSelectedTimes = arraySelection->GetNumberOfArrays();
 
         for (int i = 0; i < nSelectedTimes; ++i)
@@ -694,20 +734,21 @@ double* Foam::vtkPV3Foam::timeSteps(int& nTimeSteps)
              && timeI < times.size()
             )
             {
-#if 0
+                if (debug > 1)
+                {
                     Info<<"timeSelection["
                         << i
                         <<"] = "
                         << arraySelection->GetArraySetting(i)
                             << " is "
                         << arraySelection->GetArrayName(i) << endl;
-#endif
+                }
                 selected[timeI] = true;
                 ++nTimes;
             }
         }
 
-        if (debug)
+        if (debug > 1)
         {
             Info<< "selected " << nTimes << " times ";
             Info<< "found " << times.size() << " times: (";
@@ -732,6 +773,27 @@ double* Foam::vtkPV3Foam::timeSteps(int& nTimeSteps)
                 }
             }
         }
+
+#else /* PV3FOAM_TIMESELECTION */
+        // always skip "constant" time, unless there are no other times
+        nTimes = times.size();
+        label timeI = 0;
+
+        if (nTimes > 1)
+        {
+            timeI = 1;
+            --nTimes;
+        }
+
+        if (nTimes)
+        {
+            ts = new double[nTimes];
+            for (label stepI = 0; stepI < nTimes; ++stepI, ++timeI)
+            {
+                ts[stepI] = times[timeI].value();
+            }
+        }
+#endif /* PV3FOAM_TIMESELECTION */
     }
     else
     {
@@ -741,7 +803,7 @@ double* Foam::vtkPV3Foam::timeSteps(int& nTimeSteps)
         }
     }
 
-    // return length via the parameter
+    // return vector length via the parameter
     nTimeSteps = nTimes;
 
     return ts;
@@ -755,7 +817,7 @@ void Foam::vtkPV3Foam::addPatchNames(vtkRenderer* renderer)
 
     if (debug)
     {
-        Info<< "addPatchNames()" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addPatchNames" << endl;
     }
 
     const fvMesh& mesh = *meshPtr_;
@@ -773,7 +835,7 @@ void Foam::vtkPV3Foam::addPatchNames(vtkRenderer* renderer)
 
     if (debug)
     {
-        Info<<"patches: " << selectedPatches <<endl;
+        Info<<"... add patches: " << selectedPatches <<endl;
     }
 
     // Find the total number of zones
@@ -787,7 +849,7 @@ void Foam::vtkPV3Foam::addPatchNames(vtkRenderer* renderer)
 
     if (debug)
     {
-        Info<< "determining patch zones" << endl;
+        Info<< "... determining patch zones" << endl;
     }
 
     // Loop through all patches to determine zones, and centre of each zone
@@ -926,6 +988,11 @@ void Foam::vtkPV3Foam::addPatchNames(vtkRenderer* renderer)
 
     // Resize the patch names list to the actual number of patch names added
     patchTextActorsPtrs_.setSize(globalZoneI);
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addPatchNames)" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddFaceSetMesh.C

@@ -48,7 +48,7 @@ void Foam::vtkPV3Foam::addFaceSetMesh
 {
     if (debug)
     {
-        Info<< "entered add face set internal mesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addFaceSetMesh" << endl;
     }
 
     // Construct primitivePatch of faces in fSet.
@@ -96,6 +96,11 @@ void Foam::vtkPV3Foam::addFaceSetMesh
 
     vtkmesh->SetPolys(vtkcells);
     vtkcells->Delete();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addFaceSetMesh" << endl;
+    }
 }
 
 // ************************************************************************* //

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddFaceZoneMesh.C

@@ -47,7 +47,7 @@ void Foam::vtkPV3Foam::addFaceZoneMesh
 {
     if (debug)
     {
-        Info<< "entered addFaceZoneMesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addFaceZoneMesh" << endl;
     }
 
     // Construct primitivePatch of faces in fSet.
@@ -94,6 +94,11 @@ void Foam::vtkPV3Foam::addFaceZoneMesh
 
     vtkmesh->SetPolys(vtkcells);
     vtkcells->Delete();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addFaceZoneMesh" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddFields.H

@@ -64,7 +64,7 @@ Foam::label Foam::vtkPV3Foam::addFields
         {
             if (debug)
             {
-                Info<<"add region " << GeoField::typeName
+                Info<<"    addField to GUI " << GeoField::typeName
                     << ":" << fields[fieldI] << endl;
             }
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddLagrangianMesh.C

@@ -50,7 +50,7 @@ void Foam::vtkPV3Foam::addLagrangianMesh
 {
     if (debug)
     {
-        Info<< "entered add Lagrangian mesh with timePath "
+        Info<< "<beg> Foam::vtkPV3Foam::addLagrangianMesh - timePath "
             << mesh.time().timePath()/"lagrangian" << endl;
     }
 
@@ -61,7 +61,7 @@ void Foam::vtkPV3Foam::addLagrangianMesh
 
     if (debug && cloudDirs.size())
     {
-        Info<< "check cloudDirs: " << cloudDirs << endl;
+        Info<< "... check cloudDirs: " << cloudDirs << endl;
     }
 
     bool foundCloud = false;
@@ -99,6 +99,11 @@ void Foam::vtkPV3Foam::addLagrangianMesh
             vtkpoints->Delete();
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addLagrangianMesh" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddPatchMesh.C

@@ -48,7 +48,7 @@ void Foam::vtkPV3Foam::addPatchMesh
 {
     if (debug)
     {
-        Info<< "Adding patch: " << p.name() << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addPatchMesh - " << p.name() << endl;
     }
 
     // Convert Foam mesh vertices to VTK
@@ -84,6 +84,11 @@ void Foam::vtkPV3Foam::addPatchMesh
 
     vtkmesh->SetPolys(vtkcells);
     vtkcells->Delete();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addPatchMesh - " << p.name() << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddPointSetMesh.C

@@ -47,7 +47,7 @@ void Foam::vtkPV3Foam::addPointSetMesh
 {
     if (debug)
     {
-        Info<< "entered add point set mesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addPointSetMesh" << endl;
     }
 
     const pointField& meshPoints = mesh.points();
@@ -62,6 +62,11 @@ void Foam::vtkPV3Foam::addPointSetMesh
 
     vtkmesh->SetPoints(vtkpoints);
     vtkpoints->Delete();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addPointSetMesh" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddPointZoneMesh.C

@@ -46,7 +46,7 @@ void Foam::vtkPV3Foam::addPointZoneMesh
 {
     if (debug)
     {
-        Info<< "entered add point zone mesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addPointZoneMesh" << endl;
     }
 
     const pointField& meshPoints = mesh.points();
@@ -61,6 +61,11 @@ void Foam::vtkPV3Foam::addPointZoneMesh
 
     vtkmesh->SetPoints(vtkpoints);
     vtkpoints->Delete();
+
+    if (debug)
+    {
+        Info<< "<beg> Foam::vtkPV3Foam::addPointZoneMesh" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamAddVolumeMesh.C

@@ -54,7 +54,7 @@ void Foam::vtkPV3Foam::addVolumeMesh
 {
     if (debug)
     {
-        Info<< "entered add volume mesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::addVolumeMesh" << endl;
     }
 
     // Number of additional points needed by the decomposition of polyhedra
@@ -74,13 +74,13 @@ void Foam::vtkPV3Foam::addVolumeMesh
     // and cells
     if (debug)
     {
-        Info<< "building cell-shapes" << endl;
+        Info<< "... building cell-shapes" << endl;
     }
     const cellShapeList& cellShapes = mesh.cellShapes();
 
     if (debug)
     {
-        Info<< "scanning" << endl;
+        Info<< "... scanning" << endl;
     }
     forAll(cellShapes, cellI)
     {
@@ -133,7 +133,7 @@ void Foam::vtkPV3Foam::addVolumeMesh
 
     if (debug)
     {
-        Info<< "converting points" << endl;
+        Info<< "... converting points" << endl;
     }
 
     // Convert Foam mesh vertices to VTK
@@ -150,7 +150,7 @@ void Foam::vtkPV3Foam::addVolumeMesh
 
     if (debug)
     {
-        Info<< "converting cells" << endl;
+        Info<< "... converting cells" << endl;
     }
 
     vtkmesh->Allocate(mesh.nCells() + nAddCells);
@@ -350,6 +350,11 @@ void Foam::vtkPV3Foam::addVolumeMesh
 
     vtkmesh->SetPoints(vtkpoints);
     vtkpoints->Delete();
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::addVolumeMesh" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamConvertMesh.C

@@ -50,7 +50,7 @@ void Foam::vtkPV3Foam::convertMeshVolume
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshVolume" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshVolume" << endl;
     }
 
     const selectionInfo& selector = selectInfoVolume_;
@@ -88,6 +88,11 @@ void Foam::vtkPV3Foam::convertMeshVolume
         selectedRegionDatasetIds_[regionId] = datasetId;
         vtkmesh->Delete();
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshVolume" << endl;
+    }
 }
 
 
@@ -98,7 +103,7 @@ void Foam::vtkPV3Foam::convertMeshLagrangian
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshLagrangian" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshLagrangian" << endl;
     }
 
     const selectionInfo& selector = selectInfoLagrangian_;
@@ -131,6 +136,10 @@ void Foam::vtkPV3Foam::convertMeshLagrangian
         selectedRegionDatasetIds_[regionId] = datasetId;
         vtkmesh->Delete();
     }
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshLagrangian" << endl;
+    }
 }
 
 
@@ -141,7 +150,7 @@ void Foam::vtkPV3Foam::convertMeshPatches
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshPatches" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshPatches" << endl;
     }
 
     const selectionInfo& selector = selectInfoPatches_;
@@ -196,6 +205,11 @@ void Foam::vtkPV3Foam::convertMeshPatches
             vtkmesh->Delete();
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshPatches" << endl;
+    }
 }
 
 
@@ -206,7 +220,7 @@ void Foam::vtkPV3Foam::convertMeshCellZones
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshCellZones" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshCellZones" << endl;
     }
 
     const selectionInfo& selector = selectInfoCellZones_;
@@ -263,6 +277,11 @@ void Foam::vtkPV3Foam::convertMeshCellZones
             vtkmesh->Delete();
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshCellZones" << endl;
+    }
 }
 
 
@@ -273,7 +292,7 @@ void Foam::vtkPV3Foam::convertMeshCellSet
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshCellSet" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshCellSet" << endl;
     }
 
     const selectionInfo& selector = selectInfoCellSets_;
@@ -337,6 +356,11 @@ void Foam::vtkPV3Foam::convertMeshCellSet
             vtkmesh->Delete();
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshCellSet" << endl;
+    }
 }
 
 void Foam::vtkPV3Foam::convertMeshFaceZones
@@ -346,7 +370,7 @@ void Foam::vtkPV3Foam::convertMeshFaceZones
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshFaceZones" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshFaceZones" << endl;
     }
 
     const selectionInfo& selector = selectInfoFaceZones_;
@@ -393,6 +417,11 @@ void Foam::vtkPV3Foam::convertMeshFaceZones
             vtkmesh->Delete();
         }
     }
+    
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshFaceZones" << endl;
+    }
 }
 
 
@@ -403,7 +432,7 @@ void Foam::vtkPV3Foam::convertMeshFaceSet
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshFaceSet" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshFaceSet" << endl;
     }
 
     const selectionInfo& selector = selectInfoFaceSets_;
@@ -458,6 +487,11 @@ void Foam::vtkPV3Foam::convertMeshFaceSet
             vtkmesh->Delete();
         }
     }
+    
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshFaceSet" << endl;
+    }
 }
 
 
@@ -468,7 +502,7 @@ void Foam::vtkPV3Foam::convertMeshPointZones
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshPointZones" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshPointZones" << endl;
     }
 
     const selectionInfo& selector = selectInfoPointZones_;
@@ -515,6 +549,11 @@ void Foam::vtkPV3Foam::convertMeshPointZones
             vtkmesh->Delete();
         }
     }
+    
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshPointZones" << endl;
+    }
 }
 
 
@@ -526,7 +565,7 @@ void Foam::vtkPV3Foam::convertMeshPointSet
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::convertMeshPointSet" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::convertMeshPointSet" << endl;
     }
 
     const selectionInfo& selector = selectInfoPointSets_;
@@ -581,7 +620,11 @@ void Foam::vtkPV3Foam::convertMeshPointSet
             vtkmesh->Delete();
         }
     }
+    
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::convertMeshPointSet" << endl;
+    }
 }
 
-
 // ************************************************************************* //

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamConvertPointFields.H

@@ -66,7 +66,7 @@ void Foam::vtkPV3Foam::convertPointFields
 
                 if (debug)
                 {
-                    Info<< "converting Foam point field: " << fieldName
+                    Info<< "Foam::vtkPV3Foam::convertPointFields : " << fieldName
                         << endl;
                 }
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamUpdate.C

@@ -47,13 +47,16 @@ void Foam::vtkPV3Foam::updateFoamMesh()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateFoamMesh" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateFoamMesh" << endl;
     }
 
     if
     (
         !reader_->GetCacheMesh()
+#ifdef PV3FOAM_TIMESELECTION
+        // This is only useful if the times are individually selectable
      || reader_->GetTimeSelection()->GetArraySetting(0)
+#endif
     )
     {
         delete meshPtr_;
@@ -84,6 +87,11 @@ void Foam::vtkPV3Foam::updateFoamMesh()
             Info<< "Using existing Foam mesh" << endl;
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateFoamMesh" << endl;
+    }
 }
 
 
@@ -94,7 +102,7 @@ void Foam::vtkPV3Foam::updateVolFields
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateVolFields" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateVolFields" << endl;
     }
 
     const fvMesh& mesh = *meshPtr_;
@@ -155,6 +163,11 @@ void Foam::vtkPV3Foam::updateVolFields
     (
         mesh, pInterp, ppInterpList, objects, arraySelection, output
     );
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateVolFields" << endl;
+    }
 }
 
 
@@ -165,7 +178,7 @@ void Foam::vtkPV3Foam::updatePointFields
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updatePointFields" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updatePointFields" << endl;
     }
 
     const fvMesh& mesh = *meshPtr_;
@@ -175,11 +188,6 @@ void Foam::vtkPV3Foam::updatePointFields
 
     vtkDataArraySelection* arraySelection = reader_->GetPointFieldSelection();
 
-    // Convert point fields
-    if (debug)
-    {
-        Info<< "converting Foam point fields" << endl;
-    }
 /*
     convertPointFields<Foam::label>
     (
@@ -206,6 +214,11 @@ void Foam::vtkPV3Foam::updatePointFields
     (
         mesh, objects, arraySelection, output
     );
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updatePointFields" << endl;
+    }
 }
 
 
@@ -216,7 +229,7 @@ void Foam::vtkPV3Foam::updateLagrangianFields
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateLagrangianFields" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateLagrangianFields" << endl;
     }
 
     const fvMesh& mesh = *meshPtr_;
@@ -264,6 +277,11 @@ void Foam::vtkPV3Foam::updateLagrangianFields
     (
         mesh, objects, arraySelection, output
     );
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateLagrangianFields" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamUpdateInformation.C

@@ -86,8 +86,7 @@ void Foam::vtkPV3Foam::updateInformationInternalMesh()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationInternalMesh"
-            << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationInternalMesh" << endl;
     }
 
     vtkDataArraySelection* arraySelection = reader_->GetRegionSelection();
@@ -101,6 +100,12 @@ void Foam::vtkPV3Foam::updateInformationInternalMesh()
     selectInfoVolume_ = arraySelection->GetNumberOfArrays();
     arraySelection->AddArray("internalMesh");
     selectInfoVolume_ += 1;
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationInternalMesh" << endl;
+    }
+
 }
 
 
@@ -108,8 +113,8 @@ void Foam::vtkPV3Foam::updateInformationLagrangian()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationLagrangian "
-            << "at timePath " << dbPtr_->timePath()/"lagrangian" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationLagrangian" << nl
+            << "    " << dbPtr_->timePath()/"lagrangian" << endl;
     }
 
     vtkDataArraySelection* arraySelection = reader_->GetRegionSelection();
@@ -144,11 +149,15 @@ void Foam::vtkPV3Foam::updateInformationLagrangian()
     {
         if (debug)
         {
-            Info<<"no clouds identified in "
-                << dbPtr_->timePath()/"lagrangian" << endl;
+            Info<<"no clouds identified in " <<nl
+                << "    " <<dbPtr_->timePath()/"lagrangian" << endl;
         }
     }
 
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationLagrangian" << endl;
+    }
 }
 
 
@@ -156,7 +165,7 @@ void Foam::vtkPV3Foam::updateInformationPatches()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationPatches" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationPatches" << endl;
     }
 
     vtkDataArraySelection *arraySelection = reader_->GetRegionSelection();
@@ -198,6 +207,10 @@ void Foam::vtkPV3Foam::updateInformationPatches()
     }
     selectInfoPatches_ += nPatches;
 
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationPatches" << endl;
+    }
 }
 
 
@@ -205,7 +218,7 @@ void Foam::vtkPV3Foam::updateInformationZones()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationZones" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationZones" << endl;
     }
 
     vtkDataArraySelection *arraySelection = reader_->GetRegionSelection();
@@ -301,6 +314,12 @@ void Foam::vtkPV3Foam::updateInformationZones()
             selectInfoPointZones_ += zones.size();
         }
     }
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationZones" << endl;
+    }
+
 }
 
 
@@ -308,7 +327,7 @@ void Foam::vtkPV3Foam::updateInformationSets()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationSets" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationSets" << endl;
     }
 
     vtkDataArraySelection *arraySelection = reader_->GetRegionSelection();
@@ -346,6 +365,11 @@ void Foam::vtkPV3Foam::updateInformationSets()
         objects,
         " - pointSet"
     );
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationSets" << endl;
+    }
 }
 
 
@@ -353,7 +377,7 @@ void Foam::vtkPV3Foam::updateInformationLagrangianFields()
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationLagrangianFields"
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationLagrangianFields"
             << endl;
     }
 
@@ -415,8 +439,8 @@ void Foam::vtkPV3Foam::updateInformationLagrangianFields()
 
     if (debug)
     {
-        Info<< "lagrangian objects.size() = " << objects.size()
-            << endl;
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationLagrangianFields - "
+            << "lagrangian objects.size() = " << objects.size() << endl;
     }
 }
 

applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam/vtkPV3FoamUpdateInformationFields.H

@@ -40,7 +40,7 @@ void Foam::vtkPV3Foam::updateInformationFields
 {
     if (debug)
     {
-        Info<< "entered Foam::vtkPV3Foam::updateInformationFields" << endl;
+        Info<< "<beg> Foam::vtkPV3Foam::updateInformationFields" << endl;
     }
 
     // preserve the currently selected values
@@ -94,6 +94,11 @@ void Foam::vtkPV3Foam::updateInformationFields
         arraySelection,
         selectedEntries
     );
+
+    if (debug)
+    {
+        Info<< "<end> Foam::vtkPV3Foam::updateInformationFields" << endl;
+    }
 }
 
 

applications/utilities/postProcessing/graphics/ensightFoamReader/Allwmake

@@ -1 +1,2 @@
+#!/bin/sh
 wmake libso

applications/utilities/postProcessing/graphics/ensightFoamReader/libuserd.C

@@ -26,10 +26,9 @@ Application
     libuserd-foam
 
 Description
-    Module for EnSight 7.6 to read FOAM data directly without translation
+    EnSight library module to read OpenFOAM data directly without translation
 
-    It can currently handle cells of type:
-    Z_HEX08, Z_PEN06, Z_TET04, Z_PUR05
+    It can currently handle most cell types.
 
     See also: README_USERD_2.0
     24 Sep 2001: NN - Added support for Ensight API 2.0

applications/utilities/postProcessing/sampling/probeLocations/probeLocations.C

@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
     instantList timeDirs = timeSelector::select0(runTime, args);
 #   include "createMesh.H"
 
-    IOprobes sniff(mesh, "probesDict", true);
+    IOprobes sniff(mesh, "probesDict", IOobject::MUST_READ, true);
 
     forAll(timeDirs, timeI)
     {

applications/utilities/postProcessing/sampling/sample/sample.C

@@ -28,39 +28,39 @@ Description
 
     Keywords:
 
-    setFormat: set output format, choice of
-        xmgr
-        jplot
-        gnuplot
-        raw
+    @param setFormat : set output format, choice of \n
+      - xmgr
+      - jplot
+      - gnuplot
+      - raw
 
-    surfaceFormat: surface output format, choice of
-        null        : suppress output
-        foamFile    : separate points, faces and values file
-        dx          : DX scalar or vector format
-        vtk         : VTK ascii format
-        raw         : x y z value format for use with e.g. gnuplot 'splot'.
-        stl         : ascii stl. Does not contain values!
+    @param surfaceFormat : surface output format, choice of \n
+      - null        : suppress output
+      - foamFile    : separate points, faces and values file
+      - dx          : DX scalar or vector format
+      - vtk         : VTK ascii format
+      - raw         : x y z value format for use with e.g. gnuplot 'splot'.
+      - stl         : ascii stl. Does not contain values!
 
-    interpolationScheme: interpolation scheme, choice of
-        cell          : use cell-centre value; constant over cells (default)
-        cellPoint     : use cell-centre and vertex values
-   	    cellPointFace : use cell-centre, vertex and face values.
-          1] vertex values determined from neighbouring cell-centre values
-          2] face values determined using the current face interpolation scheme
+    @param interpolationScheme : interpolation scheme, choice of \n
+      - cell          : use cell-centre value; constant over cells (default)
+      - cellPoint     : use cell-centre and vertex values
+      - cellPointFace : use cell-centre, vertex and face values. \n
+        -# vertex values determined from neighbouring cell-centre values
+        -# face values determined using the current face interpolation scheme
            for the field (linear, limitedLinear, etc.)
 
-    fields: list of fields to sample
+    @param fields : list of fields to sample
 
-    sets: list of sets to sample, choice of
-        uniform             evenly distributed points on line
-        face                one point per face intersection
-        midPoint            one point per cell, inbetween two face intersections
-        midPointAndFace     combination of face and midPoint
+    @param sets : list of sets to sample, choice of \n
+      - uniform             evenly distributed points on line
+      - face                one point per face intersection
+      - midPoint            one point per cell, inbetween two face intersections
+      - midPointAndFace     combination of face and midPoint
 
-        curve               specified points, not nessecary on line, uses
+      - curve               specified points, not nessecary on line, uses
                             tracking
-        cloud               specified points, uses findCell
+      - cloud               specified points, uses findCell
 
         Option axis: how to write point coordinate. Choice of
           - x/y/z: x/y/z coordinate only
@@ -74,11 +74,12 @@ Description
             uniform: extra number of sampling points
             curve, cloud: list of coordinates
 
-    surfaces: list of surfaces to sample, choice of
-        plane : values on plane defined by point, normal.
-        patch : values on patch.
+    @param surfaces : list of surfaces to sample, choice of \n
+      - plane : values on plane defined by point, normal.
+      - patch : values on patch.
 
-    Runs in parallel.
+Notes
+    Runs in parallel
 
 \*---------------------------------------------------------------------------*/
 
@@ -100,8 +101,8 @@ int main(int argc, char *argv[])
     instantList timeDirs = timeSelector::select0(runTime, args);
 #   include "createMesh.H"
 
-    IOsampledSets sSets(mesh, "sampleDict", true);
-    IOsampledSurfaces sSurfaces(mesh, "sampleDict", true);
+    IOsampledSets sSets(mesh, "sampleDict", IOobject::MUST_READ, true);
+    IOsampledSurfaces sSurfs(mesh, "sampleDict", IOobject::MUST_READ, true);
 
     forAll(timeDirs, timeI)
     {
@@ -112,10 +113,10 @@ int main(int argc, char *argv[])
         polyMesh::readUpdateState state = mesh.readUpdate();
 
         sSets.readUpdate(state);
-        sSurfaces.readUpdate(state);
+        sSurfs.readUpdate(state);
 
         sSets.write();
-        sSurfaces.write();
+        sSurfs.write();
 
         Info<< endl;
     }

applications/utilities/preProcessing/applyBoundaryLayer/applyBoundaryLayer.C

@@ -95,8 +95,8 @@ int main(int argc, char *argv[])
             << exit(FatalError);
     }
 
-    Info<< "\nCreating boundary-layer for U of thickness" << ybl.value() << " m"
-        << nl << endl;
+    Info<< "\nCreating boundary-layer for U of thickness "
+        << ybl.value() << " m" << nl << endl;
 
     // Modify velocity by applying a 1/7th power law boundary-layer
     // u/U0 = (y/ybl)^(1/7)

bin/foamClearPolyMesh

@@ -35,7 +35,7 @@ usage() {
    while [ "$#" -ge 1 ]; do echo "$1" 1>&2; shift; done
    cat <<USAGE 1>&2
 
-usage: ${0##*/} [-case dir]
+usage: ${0##*/} [-case dir] [-region name]
 
     Remove the contents of the constant/polyMesh directory
     as per the Foam::polyMesh::removeFiles() method.
@@ -44,46 +44,60 @@ USAGE
    exit 1
 }
 
-unset caseDir
-unset meshDir
+unset caseDir regionName
 
-# parse options
-if [ "$#" -gt 0 ]; then
+# parse a single option
+while [ "$#" -gt 0 ]
+do
    case "$1" in
    -h | -help)
       usage
       ;;
    -case)
-      shift
-      caseDir=$1
-      [ "$#" -ge 1 ] || usage "'-case' option requires an argument"
+      [ "$#" -ge 2 ] || usage "'-case' option requires an argument"
+      caseDir=$2
+      shift 2
       cd "$caseDir" 2>/dev/null || usage "directory does not exist:  '$caseDir'"
-      meshDir="constant/polyMesh"
+      ;;
+   -region)
+      [ "$#" -ge 2 ] || usage "'-region' option requires an argument"
+      regionName=$2
+      shift 2
       ;;
    *)
       usage "unknown option/argument: '$*'"
       ;;
    esac
+done
+
+if [ -n "$regionName" ]
+then
+   meshDir=$regionName/polyMesh
+else
+   meshDir=polyMesh
 fi
 
-# meshDir is only set if -case was specified: insist upon 'constant/polyMesh'
-if [ -n "$meshDir" ]
+# if -case was specified: insist upon 'constant/polyMesh'
+if [ -n "$caseDir" ]
 then
-   if [ ! -d "$meshDir" ]
+   if [ -d constant/$meshDir ]
    then
-      echo "Error: no '$meshDir' in $caseDir" 1>&2
+      # use constant/polyMesh
+      meshDir=constant/$meshDir
+   else
+      echo "Error: no 'constant/$meshDir' in $caseDir" 1>&2
       exit 1
    fi
 else
-   if [ -d constant/polyMesh ]
+   if [ -d constant/$meshDir ]
    then
       # use constant/polyMesh
-      meshDir=constant/polyMesh
-   elif [ -d polyMesh ]
+      meshDir=constant/$meshDir
+   elif [ -d $meshDir ]
    then
-      # likely already in constant/
-      meshDir=polyMesh
-   elif [ "${PWD##*/}" = polyMesh ]
+      # likely already in constant/ - do not adjust anything
+      :
+   elif [ "${PWD##*/}" = polyMesh -a -z "$regionName" ]
    then
       # apparently already within polyMesh/
       meshDir=.

bin/foamCopySettings

@@ -84,9 +84,9 @@ for i in $fileList
 do
    name="${i##*/}"
    # skip numerical (results) directories (except 0)
-   # and things that look like queuing system output
+   # and things that look like queuing system output or log files
    case "$name" in
-   [1-9] | [0-9]?* | foam.[eo][1-9]*)
+   [1-9] | [0-9]?* | foam.[eo][1-9]* | log | *.log )
       echo "$i  [skipped]"
       continue
       ;;

bin/foamDiffSourceList

@@ -1,135 +0,0 @@
-#!/bin/sh
-#------------------------------------------------------------------------------
-# =========                 |
-# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-#  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
-#    \\/     M anipulation  |
-#-------------------------------------------------------------------------------
-# License
-#     This file is part of OpenFOAM.
-#
-#     OpenFOAM is free software; you can redistribute it and/or modify it
-#     under the terms of the GNU General Public License as published by the
-#     Free Software Foundation; either version 2 of the License, or (at your
-#     option) any later version.
-#
-#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-#     for more details.
-#
-#     You should have received a copy of the GNU General Public License
-#     along with OpenFOAM; if not, write to the Free Software Foundation,
-#     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-#
-# Script
-#     foamDiffSourceList <oldDir> <newDir> <tarFile>
-#
-# Description
-#     Packs and compresses files that have changed (diff -uw) between
-#     oldDir newDir
-#
-#------------------------------------------------------------------------------
-tmpFile=${TMPDIR:-/tmp}/foamDiffList.$$
-
-if [ $# -ne 3 ]; then
-   echo "Usage : ${0##*/} oldDir newDir tarFile"
-   echo ""
-   echo "Find the files that changed (diff -uw) between <oldDir> and <newDir>"
-   echo "and pack them into <tarFile>"
-   echo ""
-   exit 1
-fi
-
-# canonical form (no double and no trailing dashes)
-oldDir=$(echo "$1" | sed -e 's@//*@/@g' -e 's@/$@@')
-newDir=$(echo "$2" | sed -e 's@//*@/@g' -e 's@/$@@')
-packFile=$3
-
-if [ ! -d $oldDir ]; then
-   echo "Error: directory $oldDir does not exist"
-   exit 1
-fi
-
-if [ ! -d $newDir ]; then
-   echo "Error: directory $newDir does not exist"
-   exit 1
-fi
-
-if [ -f $packFile ]; then
-   echo "Error: $packFile already exists"
-   exit 1
-fi
-
-# Clean up on termination and on Ctrl-C
-trap 'rm -f $tmpFile 2>/dev/null; exit 0' EXIT TERM INT
-
-fileCount=0
-cat /dev/null > $tmpFile
-
-find -H $newDir                \
-    ! -type d -type f          \
-    ! -name "*~"               \
- -a ! -name ".*~"              \
- -a ! -name ".#*"              \
- -a ! -name "*.orig"           \
- -a ! -name "*.dep"            \
- -a ! -name "*.o"              \
- -a ! -name "*.so"             \
- -a ! -name "*.a"              \
- -a ! -name "*.tgz"            \
- -a ! -name "core"             \
- -a ! -name "core.[1-9]*"      \
- -a ! -name "log[0-9]*"        \
-| sed                          \
- -e "\@$newDir/.git/@d"        \
- -e "\@$newDir/lib/@d"         \
- -e '\@applications/bin/@d'      \
- -e '\@/t/@d'                    \
- -e '\@Make[.A-Za-z]*/[^/]*/@d'  \
- -e '\@[Dd]oxygen/html@d'        \
- -e '\@[Dd]oxygen/latex@d'       \
- -e '\@[Dd]oxygen/man@d'         \
- -e "s@$newDir/*@@"              \
- | \
- (
-    while read file
-    do
-       (( fileCount=$fileCount + 1))
-
-       if [ -f "$oldDir/$file" ]
-       then
-          diff -uw $oldDir/$file $newDir/$file >/dev/null 2>&1
-          if [ $? = 1 ]
-          then
-             echo "[DIFF]" $file
-             echo $newDir/$file >> $tmpFile
-             continue
-          fi
-       else
-          echo "[NEW]" $file
-          echo $newDir/$file >> $tmpFile
-          continue
-       fi
-       echo $fileCount $file
-    done
- )
-
-# file fileCount
-fileCount=$(cat $tmpFile | wc -l)
-echo "----------------------------------------------------------------------"
-echo "pack $fileCount changed/new files"
-
-tar -czpf $packFile --files-from $tmpFile
-
-if [ $? = 0 ]
-then
-   echo "Finished packing changed files from $newDir into $packFile"
-else
-   echo "Error: failure packing changed files from $newDir into $packFile"
-   rm -f $packFile 2>/dev/null
-fi
-echo "----------------------------------------------------------------------"
-
-# ----------------------------------------------------------------------------

bin/foamExec

@@ -37,13 +37,11 @@
 #         foamExec -v <foamVersion> <foamCommand> ... -parallel
 #
 #------------------------------------------------------------------------------
-Script=${0##*/}
-
 usage() {
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
    cat<<USAGE
 
-usage: $Script [OPTION] <application> ...
+usage: ${0##*/} [OPTION] <application> ...
 
 options:
   -v ver        specify OpenFOAM version

bin/foamJob

@@ -29,13 +29,11 @@
 # Description
 #
 #------------------------------------------------------------------------------
-Script=${0##*/}
-
 usage() {
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
    cat<<USAGE
 
-usage: $Script [OPTION] <application> ...
+usage: ${0##*/} [OPTION] <application> ...
 
 options:
   -case dir     specify case directory
@@ -108,9 +106,9 @@ do
       usage
       ;;
    -case)
-      shift
-      caseDir=$1
-      [ "$#" -ge 1 ] || usage "'-case' option requires an argument"
+      [ "$#" -ge 2 ] || usage "'-case' option requires an argument"
+      caseDir=$2
+      shift 2
       cd "$caseDir" 2>/dev/null || usage "directory does not exist:  '$caseDir'"
       ;;
    -s)

bin/foamNew

@@ -30,13 +30,11 @@
 #     Create a new standard OpenFOAM source file
 #
 #------------------------------------------------------------------------------
-Script=${0##*/}
-
 usage() {
     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
     cat<<USAGE
 
-usage: $Script <type> {args}
+usage: ${0##*/} <type> {args}
 
 * create a new standard OpenFOAM source file
 

bin/foamPack

@@ -43,7 +43,8 @@ then
 fi
 
 # add optional output directory
-if [ -d "$1" ]; then
+if [ -d "$1" ]
+then
    packFile="$1/$packFile"
 fi