From d8c7792e9c9e759b854caf29468dbc7bcf9b6212 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:42:26 +0100
Subject: [PATCH 1/6] ENH: renumberMesh.C : renumber XXXXProcAddressing maps in
 parallel

---
 .../manipulation/renumberMesh/renumberMesh.C  | 89 ++++++++++++++++++-
 1 file changed, 88 insertions(+), 1 deletion(-)

diff --git a/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C b/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C
index 3394b928b2..c04d87bc91 100644
--- a/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C
+++ b/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();
 

From d5fc3e2475268c292f9398a47d54a26629dfed75 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:42:58 +0100
Subject: [PATCH 2/6] BUG: paraFoam : load pointFields

---
 .../PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C    |  1 +
 .../PV3FoamReader/vtkPV3Foam/vtkPV3FoamPointFields.H   | 10 +++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C b/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C
index a9e39afbb7..0f0ea82066 100644
--- a/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C
+++ b/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"
diff --git a/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamPointFields.H b/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamPointFields.H
index c8e9dd2925..027b8fd142 100644
--- a/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamPointFields.H
+++ b/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>)"
-    pointData->SetName(tf.name().c_str());
+
+    if (&tf != &GeometricField<Type, fvPatchField, volMesh>::null())
+    {
+        pointData->SetName(tf.name().c_str());
+    }
+    else
+    {
+        pointData->SetName(ptf.name().c_str());
+    }
 
     if (debug)
     {

From 502987ac7adfafb31b2cc62053fe33736d03ac5f Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:43:44 +0100
Subject: [PATCH 3/6] BUG:foamExec : save arguments; handle debian naming

---
 bin/foamExec | 45 +++++++++++++++++++++++++++++++++++++++------
 1 file changed, 39 insertions(+), 6 deletions(-)

diff --git a/bin/foamExec b/bin/foamExec
index 84bf043511..d5d56a4cfb 100755
--- a/bin/foamExec
+++ b/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
@@ -54,14 +58,39 @@ USAGE
 
 
 # This script should exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
+# or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
 # extract the <foamInstall> and <version> elements
 # using a function preserves the command args
 getDefaults() {
     set -- $(echo $0 | sed -e 's@/OpenFOAM-\([^/]*\)/bin/[^/]*$@ \1@')
     foamInstall=$1
-    version=$2
+    foamName='OpenFOAM-'
+    versionFile=$2
+    versionString=$2
+
+    if [ -z "$versionFile" ]
+    then
+        # Try debian package name
+        #echo "Assuming debian naming convention 'openfoam<version>'"
+        set -- $(echo $0 | sed -e 's@/openfoam\([0-9]*\)/bin/[^/]*$@ \1@')
+        foamInstall=$1
+        foamName='openfoam'
+        versionFile=$2
+        versionString=$WM_PROJECT_VERSION
+        #echo "foamInstall=$foamInstall"
+        #echo "foamName=$foamName"
+        #echo "versionFile=$versionFile"
+        #echo "versionString=$versionString"
+    fi
 }
 
+
+foamInstall=''      # path before OpenFOAM-1.7.0
+foamName=''         # OpenFOAM- or openfoam
+versionFile=''      # 170 so what the WM_PROJECT_INST_DIR exists as 
+versionString=''    # 1.7.0
+
+# Get above settings from $0
 getDefaults
 
 # parse options
@@ -73,7 +102,8 @@ do
         ;;
     -v)
         shift
-        version=$1
+        versionString=$1
+        versionFile=$1
         shift
         ;;
     --)
@@ -89,15 +119,18 @@ do
     esac
 done
 
+#echo "Detected version $versionString with path name $foamName$versionFile"
+
 if [ "$#" -lt 1 ]
 then
     usage "no application specified"
 fi
 
 unset foamDotFile
+args="$*"
 
 # Check user-specific OpenFOAM bashrc file
-foamDotFile="$HOME/.OpenFOAM/$version/bashrc"
+foamDotFile="$HOME/.OpenFOAM/$versionString/bashrc"
 if [ -f $foamDotFile ]
 then
     . $foamDotFile
@@ -106,7 +139,7 @@ else
     # Use the FOAM_INST_DIR variable for locating the installed version
     for FOAM_INST_DIR in $foamInstall $WM_PROJECT_INST_DIR
     do
-        foamDotFile="$FOAM_INST_DIR/OpenFOAM-$version/etc/bashrc"
+        foamDotFile="$FOAM_INST_DIR/$foamName$versionFile/etc/bashrc"
         if [ -f $foamDotFile ]
         then
             . $foamDotFile
@@ -119,11 +152,11 @@ fi
 
 if [ "$foamDotFile" != okay ]
 then
-    echo "Error : bashrc file could not be found for OpenFOAM-$version" 1>&2
+    echo "Error : bashrc file could not be found for OpenFOAM-$versionString" 1>&2
     exit 1
 fi
 
 # Pass on the rest of the arguments
-exec $*
+exec $args
 
 #------------------------------------------------------------------------------

From 50fc6c846a127dd078fad48e679ee5dca0842657 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:44:37 +0100
Subject: [PATCH 4/6] ENH: apps/paraview3 : upgrade to 3.8.0

---
 etc/apps/paraview3/bashrc | 3 ++-
 etc/apps/paraview3/cshrc  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/etc/apps/paraview3/bashrc b/etc/apps/paraview3/bashrc
index 0ff28f0caf..51965e47d6 100644
--- a/etc/apps/paraview3/bashrc
+++ b/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
diff --git a/etc/apps/paraview3/cshrc b/etc/apps/paraview3/cshrc
index ddb4502c27..a69608c9d3 100644
--- a/etc/apps/paraview3/cshrc
+++ b/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

From 24734787b869346510455f575a41ccebcaf6eb06 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:46:00 +0100
Subject: [PATCH 5/6] BUG: etc/settings.*sh : make SYSTEMOPENMPI work with
 multiple paths

---
 etc/settings.csh | 18 ++++++++++++------
 etc/settings.sh  | 14 +++++++++-----
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/etc/settings.csh b/etc/settings.csh
index 5df50a809a..8b51bb7b41 100644
--- a/etc/settings.csh
+++ b/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 "    compile flags : `mpicc --showme:compile`"
-        echo "    link flags    : `mpicc --showme:link`"
+        echo "Using system installed MPI:"
+        echo "    compile flags : $PINC"
+        echo "    link flags    : $PLIBS"
         echo "    libmpi dir    : $libDir"
     endif
 
diff --git a/etc/settings.sh b/etc/settings.sh
index 17f029539a..aae19a764b 100644
--- a/etc/settings.sh
+++ b/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 "    compile flags : `mpicc --showme:compile`"
-        echo "    link flags    : `mpicc --showme:link`"
+        echo "Using system installed MPI:"
+        echo "    compile flags : $PINC"
+        echo "    link flags    : $PLIBS"
         echo "    libmpi dir    : $libDir"
     fi
 

From 4b307cf543d4349c5e308afdaa9f96adfd320c51 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 6 Jul 2010 11:48:46 +0100
Subject: [PATCH 6/6] STYLE: etc/*rc : update version number, add comment

---
 etc/bashrc | 4 ++--
 etc/cshrc  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/etc/bashrc b/etc/bashrc
index d7dae2ae46..ad866d049b 100644
--- a/etc/bashrc
+++ b/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
 
 
diff --git a/etc/cshrc b/etc/cshrc
index 1ef3458f8e..9f55d62ab6 100644
--- a/etc/cshrc
+++ b/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