Merge remote branch 'OpenCFD/master' into olesenm

Conflicts:
	bin/foamExec

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

@@ -430,6 +430,59 @@ int main(int argc, char *argv[])
         << "Band before renumbering: "
         << returnReduce(band, maxOp<label>()) << nl << endl;
 
+
+    // Read parallel reconstruct maps
+    labelIOList cellProcAddressing
+    (
+        IOobject
+        (
+            "cellProcAddressing",
+            mesh.facesInstance(),
+            polyMesh::meshSubDir,
+            mesh,
+            IOobject::READ_IF_PRESENT
+        ),
+        labelList(0)
+    );
+
+    labelIOList faceProcAddressing
+    (
+        IOobject
+        (
+            "faceProcAddressing",
+            mesh.facesInstance(),
+            polyMesh::meshSubDir,
+            mesh,
+            IOobject::READ_IF_PRESENT
+        ),
+        labelList(0)
+    );
+    labelIOList pointProcAddressing
+    (
+        IOobject
+        (
+            "pointProcAddressing",
+            mesh.pointsInstance(),
+            polyMesh::meshSubDir,
+            mesh,
+            IOobject::READ_IF_PRESENT
+        ),
+        labelList(0)
+    );
+    labelIOList boundaryProcAddressing
+    (
+        IOobject
+        (
+            "boundaryProcAddressing",
+            mesh.pointsInstance(),
+            polyMesh::meshSubDir,
+            mesh,
+            IOobject::READ_IF_PRESENT
+        ),
+        labelList(0)
+    );
+
+
     // Read objects in time directory
     IOobjectList objects(mesh, runTime.timeName());
 
@@ -579,6 +632,39 @@ int main(int argc, char *argv[])
     // Update fields
     mesh.updateMesh(map);
 
+    // Update proc maps
+    if (cellProcAddressing.headerOk())
+    {
+        Info<< "Renumbering processor cell decomposition map "
+            << cellProcAddressing.name() << endl;
+
+        cellProcAddressing = labelList
+        (
+            UIndirectList<label>(cellProcAddressing, map().cellMap())
+        );
+    }
+    if (faceProcAddressing.headerOk())
+    {
+        Info<< "Renumbering processor face decomposition map "
+            << faceProcAddressing.name() << endl;
+
+        faceProcAddressing = labelList
+        (
+            UIndirectList<label>(faceProcAddressing, map().faceMap())
+        );
+    }
+    if (pointProcAddressing.headerOk())
+    {
+        Info<< "Renumbering processor point decomposition map "
+            << pointProcAddressing.name() << endl;
+
+        pointProcAddressing = labelList
+        (
+            UIndirectList<label>(pointProcAddressing, map().pointMap())
+        );
+    }
+
+
     // Move mesh (since morphing might not do this)
     if (map().hasMotionPoints())
     {
@@ -652,7 +738,8 @@ int main(int argc, char *argv[])
     {
         mesh.setInstance(oldInstance);
     }
-    Info<< "Writing mesh to " << runTime.timeName() << endl;
+
+    Info<< "Writing mesh to " << mesh.facesInstance() << endl;
 
     mesh.write();
 

applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C

@@ -31,6 +31,7 @@ License
 #include "cellModeller.H"
 #include "vtkOpenFOAMPoints.H"
 #include "Swap.H"
+#include "longLong.H"
 
 // VTK includes
 #include "vtkCellArray.h"

applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamPointFields.H

@@ -195,7 +195,15 @@ void Foam::vtkPV3Foam::convertPointField
 
     // Note: using the name of the original volField
     // not the name generated by the interpolation "volPointInterpolate(<name>)"
+
+    if (&tf != &GeometricField<Type, fvPatchField, volMesh>::null())
+    {
         pointData->SetName(tf.name().c_str());
+    }
+    else
+    {
+        pointData->SetName(ptf.name().c_str());
+    }
 
     if (debug)
     {

bin/foamEtcFile

@@ -82,6 +82,9 @@ mode=ugo
 prefix="$WM_PROJECT_INST_DIR"
 version="$WM_PROJECT_VERSION"
 
+# default naming convention is "OpenFOAM-<VERSION>"
+projectNamePrefix="${WM_PROJECT:-OpenFOAM}-"
+
 
 unset listOpt quietOpt
 # parse options
@@ -132,6 +135,23 @@ do
     esac
 done
 
+
+#
+# handle standard and debian naming convention
+#
+case "$version" in
+OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
+    projectNamePrefix="OpenFOAM-"
+    version="${version##OpenFOAM-}"
+    ;;
+
+openfoam[0-9]*)     # debian naming convention 'openfoam<VERSION>'
+    projectNamePrefix="openfoam"
+    version="${version##openfoam}"
+    ;;
+esac
+
+
 # Save the essential bits of information:
 nArgs=$#
 fileName="$1"
@@ -154,7 +174,7 @@ esac
 
 case "$mode" in
 *o*)  # other (shipped)
-    dirList="$dirList $prefix/${WM_PROJECT:-OpenFOAM}-$version/etc"
+    dirList="$dirList $prefix/$projectNamePrefix$version/etc"
     ;;
 esac
 set -- $dirList

bin/foamExec

@@ -35,6 +35,10 @@
 #     mpirun -np <nProcs> \
 #         foamExec -v <foamVersion> <foamCommand> ... -parallel
 #
+#     Note: - not consistent with foamEtcFiles - does not search 'site'
+#             directories
+#           - version switch -v will not work with the debian naming
+#             openfoamXXX
 #------------------------------------------------------------------------------
 usage() {
     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
@@ -54,7 +58,7 @@ USAGE
 }
 
 # This script must exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
-# or <foamInstall>/openfoamVERSION/bin/
+# or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
 #
 
 # the bindir:
@@ -71,12 +75,31 @@ foamInstall="$prefixDir"
 # the name used for the project directory
 projectDirName="${projectDir##*/}"
 
-# version from OpenFOAM-VERSION (normal) or openfoamVERSION (debian)
+#
-version=$(echo $projectDirName | sed -e 's@^openfoam-*@@i')
+# handle standard and debian naming convention
+#
+case "$projectDirName" in
+OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
+    projectNamePrefix="OpenFOAM-"
+    version="${projectDirName##OpenFOAM-}"
+    versionNum=$version
+    ;;
+
+openfoam[0-9]*)     # debian naming convention 'openfoam<VERSION>'
+    projectNamePrefix="openfoam"
+    versionNum="${projectDirName##openfoam}"
+    version=$WM_PROJECT_DIR
+    ;;
+*)
+    echo "Error : unknown/unsupported naming convention"
+    exit 1
+    ;;
+esac
+
 
 # debugging:
 # echo "Installed locations:"
-# for i in projectDir prefixDir foamInstall projectDirName version
+# for i in projectDir prefixDir foamInstall projectDirName version versionNum
 # do
 #     eval echo "$i=\$$i"
 # done
@@ -92,6 +115,7 @@ do
     -v | version)
         [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
         version=$2
+        versionNum=$version
         shift 2
         ;;
     --)

etc/apps/paraview3/bashrc

@@ -51,7 +51,7 @@ done
 
 
 # set VERSION and MAJOR (version) variables if not already set
-[ -n "$ParaView_VERSION" ] || ParaView_VERSION=3.6.1
+[ -n "$ParaView_VERSION" ] || ParaView_VERSION=3.8.0
 [ -n "$ParaView_MAJOR" ]   || ParaView_MAJOR=unknown
 
 # if needed, set MAJOR version to correspond to VERSION
@@ -75,6 +75,7 @@ export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/paraview-
 if [ -r $ParaView_DIR -o -r $paraviewInstDir ]
 then
     export PATH=$ParaView_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$ParaView_DIR/lib/paraview-$ParaView_MAJOR:$LD_LIBRARY_PATH
     export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
 
     # add in python libraries if required

etc/apps/paraview3/cshrc

@@ -49,7 +49,7 @@ foreach cmake ( cmake-2.8.1 cmake-2.8.0 cmake-2.6.4 )
 end
 
 # set VERSION and MAJOR (version) variables if not already set
-if ( ! $?ParaView_VERSION ) setenv ParaView_VERSION 3.6.1
+if ( ! $?ParaView_VERSION ) setenv ParaView_VERSION 3.8.0
 if ( ! $?ParaView_MAJOR ) setenv ParaView_MAJOR unknown
 
 # if needed, set MAJOR version to correspond to VERSION
@@ -73,6 +73,7 @@ setenv ParaView_DIR $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/paraview-
 # set paths if binaries or source are present
 if ( -r $ParaView_DIR || -r $paraviewInstDir ) then
     setenv PATH ${ParaView_DIR}/bin:${PATH}
+    setenv LD_LIBRARY_PATH "${ParaView_DIR}/lib/paraview-${ParaView_MAJOR}:${LD_LIBRARY_PATH}"
     setenv PV_PLUGIN_PATH $FOAM_LIBBIN/paraview-${ParaView_MAJOR}
 
     # add in python libraries if required

etc/bashrc

@@ -32,7 +32,7 @@
 #------------------------------------------------------------------------------
 
 export WM_PROJECT=OpenFOAM
-[ -z "$WM_PROJECT_VERSION" ] && export WM_PROJECT_VERSION=1.6
+[ -z "$WM_PROJECT_VERSION" ] && export WM_PROJECT_VERSION=dev
 
 ################################################################################
 # USER EDITABLE PART. Note changes made here may be lost with the next upgrade
@@ -131,7 +131,7 @@ unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH
 # WM_COMPILE_OPTION = Opt | Debug | Prof
 : ${WM_COMPILE_OPTION:=Opt}; export WM_COMPILE_OPTION
 
-# WM_MPLIB = | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI
+# WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI
 : ${WM_MPLIB:=OPENMPI}; export WM_MPLIB
 
 

etc/cshrc

@@ -31,7 +31,7 @@
 #------------------------------------------------------------------------------
 
 setenv WM_PROJECT OpenFOAM
-if ( ! $?WM_PROJECT_VERSION ) setenv WM_PROJECT_VERSION 1.6
+if ( ! $?WM_PROJECT_VERSION ) setenv WM_PROJECT_VERSION dev
 
 ################################################################################
 # USER EDITABLE PART. Note changes made here may be lost with the next upgrade
@@ -119,7 +119,7 @@ if ( ! $?WM_PRECISION_OPTION ) setenv WM_PRECISION_OPTION DP
 # WM_COMPILE_OPTION = Opt | Debug | Prof
 if ( ! $?WM_COMPILE_OPTION ) setenv WM_COMPILE_OPTION Opt
 
-# WM_MPLIB = | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI
+# WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI
 if ( ! $?WM_MPLIB ) setenv WM_MPLIB OPENMPI
 
 

etc/settings.csh

@@ -82,7 +82,7 @@ unsetenv MPFR_ARCH_PATH
 # Select compiler installation
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # compilerInstall = OpenFOAM | system
-if ( ! $?compilerInstall ) set compilerInstall=OpenFOAM
+if ( ! $?compilerInstall ) set compilerInstall=system
 
 switch ("$compilerInstall")
 case OpenFOAM:
@@ -209,14 +209,20 @@ case OPENMPI:
     breaksw
 
 case SYSTEMOPENMPI:
-    # use the system installed openmpi, get library directory via mpicc
+
+    # This uses the installed openmpi. It needs mpicc installed!
+
     set mpi_version=openmpi-system
-    set libDir=`mpicc --showme:link | sed -e 's/.*-L\([^ ]*\).*/\1/'`
+
+    # Set compilation flags here instead of in wmake/rules/../mplibSYSTEMOPENMPI
+    setenv PINC "`mpicc --showme:compile`"
+    setenv PLIBS "`mpicc --showme:link`"
+    set libDir=`echo "$PLIBS" | sed -e 's/.*-L\([^ ]*\).*/\1/'`
 
     if ($?FOAM_VERBOSE && $?prompt) then
-        echo "Using system installed OpenMPI:"
+        echo "Using system installed MPI:"
-        echo "    compile flags : `mpicc --showme:compile`"
+        echo "    compile flags : $PINC"
-        echo "    link flags    : `mpicc --showme:link`"
+        echo "    link flags    : $PLIBS"
         echo "    libmpi dir    : $libDir"
     endif
 

etc/settings.sh

@@ -105,7 +105,7 @@ unset MPFR_ARCH_PATH
 # Select compiler installation
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # compilerInstall = OpenFOAM | system
-: ${compilerInstall:=OpenFOAM}
+: ${compilerInstall:=system}
 
 case "${compilerInstall:-OpenFOAM}" in
 OpenFOAM)
@@ -237,13 +237,17 @@ OPENMPI)
 SYSTEMOPENMPI)
     # use the system installed openmpi, get library directory via mpicc
     mpi_version=openmpi-system
-    libDir=`mpicc --showme:link | sed -e 's/.*-L\([^ ]*\).*/\1/'`
+
+    # Set compilation flags here instead of in wmake/rules/../mplibSYSTEMOPENMPI
+    export PINC="`mpicc --showme:compile`"
+    export PLIBS="`mpicc --showme:link`"
+    libDir=`echo "$PLIBS" | sed -e 's/.*-L\([^ ]*\).*/\1/'`
 
     if [ "$FOAM_VERBOSE" -a "$PS1" ]
     then
-        echo "Using system installed OpenMPI:"
+        echo "Using system installed MPI:"
-        echo "    compile flags : `mpicc --showme:compile`"
+        echo "    compile flags : $PINC"
-        echo "    link flags    : `mpicc --showme:link`"
+        echo "    link flags    : $PLIBS"
         echo "    libmpi dir    : $libDir"
     fi