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

.gitignore

@@ -60,8 +60,8 @@ doc/[Dd]oxygen/man
 # untracked configuration files
 /etc/prefs.csh
 /etc/prefs.sh
-/etc/config/*.csh
-/etc/config/*.sh
+/etc/config/prefs.csh
+/etc/config/prefs.sh
 
 # source packages - anywhere
 *.tar.bz2

ReleaseNotes-dev

@@ -241,9 +241,11 @@
       - works in parallel
     + =snappyHexMesh=:
       + extrude across multi-processor boundaries
-      + preserve faceZones during layering
-      + combining patch faces after snapping
+      + preserve faceZones shape during layering
+      + combining coincident patch faces is now default after snapping
       + *Warning*:
+            - snapControls::tolerance setting fixed w.r.t. 17x. Is the
+              multiplication to calculate the local search distance for nearest.
             - minMedianAxisAngle angle fixed w.r.t. 17x. Set to
               90 to get same behaviour as 130 in 17x.
             - nGrow did not work in 17x. Set to 0
@@ -308,6 +310,8 @@
     + multipleBoxes, hotBoxes, panel, evaporationTest
   + =interDyMFoam= tutorials:
     + testTubeMixer: showcases =solidBodyMotionFunction=
+  + =snappyHexMesh= tutorials:
+    + flange: demonstration of feature lines in snappyHexMesh
 
 * Other
   + compilable with =clang=

applications/solvers/basic/potentialFoam/potentialFoam.C

@@ -49,6 +49,10 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Calculating potential flow" << endl;
 
+    // Since solver contains no time loop it would never execute
+    // function objects so do it ourselves.
+    runTime.functionObjects().start();
+
     adjustPhi(phi, U, p);
 
     for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
@@ -99,6 +103,9 @@ int main(int argc, char *argv[])
         p.write();
     }
 
+    runTime.functionObjects().end();
+
+
     Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
         << "  ClockTime = " << runTime.elapsedClockTime() << " s"
         << nl << endl;

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

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -453,6 +453,7 @@ void Foam::createShellMesh::setRefinement
             label region0 = pointRegions_[eFaces[0]][fp0];
             label region1 = pointRegions_[eFaces[0]][fp1];
 
+            // Pick up points with correct normal
             if (layerI == 0)
             {
                 newF[0] = f[fp0];
@@ -468,6 +469,22 @@ void Foam::createShellMesh::setRefinement
                 newF[3] = addedPoints[nLayers*region0+layerI];
             }
 
+            // Optionally rotate so e[0] is always 0th vertex. Note that
+            // this normally is automatically done by coupled face ordering
+            // but with NOORDERING we have to do it ourselves.
+            if (f[fp0] != e[0])
+            {
+                // rotate one back to get newF[1] (originating from e[0])
+                // into newF[0]
+                label v0 = newF[0];
+                for (label i = 0; i < newF.size()-1; i++)
+                {
+                    newF[i] = newF[newF.fcIndex(i)];
+                }
+                newF.last() = v0;
+            }
+
+
             label minCellI = addedCells[nLayers*eFaces[0]+layerI];
             label maxCellI;
             label patchI;
@@ -569,6 +586,21 @@ void Foam::createShellMesh::setRefinement
                         newF[3] = addedPoints[nLayers*region0+layerI];
                     }
 
+
+                    // Optionally rotate so e[0] is always 0th vertex. Note that
+                    // this normally is automatically done by coupled face
+                    // ordering but with NOORDERING we have to do it ourselves.
+                    if (f[fp0] != e[0])
+                    {
+                        // rotate one back to get newF[1] (originating
+                        // from e[0]) into newF[0].
+                        label v0 = newF[0];
+                        for (label i = 0; i < newF.size()-1; i++)
+                        {
+                            newF[i] = newF[newF.fcIndex(i)];
+                        }
+                        newF.last() = v0;
+                    }
                     ////if (ePatches.size() == 0)
                     //{
                     //    Pout<< "Adding from MULTI face:"

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -220,7 +220,7 @@ snapControls
     //- Maximum relative distance for points to be attracted by surface.
     //  True distance is this factor times local maximum edge length.
     // Note: changed(corrected) w.r.t 17x! (17x used 2* tolerance)
-    tolerance 2.0;
+    tolerance 1.0;
 
     //- Number of mesh displacement relaxation iterations.
     nSolveIter 30;
@@ -228,6 +228,10 @@ snapControls
     //- Maximum number of snapping relaxation iterations. Should stop
     //  before upon reaching a correct mesh.
     nRelaxIter 5;
+
+    //- Highly experimental and wip: number of feature edge snapping
+    //  iterations. Leave out altogether to disable.
+    //nFeatureSnapIter 10;
 }
 
 
@@ -258,6 +262,9 @@ addLayersControls
 
 
     //- Wanted thickness of final added cell layer. If multiple layers
+    //  is the
+    //  thickness of the layer furthest away from the wall.
+    //  Relative to undistorted size of cell outside layer.
     //  is the thickness of the layer furthest away from the wall.
     //  See relativeSizes parameter.
     finalLayerThickness 0.3;
@@ -410,7 +417,7 @@ debug 0;
 
 // Merge tolerance. Is fraction of overall bounding box of initial mesh.
 // Note: the write tolerance needs to be higher than this.
-mergeTolerance 1E-6;
+mergeTolerance 1e-6;
 
 
 // ************************************************************************* //

applications/utilities/miscellaneous/foamFormatConvert/foamFormatConvert.C

@@ -144,10 +144,30 @@ bool writeZones(const word& name, const fileName& meshDir, Time& runTime)
 int main(int argc, char *argv[])
 {
     timeSelector::addOptions();
+    argList::addBoolOption
+    (
+        "noConstant",
+        "exclude the 'constant/' dir in the times list"
+    );
+
 #   include "addRegionOption.H"
 #   include "setRootCase.H"
+
+    // enable noConstant by switching
+    if (!args.optionFound("noConstant"))
+    {
+        args.setOption("constant", "");
+    }
+    else
+    {
+        args.unsetOption("constant");
+        Info<< "Excluding the constant directory." << nl << endl;
+    }
+
+
 #   include "createTime.H"
 
+
     // Make sure we do not use the master-only reading since we read
     // fields (different per processor) as dictionaries.
     regIOobject::fileModificationChecking = regIOobject::timeStamp;

applications/utilities/parallelProcessing/redistributeMeshPar/redistributeMeshPar.C

@@ -98,6 +98,44 @@ autoPtr<fvMesh> createMesh
             xferCopy(labelList()),
             false
         );
+        // Add some dummy zones so upon reading it does not read them
+        // from the undecomposed case. Should be done as extra argument to
+        // regIOobject::readStream?
+        List<pointZone*> pz
+        (
+            1,
+            new pointZone
+            (
+                "dummyPointZone",
+                labelList(0),
+                0,
+                dummyMesh.pointZones()
+            )
+        );
+        List<faceZone*> fz
+        (
+            1,
+            new faceZone
+            (
+                "dummyFaceZone",
+                labelList(0),
+                boolList(0),
+                0,
+                dummyMesh.faceZones()
+            )
+        );
+        List<cellZone*> cz
+        (
+            1,
+            new cellZone
+            (
+                "dummyCellZone",
+                labelList(0),
+                0,
+                dummyMesh.cellZones()
+            )
+        );
+        dummyMesh.addZones(pz, fz, cz);
         //Pout<< "Writing dummy mesh to " << dummyMesh.polyMesh::objectPath()
         //    << endl;
         dummyMesh.write();
@@ -239,7 +277,11 @@ autoPtr<fvMesh> createMesh
 
     if (!haveMesh)
     {
-        // Add the zones
+        // Add the zones. Make sure to remove the old dummy ones first
+        mesh.pointZones().clear();
+        mesh.faceZones().clear();
+        mesh.cellZones().clear();
+
         List<pointZone*> pz(pointZoneNames.size());
         forAll(pointZoneNames, i)
         {
@@ -389,6 +431,12 @@ void printMeshData(const polyMesh& mesh)
 
     globalIndex globalBoundaryFaces(mesh.nFaces()-mesh.nInternalFaces());
 
+    label maxProcCells = 0;
+    label totProcFaces = 0;
+    label maxProcPatches = 0;
+    label totProcPatches = 0;
+    label maxProcFaces = 0;
+
     for (label procI = 0; procI < Pstream::nProcs(); procI++)
     {
         Info<< endl
@@ -413,7 +461,32 @@ void printMeshData(const polyMesh& mesh)
             << "    Number of processor faces = " << nProcFaces << nl
             << "    Number of boundary faces = "
             << globalBoundaryFaces.localSize(procI) << endl;
+
+        maxProcCells = max(maxProcCells, globalCells.localSize(procI));
+        totProcFaces += nProcFaces;
+        totProcPatches += nei.size();
+        maxProcPatches = max(maxProcPatches, nei.size());
+        maxProcFaces = max(maxProcFaces, nProcFaces);
     }
+
+    // Stats
+
+    scalar avgProcCells = scalar(globalCells.size())/Pstream::nProcs();
+    scalar avgProcPatches = scalar(totProcPatches)/Pstream::nProcs();
+    scalar avgProcFaces = scalar(totProcFaces)/Pstream::nProcs();
+
+    Info<< nl
+        << "Number of processor faces = " << totProcFaces/2 << nl
+        << "Max number of cells = " << maxProcCells
+        << " (" << 100.0*(maxProcCells-avgProcCells)/avgProcCells
+        << "% above average " << avgProcCells << ")" << nl
+        << "Max number of processor patches = " << maxProcPatches
+        << " (" << 100.0*(maxProcPatches-avgProcPatches)/avgProcPatches
+        << "% above average " << avgProcPatches << ")" << nl
+        << "Max number of faces between processors = " << maxProcFaces
+        << " (" << 100.0*(maxProcFaces-avgProcFaces)/avgProcFaces
+        << "% above average " << avgProcFaces << ")" << nl
+        << endl;
 }
 
 
@@ -641,6 +714,16 @@ int main(int argc, char *argv[])
     );
 #   include "setRootCase.H"
 
+    if (env("FOAM_SIGFPE"))
+    {
+        WarningIn(args.executable())
+            << "Detected floating point exception trapping (FOAM_SIGFPE)."
+            << " This might give" << nl
+            << "    problems when mapping fields. Switch it off in case"
+            << " of problems." << endl;
+    }
+
+
     // Create processor directory if non-existing
     if (!Pstream::master() && !isDir(args.path()))
     {
@@ -906,7 +989,7 @@ int main(int argc, char *argv[])
 
     // Debugging: Create additional volField that will be mapped.
     // Used to test correctness of mapping
-    volVectorField mapCc("mapCc", 1*mesh.C());
+    //volVectorField mapCc("mapCc", 1*mesh.C());
 
     // Global matching tolerance
     const scalar tolDim = getMergeDistance
@@ -948,7 +1031,7 @@ int main(int argc, char *argv[])
 
 
     // Debugging: test mapped cellcentre field.
-    compareFields(tolDim, mesh.C(), mapCc);
+    //compareFields(tolDim, mesh.C(), mapCc);
 
     // Print nice message
     // ~~~~~~~~~~~~~~~~~~

bin/paraFoam

@@ -37,7 +37,7 @@ usage() {
     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
     cat<<USAGE
 
-Usage: ${0##*/} [OPTION]
+Usage: ${0##*/} [OPTION] [PARAVIEW_OPTION]
 options:
   -block            use blockMesh reader  (uses .blockMesh extension)
   -builtin          use VTK builtin OpenFOAM reader  (uses .foam extension)
@@ -47,6 +47,9 @@ options:
   -touchAll         create .blockMesh, .OpenFOAM files (and for all regions)
   -help             print the usage
 
+
+paraview options start with a double dashes
+
 * start paraview $ParaView_VERSION with the OpenFOAM libraries
 
 USAGE
@@ -57,7 +60,7 @@ USAGE
 # to clean up
 unset FOAM_ABORT
 
-unset regionName touchOpt
+unset regionName optTouch
 
 # reader extension
 extension=OpenFOAM
@@ -88,12 +91,19 @@ do
         shift 2
         ;;
     -touch)
-        touchOpt=true
+        optTouch=true
         shift
         ;;
     -touchAll)
-        touchOpt=all
+        optTouch=all
+        shift
+        ;;
+    --)
         shift
+        break    # stop here, treat balance as paraview options
+        ;;
+    --*)
+        break    # stop here, treat this and balance as paraview options
         ;;
     *)
         usage "unknown option/argument: '$*'"
@@ -101,6 +111,28 @@ do
     esac
 done
 
+
+#
+# check for --data=... argument
+#
+hasDataArg()
+{
+    hasData=false
+    while [ "$#" -gt 0 ]
+    do
+        case "$1" in
+        (--data=*)
+            hasData=true
+            break
+            ;;
+        esac
+        shift
+    done
+}
+
+hasDataArg $@
+
+
 # get a sensible caseName from the directory name
 caseName=${PWD##*/}
 caseFile="$caseName.$extension"
@@ -112,7 +144,7 @@ then
     fvControls="$fvControls/$regionName"
 fi
 
-case "${touchOpt:-false}" in
+case "${optTouch:-false}" in
 all)
     extension=OpenFOAM
     if [ -f constant/polyMesh/blockMeshDict ]
@@ -149,33 +181,56 @@ case "$caseName" in
 esac
 
 
-#
-# check existence of essential files
-#
-case $extension in
-blockMesh)
-    for check in system/controlDict constant/polyMesh/blockMeshDict
-    do
-        [ -s "$parentDir/$check" ] || usage "file does not exist:  '$parentDir/$check'"
-    done
-    ;;
+if [ "${hasData:-false}" = true ]
+then
 
-builtin | OpenFOAM)
-    for check in system/controlDict $fvControls/fvSchemes $fvControls/fvSolution
-    do
-        [ -s "$parentDir/$check" ] || usage "file does not exist:  '$parentDir/$check'"
-    done
-    ;;
-esac
+    # has --data=.., send directly to paraview
+    exec paraview "$@"
+
+else
+
+    # check existence of essential files
+    warn="WARN file does not exist:"
+    case $extension in
+    blockMesh)
+        for check in \
+            system/controlDict \
+            constant/polyMesh/blockMeshDict \
+            ;
+        do
+            [ -s "$parentDir/$check" ] || {
+                [ -n "$warn" ] && echo "$warn" 1>&2
+                echo "    $parentDir/$check" 1>&2
+                unset warn
+            }
+        done
+        ;;
+
+    builtin | OpenFOAM)
+        for check in \
+            system/controlDict \
+            $fvControls/fvSchemes \
+            $fvControls/fvSolution \
+            ;
+        do
+            [ -s "$parentDir/$check" ] || {
+                [ -n "$warn" ] && echo "$warn" 1>&2
+                echo "    $parentDir/$check" 1>&2
+                unset warn
+            }
+        done
+        ;;
+    esac
 
+    # only create/remove caseFile if it didn't already exist
+    [ -e $caseFile ] || {
+        trap "rm -f $caseFile 2>/dev/null; exit 0" EXIT TERM INT
+        touch "$caseFile"
+        echo "created temporary '$caseFile'"
+    }
 
-# only create/remove caseFile if it didn't already exist
-[ -e $caseFile ] || {
-    trap "rm -f $caseFile 2>/dev/null; exit 0" EXIT TERM INT
-    touch "$caseFile"
-    echo "created temporary '$caseFile'"
-}
+    paraview --data="$caseFile" "$@"
+fi
 
-paraview --data="$caseFile"
 
 #------------------------------------------------------------------------------

bin/tools/foamConfigurePaths

@@ -131,7 +131,7 @@ do
         paraviewInstall="$2"
         # replace ParaView_DIR=...
         _inlineSed \
-            etc/apps/paraview3/bashrc \
+            etc/config/paraview.sh \
             '/^[^#]/s@ParaView_DIR=.*@ParaView_DIR='"$paraviewInstall@" \
              "Replacing ParaView_DIR setting by '$paraviewInstall'"
         shift 2

etc/bashrc

@@ -120,7 +120,12 @@ export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
 # Location of site-specific templates etc
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # unset is equivalent to $WM_PROJECT_INST_DIR/site
-unset WM_PROJECT_SITE
+if [ -d "$WM_PROJECT_SITE" ]
+then
+    export WM_PROJECT_SITE
+else
+    unset WM_PROJECT_SITE
+fi
 
 # Location of user files
 # ~~~~~~~~~~~~~~~~~~~~~~
@@ -177,7 +182,7 @@ _foamEval()
 _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
 
 # Evaluate command-line parameters and record settings for later
-# these can be used to set/unset values, or specify prefs files
+# these can be used to set/unset values, or specify alternative pref files
 export FOAM_SETTINGS="$@"
 _foamEval $@
 
@@ -200,14 +205,14 @@ export PATH LD_LIBRARY_PATH MANPATH
 
 # Source project setup files
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~
-_foamSource $WM_PROJECT_DIR/etc/settings.sh
-_foamSource $WM_PROJECT_DIR/etc/aliases.sh
+_foamSource $WM_PROJECT_DIR/etc/config/settings.sh
+_foamSource $WM_PROJECT_DIR/etc/config/aliases.sh
 
 
 # Source user setup files for optional packages
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile apps/paraview3/bashrc`
-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile apps/ensight/bashrc`
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/paraview.sh`
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/ensight.sh`
 
 
 # Clean environment paths again. Only remove duplicates

etc/config/README

+The main OpenFOAM settings are located in the parent etc/ directory
+
+* bashrc, cshrc
+  entry point for sourcing
+
+* prefs.csh, prefs.sh
+  these files are untracked and can be used for some site-defined
+  settings
+
+
+The etc/config/ directory contains various configuration files in
+sh/csh variants:
+
+* settings.csh, settings.sh
+  core settings
+
+* aliases.csh, aliases.sh
+  aliases for interactive shells
+
+* unset.csh, unset.sh
+  sourced to clear as many OpenFOAM environment settings as possible
+
+
+* ensight.csh, ensight.sh
+  application settings for EnSight
+
+* paraview.csh, paraview.sh
+  application settings for ParaView
+
+* scotch.sh
+  application settings for compiling against scotch
+
+---
+
+The config/example directory contains various example configuration files
+in sh/csh variants
+
+* compiler.csh, compiler.sh
+  an example of fine tuning ThirdParty compiler settings for OpenFOAM
+
+* openmpi.csh, openmpi.sh
+  an example of fine tuning openmpi settings for OpenFOAM
+
+* paraview.csh, paraview.sh
+  an example of chaining to the standard config/paraview.sh with a
+  different ParaView_VERSION
+
+* prefs.csh, prefs.sh
+  an example of supplying alternative site-defined settings
+
+---

etc/aliases.csh → etc/config/aliases.csh

@@ -22,7 +22,7 @@
 #     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 #
 # File
-#     etc/aliases.csh
+#     etc/config/aliases.csh
 #
 # Description
 #     Aliases for working with OpenFOAM
@@ -39,7 +39,7 @@ alias wmSP 'wmSET WM_PRECISION_OPTION=SP'
 alias wmDP 'wmSET WM_PRECISION_OPTION=DP'
 
 # clear env
-alias wmUNSET='source $WM_PROJECT_DIR/etc/unset.csh'
+alias wmUNSET='source $WM_PROJECT_DIR/etc/config/unset.csh'
 
 # Toggle wmakeScheduler on/off
 #  - also need to set WM_HOSTS
@@ -49,7 +49,7 @@ alias wmSchedOFF 'unsetenv WM_SCHEDULER'
 
 # Change ParaView version
 # ~~~~~~~~~~~~~~~~~~~~~~~
-alias foamPV 'source `$WM_PROJECT_DIR/etc/apps/paraview3/cshrc` ParaView_VERSION=\!*; echo paraview-$ParaView_VERSION'
+alias foamPV 'source `$WM_PROJECT_DIR/etc/config/paraview.csh` ParaView_VERSION=\!*; echo paraview-$ParaView_VERSION'
 
 
 # Change directory aliases

etc/aliases.sh → etc/config/aliases.sh

@@ -22,7 +22,7 @@
 #     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 #
 # File
-#     etc/aliases.sh