Merge branch 'develop' of develop.openfoam.com:Development/OpenFOAM-plus into develop

applications/Allwmake

@@ -20,8 +20,8 @@ wmakeCheckPwd "$WM_PROJECT_DIR/applications" || {
 
 set -x
 
-wmake -all utilities $*
 wmake -all solvers $*
+wmake -all utilities $*
 
 
 #------------------------------------------------------------------------------

applications/utilities/mesh/conversion/Optional/Allwmake

@@ -6,13 +6,17 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for compilation (at least for error catching)
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+# Get version info and arch-path
+. $WM_PROJECT_DIR/etc/config.sh/functions
+_foamSource $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/libccmio)
+
 set -x
 
-# build libccmio and create lnInclude directory
+# Build libccmio (.so)
-$WM_THIRD_PARTY_DIR/AllwmakeLibccmio
+$WM_THIRD_PARTY_DIR/makeCCMIO
 
-# if the library built properly, the headers should exist too
+if [ -e $CCMIO_ARCH_PATH/include/libccmio/ccmio.h \
-if [ -e $FOAM_EXT_LIBBIN/libccmio.so ]
+  -a -e $FOAM_EXT_LIBBIN/libccmio.so ]
 then
     wmake ccm26ToFoam
 fi

applications/utilities/mesh/conversion/Optional/ccm26ToFoam/Make/options

@@ -1,10 +1,7 @@
-LIBCCMIO_DIR = $(WM_THIRD_PARTY_DIR)/libccmio-2.6.1
-
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(LIBCCMIO_DIR) \
+    -I$(CCMIO_ARCH_PATH)/include
-    -I$(LIBCCMIO_DIR)/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \

applications/utilities/mesh/conversion/Optional/ccm26ToFoam/ccm26ToFoam.C

@@ -49,7 +49,7 @@ Description
 #include "SortableList.H"
 #include "cellSet.H"
 
-#include <ccmio.h>
+#include "libccmio/ccmio.h"
 #include <vector>
 
 using namespace Foam;

applications/utilities/mesh/generation/Allwmake

@@ -3,12 +3,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 # Parse arguments for compilation (at least for error catching)
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-
-# Get CGAL and boost versions
-. $WM_PROJECT_DIR/etc/config.sh/functions
-_foamEval SOURCE_CGAL_VERSIONS_ONLY=yes \
-          $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/CGAL)
-
 set -x
 
 wmake -all blockMesh
@@ -16,10 +10,6 @@ wmake -all extrude
 wmake -all extrude2DMesh
 wmake -all snappyHexMesh
 
-if [ -n "$CGAL_ARCH_PATH" -o "$cgal_version" = "cgal-system" ]
+foamyMesh/Allwmake $*
-then
-    foamyMesh/Allwmake $*
-fi
-
 
 #------------------------------------------------------------------------------

applications/utilities/mesh/generation/foamyMesh/Allwmake

@@ -4,15 +4,21 @@ cd ${0%/*} || exit 1    # Run from this directory
 # Parse arguments for library compilation
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
-wmake $targetType conformalVoronoiMesh
+if [ -d "$CGAL_ARCH_PATH/include/CGAL" ] || \
-wmake $targetType conformalVoronoi2DMesh
+   [ "${CGAL_ARCH_PATH##*-}" = system -a -d /usr/include/CGAL ]
-wmake foamyQuadMesh
+then
-wmake foamyHexMesh
+    set -x
-#wmake foamyHexMeshBackgroundMesh
-#(cd foamyHexMeshSurfaceSimplify && ./Allwmake)
-#wmake cellSizeAndAlignmentGrid
 
+    wmake $targetType conformalVoronoiMesh
+    wmake $targetType conformalVoronoi2DMesh
+    wmake foamyQuadMesh
+    wmake foamyHexMesh
+    # wmake foamyHexMeshBackgroundMesh
+    # (cd foamyHexMeshSurfaceSimplify && ./Allwmake)
+    # wmake cellSizeAndAlignmentGrid
+else
+    echo "WARNING: cannot build ${PWD##*/} without CGAL"
+fi
 
 #------------------------------------------------------------------------------

applications/utilities/mesh/manipulation/insideCells/insideCells.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -39,6 +39,7 @@ Description
 #include "triSurface.H"
 #include "triSurfaceSearch.H"
 #include "cellSet.H"
+#include "globalMeshData.H"
 
 using namespace Foam;
 
@@ -54,7 +55,6 @@ int main(int argc, char *argv[])
         "Surface must be closed and singly connected."
     );
 
-    argList::noParallel();
     argList::validArgs.append("surfaceFile");
     argList::validArgs.append("cellSet");
 
@@ -87,7 +87,8 @@ int main(int argc, char *argv[])
     }
 
 
-    Info<< "Selected " << insideCells.size() << " of " << mesh.nCells()
+    Info<< "Selected " << returnReduce(insideCells.size(), sumOp<label>())
+        << " of " << mesh.globalData().nTotalCells()
         << " cells" << nl << nl
         << "Writing selected cells to cellSet " << insideCells.name()
         << nl << nl

applications/utilities/parallelProcessing/decomposePar/decomposePar.C

@@ -1104,6 +1104,10 @@ int main(int argc, char *argv[])
                 {
                     const fileName timePath = processorDb.timePath();
 
+                    // If no fields have been decomposed the destination
+                    // directory will not have been created so make sure.
+                    mkDir(timePath);
+
                     if (copyUniform || mesh.distributed())
                     {
                         cp

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

@@ -81,6 +81,8 @@ Note
 #include "cellSet.H"
 #include "fvMeshSubset.H"
 
+#include "memInfo.H"
+
 using namespace Foam;
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -156,6 +158,11 @@ int main(int argc, char *argv[])
     const bool binary = !args.optionFound("ascii");
     const bool nodeValues = args.optionFound("nodeValues");
 
+    cpuTime timer;
+    memInfo mem;
+    Info<< "Initial memory "
+        << mem.update().size() << " kB" << endl;
+
     #include "createTime.H"
 
     instantList Times = timeSelector::select0(runTime, args);
@@ -746,6 +753,10 @@ int main(int argc, char *argv[])
                 }
             }
         }
+
+        Info<< "Wrote in "
+            << timer.cpuTimeIncrement() << " s, "
+            << mem.update().size() << " kB" << endl;
     }
 
     #include "ensightCaseTail.H"
@@ -755,7 +766,9 @@ int main(int argc, char *argv[])
         delete ensightCaseFilePtr;
     }
 
-    Info<< "End\n" << endl;
+    Info<< "\nEnd: "
+        << timer.elapsedCpuTime() << " s, "
+        << mem.update().peak() << " kB (peak)\n" << endl;
 
     return 0;
 }

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/foamToEnsightParts.C

@@ -74,6 +74,8 @@ Note
 #include "ensightParts.H"
 #include "ensightOutputFunctions.H"
 
+#include "memInfo.H"
+
 using namespace Foam;
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -135,6 +137,12 @@ int main(int argc, char *argv[])
     const char* geometryName = "geometry";
 
     #include "setRootCase.H"
+
+    cpuTime timer;
+    memInfo mem;
+    Info<< "Initial memory "
+        << mem.update().size() << " kB" << endl;
+
     #include "createTime.H"
 
     // get times list
@@ -471,11 +479,17 @@ int main(int argc, char *argv[])
             // remember the time index
             cloudTimesUsed[cloudName].append(timeIndex);
         }
+
+        Info<< "Wrote in "
+            << timer.cpuTimeIncrement() << " s, "
+            << mem.update().size() << " kB" << endl;
     }
 
     #include "ensightOutputCase.H"
 
-    Info<< "\nEnd\n"<< endl;
+    Info<< "\nEnd: "
+        << timer.elapsedCpuTime() << " s, "
+        << mem.update().peak() << " kB (peak)\n" << endl;
 
     return 0;
 }

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

@@ -163,6 +163,7 @@ Note
 #include "surfaceMeshWriter.H"
 #include "writeSurfFields.H"
 
+#include "memInfo.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -322,6 +323,12 @@ int main(int argc, char *argv[])
     );
 
     #include "setRootCase.H"
+
+    cpuTime timer;
+    memInfo mem;
+    Info<< "Initial memory "
+        << mem.update().size() << " kB" << endl;
+
     #include "createTime.H"
 
     const bool doWriteInternal = !args.optionFound("noInternal");
@@ -432,10 +439,13 @@ int main(int argc, char *argv[])
 
     mkDir(fvPath);
 
-
     // Mesh wrapper; does subsetting and decomposition
     vtkMesh vMesh(mesh, cellSetName);
 
+    Info<< "VTK mesh topology: "
+        << timer.cpuTimeIncrement() << " s, "
+        << mem.update().size() << " kB" << endl;
+
 
     // Scan for all possible lagrangian clouds
     HashSet<fileName> allCloudDirs;
@@ -1245,6 +1255,10 @@ int main(int argc, char *argv[])
                 writer.writeParcelHeader(0);
             }
         }
+
+        Info<< "Wrote in "
+            << timer.cpuTimeIncrement() << " s, "
+            << mem.update().size() << " kB" << endl;
     }
 
 
@@ -1305,7 +1319,9 @@ int main(int argc, char *argv[])
         }
     }
 
-    Info<< "End\n" << endl;
+    Info<< "\nEnd: "
+        << timer.elapsedCpuTime() << " s, "
+        << mem.update().peak() << " kB (peak)\n" << endl;
 
     return 0;
 }

applications/utilities/postProcessing/graphics/PV3Readers/Allwmake

@@ -1,32 +1,66 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
 
+# Optional unit: continue-on-error
+export WM_CONTINUE_ON_ERROR=true
+
 # Parse arguments for library compilation
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-#set -x
 
+#
+# There are several prerequisites for building a plugin
+#
+#set -x
+canBuildPlugin()
+{
+    [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ] || {
+        echo
+        echo "WARNING: cannot build ParaView plugin(s) without paraview directory"
+        echo "    ParaView_DIR=$ParaView_DIR"
+        echo
+        return 1
+    }
+
+    [ -n "$PV_PLUGIN_PATH" ] || {
+        echo
+        echo "${PWD##*/} : invalid PV_PLUGIN_PATH for building ParaView plugin(s)"
+        echo "    PV_PLUGIN_PATH=${PV_PLUGIN_PATH:-unset}"
+        echo
+        return 1
+    }
+
+    type cmake > /dev/null 2>&1 || {
+        echo
+        echo "WARNING: cannot build ParaView plugin(s) without cmake"
+        echo
+        return 1
+    }
+
+    return 0 # success
+}
+
+
+# -----------------------------------------------------------------------------
 case "$ParaView_VERSION" in
 3*)
-    if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
+    if canBuildPlugin
     then
-        [ -n "$PV_PLUGIN_PATH" ] || {
+    (
-            echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
+        # C++ compiler for CMake
-            exit 1
-        }
-
-        # ensure CMake gets the correct C++ compiler
         [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
 
         wmake $targetType vtkPV3Readers
         PV3blockMeshReader/Allwmake $*
         PV3FoamReader/Allwmake $*
-    else
+    )
-        echo "ERROR: ParaView not found in $ParaView_DIR"
     fi
     ;;
 *)
-    echo "WARN: PV3 readers not building: ParaView_VERSION=$ParaView_VERSION"
+    echo
+    echo "NOTE: skipping build of ParaView V3 plugin(s)"
+    echo "    different version: ParaView_VERSION=$ParaView_VERSION"
+    echo
     ;;
 esac
 

applications/utilities/postProcessing/graphics/PVReaders/Allwclean

@@ -6,4 +6,7 @@ wclean libso vtkPVReaders
 PVblockMeshReader/Allwclean
 PVFoamReader/Allwclean
 
+# remove dummy directory (see Allwmake)
+rmdir Make 2>/dev/null
+
 #------------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/PVReaders/Allwmake

@@ -1,32 +1,70 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
 
+# Optional unit: continue-on-error
+export WM_CONTINUE_ON_ERROR=true
+
 # Parse arguments for library compilation
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-#set -x
 
+#
+# There are several prerequisites for building a plugin
+#
+#set -x
+canBuildPlugin()
+{
+    [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ] || {
+        echo
+        echo "WARNING: cannot build ParaView plugin(s) without paraview directory"
+        echo "    ParaView_DIR=$ParaView_DIR"
+        echo
+        return 1
+    }
+
+    [ -n "$PV_PLUGIN_PATH" ] || {
+        echo
+        echo "${PWD##*/} : invalid PV_PLUGIN_PATH for building ParaView plugin(s)"
+        echo "    PV_PLUGIN_PATH=${PV_PLUGIN_PATH:-unset}"
+        echo
+        return 1
+    }
+
+    type cmake > /dev/null 2>&1 || {
+        echo
+        echo "WARNING: cannot build ParaView plugin(s) without cmake"
+        echo
+        return 1
+    }
+
+    return 0 # success
+}
+
+
+# -----------------------------------------------------------------------------
 case "$ParaView_VERSION" in
 4* | 5*)
-    if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
+    if canBuildPlugin
     then
-        [ -n "$PV_PLUGIN_PATH" ] || {
+    (
-            echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
+        # C++ compiler for CMake
-            exit 1
-        }
-
-        # ensure CMake gets the correct C++ compiler
         [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
 
         wmake $targetType vtkPVReaders
         PVblockMeshReader/Allwmake $*
         PVFoamReader/Allwmake $*
-    else
+
-        echo "ERROR: ParaView not found in $ParaView_DIR"
+        # dummy directory to trigger proper 'wclean all' behaviour
+        # - the Allwclean will otherwise not be used
+        mkdir -p Make
+    )
     fi
     ;;
 *)
-    echo "WARN: PV readers not building: ParaView_VERSION=$ParaView_VERSION"
+    echo
+    echo "NOTE: skipping build of ParaView plugin(s)"
+    echo "    different version: ParaView_VERSION=$ParaView_VERSION"
+    echo
     ;;
 esac
 

applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/Allwclean

@@ -1,11 +1,19 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
+
+# Source the wmake functions
+. $WM_DIR/scripts/wmakeFunctions
+
 set -x
 
 # deal with client/server vs combined plugins
 rm -f $FOAM_LIBBIN/libPVFoamReader* 2>/dev/null
 
-rm -rf PVFoamReader/Make
+rm -rf PVFoamReader/Make        # safety: old build location
 wclean libso vtkPVFoam
 
+# Where are the generated files stored?
+findObjectDir $PWD # remove entire top-level
+rm -rf "$objectsDir" > /dev/null 2>&1
+
 #------------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/Allwmake

@@ -4,18 +4,30 @@ cd ${0%/*} || exit 1    # Run from this directory
 # Parse arguments for library compilation
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
+# Source the wmake functions
+. $WM_DIR/scripts/wmakeFunctions
+
+# C++ compiler for CMake
+[ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+
+set -x
 if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
 then
     wmake $targetType vtkPVFoam
+    sourceDir=$PWD/PVFoamReader
+
+    # Where are any generated files stored?
+    findObjectDir $sourceDir
     (
-        cd PVFoamReader
+        mkdir -p $objectsDir \
-        mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1
+        && cd $objectsDir \
-        cd Make/$WM_OPTIONS
+        && cmake $sourceDir \
-        cmake ../..
+        && make
-        make
+    ) || {
-    )
+        echo
+        echo "WARNING: incomplete build of ParaView OpenFOAM plugin"
+    }
 fi
 
 #------------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/Allwclean

@@ -1,11 +1,19 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
+
+# Source the wmake functions
+. $WM_DIR/scripts/wmakeFunctions
+
 set -x
 
 # deal with client/server vs combined plugins
-rm -f $FOAM_LIBBIN/libPVblockMeshReader*  2>/dev/null
+rm -f $FOAM_LIBBIN/libPVblockMeshReader* 2>/dev/null
 
-rm -rf PVblockMeshReader/Make
+rm -rf PVblockMeshReader/Make   # safety: old build location
 wclean libso vtkPVblockMesh
 
+# Where are the generated files stored?
+findObjectDir $PWD # remove entire top-level
+rm -rf "$objectsDir" > /dev/null 2>&1
+
 #------------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/Allwmake

@@ -4,18 +4,30 @@ cd ${0%/*} || exit 1    # Run from this directory
 # Parse arguments for library compilation
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-set -x
 
+# Source the wmake functions
+. $WM_DIR/scripts/wmakeFunctions
+
+# C++ compiler for CMake
+[ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+
+set -x
 if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
 then
     wmake $targetType vtkPVblockMesh
+    sourceDir=$PWD/PVblockMeshReader
+
+    # Where are any generated files stored?
+    findObjectDir $sourceDir
     (
-        cd PVblockMeshReader
+        mkdir -p $objectsDir \
-        mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1
+        && cd $objectsDir \
-        cd Make/$WM_OPTIONS
+        && cmake $sourceDir \
-        cmake ../..
+        && make
-        make
+    ) || {
-    )
+        echo
+        echo "WARNING: incomplete build of ParaView BlockMesh plugin"
+    }
 fi
 
 #------------------------------------------------------------------------------

applications/utilities/surface/surfaceBooleanFeatures/Allwmake

@@ -2,14 +2,18 @@
 cd ${0%/*} || exit 1    # Run from this directory
 set -x
 
-if [ -z "$CGAL_ARCH_PATH" ]
+unset COMPILE_FLAGS LINK_FLAGS
+
+if [ -d "$CGAL_ARCH_PATH/include/CGAL" ] || \
+   [ "${CGAL_ARCH_PATH##*-}" = system -a -d /usr/include/CGAL ]
 then
-    export COMPILE_FLAGS="-DNO_CGAL"
-else
     wmake PolyhedronReader
     export COMPILE_FLAGS='-IPolyhedronReader'
     export LINK_FLAGS='${CGAL_LIBS} -lPolyhedronReader'
+else
+    export COMPILE_FLAGS="-DNO_CGAL"
 fi
+
 wmake
 
 # ----------------------------------------------------------------- end-of-file

applications/utilities/surface/surfaceBooleanFeatures/Make/options

@@ -15,7 +15,6 @@ EXE_INC = \
     ${CGAL_INC} \
     ${c++CGALWARN} \
     $(COMPILE_FLAGS) \
-    -IPolyhedronReader \
     -I$(FOAM_SRC)/surfMesh/lnInclude \
     -I$(FOAM_SRC)/triSurface/lnInclude \
     -I$(LIB_SRC)/edgeMesh/lnInclude \

etc/bashrc

@@ -62,7 +62,7 @@ foamInstall=$HOME/$WM_PROJECT
 export WM_COMPILER_TYPE=system
 
 #- Compiler:
-#    WM_COMPILER = Gcc | Gcc45 | Gcc46 | Gcc47 | Gcc48 | Gcc49| Clang | Icc
+#    WM_COMPILER = Gcc | Gcc4[5-9] | Gcc5[1-4] | Gcc61 | Clang | Icc
 export WM_COMPILER=Gcc
 unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH
 

etc/config.csh/CGAL

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2014-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -22,33 +22,60 @@
 #     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 #
 # File
-#     config.csh/CGAL
+#     etc/config.csh/CGAL
 #
 # Description
 #     Setup file for CGAL (& boost) include/libraries.
 #     Sourced from OpenFOAM-<VERSION>/etc/cshrc
-##------------------------------------------------------------------------------
+#
+#     If using system-wide installations, use the following settings:
+#
+#         boost_version=boost-system
+#         cgal_version=cgal-system
+#
+#     If the system boost/cgal is unusable (eg, too old) and you don't
+#     have or want a ThirdParty installation:
+#
+#         boost_version=boost-none
+#         cgal_version=cgal-none
+#
+#     If using a central installation, but not located under ThirdParty:
+#         - specify boost-system / cgal-system
+#         - provide full paths for BOOST_ARCH_PATH / CGAL_ARCH_PATH
+#
+# Note
+#     When building OpenFOAM, any changes made here MUST be made in the
+#     equivalent config.sh version too, since that is the one which will
+#     be used during the build process.
+#
+#------------------------------------------------------------------------------
 
 set boost_version=boost-system
-set cgal_version=CGAL-4.7
+set cgal_version=CGAL-4.8
 
 setenv BOOST_ARCH_PATH $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version
 setenv CGAL_ARCH_PATH $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version
 
+#------------------------------------------------------------------------------
 if ($?FOAM_VERBOSE && $?prompt) then
-    echo "Using CGAL and boost"
+    echo "Using boost ($boost_version)  ->  $BOOST_ARCH_PATH"
-    echo "    $cgal_version at $CGAL_ARCH_PATH"
+    echo "Using CGAL ($cgal_version)  ->  $CGAL_ARCH_PATH"
-    echo "    $boost_version at $BOOST_ARCH_PATH"
 endif
 
-if ( -d "$CGAL_ARCH_PATH" ) then
+# If BOOST_ARCH_PATH, CGAL_ARCH_PATH do not end with '-system' or '-none',
-    _foamAddLib $CGAL_ARCH_PATH/lib
+# they are either located within ThirdParty, or a central installation
-endif
+# outside of ThirdParty and must be added to the lib-path.
 
-if ( -d "$BOOST_ARCH_PATH" ) then
+set ending="${BOOST_ARCH_PATH:t}"
+if ( "$ending" != "boost-none" && "$ending" != "boost-system" ) then
     _foamAddLib $BOOST_ARCH_PATH/lib
 endif
 
-unset boost_version cgal_version
+set ending="${CGAL_ARCH_PATH:t}"
+if ( "$ending" != "cgal-none" && "$ending" != "cgal-system" ) then
+    _foamAddLib $CGAL_ARCH_PATH/lib
+endif
+
+unset boost_version cgal_version ending
 
 #------------------------------------------------------------------------------

etc/config.csh/compiler

@@ -0,0 +1,90 @@
+#----------------------------------*-sh-*--------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2016 OpenFOAM Foundation
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM.
+#
+#     OpenFOAM is free software: you can redistribute it and/or modify it
+#     under the terms of the GNU General Public License as published by
+#     the Free Software Foundation, either version 3 of the License, or
+#     (at your option) any later version.
+#
+#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#     for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#
+# File
+#     etc/config.csh/compiler
+#
+# Description
+#     Startup file for custom compiler versions for OpenFOAM
+#     Sourced from OpenFOAM-<VERSION>/etc/config.csh/settings
+#
+#------------------------------------------------------------------------------
+
+switch ("$WM_COMPILER_TYPE")
+case OpenFOAM:
+case ThirdParty:
+    # Default versions of GMP, MPFR and MPC, override as necessary
+    set gmp_version=gmp-system
+    set mpfr_version=mpfr-system
+    set mpc_version=mpc-system
+
+    switch ("$WM_COMPILER")
+    case Gcc:
+    case Gcc48:
+        set gcc_version=gcc-4.8.5
+        breaksw
+    case Gcc45:
+        set gcc_version=gcc-4.5.4
+        breaksw
+    case Gcc46:
+        set gcc_version=gcc-4.6.4
+        breaksw
+    case Gcc47:
+        set gcc_version=gcc-4.7.4
+        breaksw
+    case Gcc49:
+        set gcc_version=gcc-4.9.3
+        breaksw
+    case Gcc51:
+        set gcc_version=gcc-5.1.0
+        breaksw
+    case Gcc52:
+        set gcc_version=gcc-5.2.0
+        breaksw
+    case Gcc53:
+        set gcc_version=gcc-5.3.0
+        breaksw
+    case Gcc54:
+        set gcc_version=gcc-5.4.0
+        breaksw
+    case Gcc61:
+        set gcc_version=gcc-6.1.0
+        breaksw
+    case Clang:
+        # Using clang - not gcc
+        setenv WM_CC 'clang'
+        setenv WM_CXX 'clang++'
+        set clang_version=llvm-3.7.0
+        # set clang_version=llvm-3.8.0
+        breaksw
+    default:
+        echo
+        echo "Warning in $WM_PROJECT_DIR/etc/config.csh/compiler:"
+        echo "    Unknown OpenFOAM compiler type '$WM_COMPILER'"
+        echo "    Please check your settings"
+        echo
+        breaksw
+    endsw
+endsw
+
+#------------------------------------------------------------------------------

etc/config.csh/mpi

@@ -61,11 +61,7 @@ case OPENMPI:
     setenv OPAL_PREFIX $MPI_ARCH_PATH
 
     _foamAddPath    $MPI_ARCH_PATH/bin
-
-    # 64-bit on OpenSuSE 12.1 uses lib64 others use lib
     _foamAddLib     $MPI_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH
-    _foamAddLib     $MPI_ARCH_PATH/lib
-
     _foamAddMan     $MPI_ARCH_PATH/share/man
     breaksw
 
@@ -261,7 +257,6 @@ if ( "$FOAM_MPI" != dummy ) then
 endif
 
 
-
 # Set the minimum MPI buffer size (used by all platforms except SGI MPI)
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 if ( ! $?minBufferSize ) set minBufferSize=20000000
@@ -274,4 +269,8 @@ else
     setenv MPI_BUFFER_SIZE $minBufferSize
 endif
 
+# Cleanup environment:
+# ~~~~~~~~~~~~~~~~~~~~
+unset minBufferSize
+
 #------------------------------------------------------------------------------

etc/config.csh/paraview

@@ -25,7 +25,7 @@
 #     config.csh/paraview
 #
 # Description
-#     Setup file for paraview-[3-5].x
+#     Setup file for paraview
 #     Sourced from OpenFOAM-<VERSION>/etc/cshrc or from foamPV alias
 #
 # Note
@@ -49,12 +49,8 @@ foreach cmake ( cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 c
 end
 
 #- ParaView version, automatically determine major version:
-#setenv ParaView_VERSION 3.12.0
-#setenv ParaView_VERSION 4.0.1
-#setenv ParaView_VERSION 4.1.0
-#setenv ParaView_VERSION 4.3.1
 #setenv ParaView_VERSION 4.4.0
-setenv ParaView_VERSION 5.0.0
+setenv ParaView_VERSION 5.0.1
 setenv ParaView_MAJOR detect
 
 

etc/config.csh/settings

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -202,7 +202,7 @@ _foamAddLib  ${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}:${FOAM_LIBBIN}:${FOAM_EXT_L
 # Compiler settings
 # ~~~~~~~~~~~~~~~~~
 unset gcc_version gmp_version mpfr_version mpc_version
-unsetenv MPFR_ARCH_PATH GMP_ARCH_PATH
+unsetenv GMP_ARCH_PATH MPFR_ARCH_PATH
 
 
 # Location of compiler installation
@@ -213,64 +213,25 @@ if ( ! $?WM_COMPILER_TYPE ) then
     echo "    WM_COMPILER_TYPE not set, using '$WM_COMPILER_TYPE'"
 endif
 
+# Load configured compiler versions, regardless of the compiler type
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/compiler`
+
 switch ("$WM_COMPILER_TYPE")
+case system:
+    # Use system compiler
+    breaksw
+
 case OpenFOAM:
 case ThirdParty:
-    # Default versions of GMP, MPFR and MPC, overide as necessary
-    set gmp_version=gmp-5.1.2
-    set mpfr_version=mpfr-3.1.2
-    set mpc_version=mpc-1.0.1
-    switch ("$WM_COMPILER")
-    case Gcc:
-    case Gcc48:
-        set gcc_version=gcc-4.8.5
-        breaksw
-    case Gcc45:
-        set gcc_version=gcc-4.5.4
-        breaksw
-    case Gcc46:
-        set gcc_version=gcc-4.6.4
-        breaksw
-    case Gcc47:
-        set gcc_version=gcc-4.7.4
-        breaksw
-    case Gcc49:
-        set gcc_version=gcc-4.9.3
-        breaksw
-    case Gcc51:
-        set gcc_version=gcc-5.1.0
-        breaksw
-    case Gcc52:
-        set gcc_version=gcc-5.2.0
-        breaksw
-    case Gcc53:
-        set gcc_version=gcc-5.3.0
-        breaksw
-    case Clang:
-        # Using clang - not gcc
-        setenv WM_CC 'clang'
-        setenv WM_CXX 'clang++'
-        set clang_version=llvm-3.7.0
-        breaksw
-    default:
-        echo
-        echo "Warning in $WM_PROJECT_DIR/etc/config.csh/settings:"
-        echo "    Unknown OpenFOAM compiler type '$WM_COMPILER'"
-        echo "    Please check your settings"
-        echo
-        breaksw
-    endsw
-
-    # Optional configuration tweaks:
-    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/compiler`
-
     if ( $?gcc_version ) then
+        if ( ! $?gmp_version  ) set gmp_version=gmp-system
+        if ( ! $?mpfr_version ) set mpfr_version=mpfr-system
+        if ( ! $?mpc_version  ) set mpc_version=mpc-system
         set gccDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$gcc_version
         set gmpDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$gmp_version
         set mpfrDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpfr_version
-        if ( $?mpc_version ) then
+        set mpcDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpc_version
-            set mpcDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpc_version
-        endif
 
         # Check that the compiler directory can be found
         if ( ! -d "$gccDir" ) then
@@ -286,21 +247,28 @@ case ThirdParty:
         _foamAddMan     $gccDir/man
         _foamAddPath    $gccDir/bin
 
-        # Add compiler libraries to run-time environment
+        # Add ThirdParty compiler libraries to run-time environment
         _foamAddLib     $gccDir/lib$WM_COMPILER_LIB_ARCH
 
-        # Add gmp/mpfr libraries to run-time environment
+        # Add ThirdParty gmp/mpfr/mpc libraries to run-time environment
-        _foamAddLib     $gmpDir/lib
+        if ( "${gmpDir:t}" != "gmp-system" ) then
-        _foamAddLib     $mpfrDir/lib
+            _foamAddLib $gmpDir/lib$WM_COMPILER_LIB_ARCH
-
+        endif
-        # Add mpc libraries (not need for older gcc) to run-time environment
+        if ( "${mpfrDir:t}" != "mpfr-system" ) then
-        if ( $?mpc_version ) then
+            _foamAddLib $mpfrDir/lib$WM_COMPILER_LIB_ARCH
-            _foamAddLib     $mpcDir/lib
+        endif
+        if ( "${mpcDir:t}" != "mpc-system" ) then
+            _foamAddLib $mpcDir/lib$WM_COMPILER_LIB_ARCH
         endif
 
         # Used by boost/CGAL:
-        setenv MPFR_ARCH_PATH $mpfrDir
         setenv GMP_ARCH_PATH $gmpDir
+        setenv MPFR_ARCH_PATH $mpfrDir
+
+        if ($?FOAM_VERBOSE && $?prompt) then
+            echo "Using ThirdParty compiler"
+            echo "    ${gccDir:t} (${gmpDir:t} ${mpfrDir:t} ${mpcDir:t})"
+        endif
     endif
     unset gcc_version gccDir
     unset gmp_version gmpDir  mpfr_version mpfrDir  mpc_version mpcDir
@@ -321,13 +289,13 @@ case ThirdParty:
 
         _foamAddMan     $clangDir/man
         _foamAddPath    $clangDir/bin
+
+        if ($?FOAM_VERBOSE && $?prompt) then
+            echo "Using ThirdParty compiler"
+            echo "    ${clangDir:t}"
+        endif
     endif
     unset clang_version clangDir
-
-    breaksw
-
-case system:
-    # Use system compiler
     breaksw
 
 default:
@@ -340,7 +308,6 @@ endsw
 # Cleanup environment:
 # ~~~~~~~~~~~~~~~~~~~~
 #- keep _foamAddPath _foamAddLib _foamAddMan
-unset minBufferSize
 unsetenv WM_COMPILER_TYPE
 
 #------------------------------------------------------------------------------

etc/config.csh/unset

@@ -166,6 +166,7 @@ unalias wm32
 unalias wmSP
 unalias wmDP
 
+unalias wmREFRESH
 unalias wmUNSET
 
 unalias wmSchedON

etc/config.sh/CGAL

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2014-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -28,42 +28,60 @@
 #     Setup file for CGAL (& boost) include/libraries.
 #     Sourced from OpenFOAM-<VERSION>/etc/bashrc
 #
-#     If using system-wide installations for either one, use the following
+#     If using system-wide installations, use the following settings:
-#     version settings:
 #
 #         boost_version=boost-system
 #         cgal_version=cgal-system
+#
+#     If the system boost/cgal is unusable (eg, too old) and you don't
+#     have or want a ThirdParty installation:
+#
+#         boost_version=boost-none
+#         cgal_version=cgal-none
+#
+#     If using a central installation, but not located under ThirdParty:
+#         - specify boost-system / cgal-system
+#         - provide full paths for BOOST_ARCH_PATH / CGAL_ARCH_PATH
+#
+# Note
+#     When _foamAddLib is unset (eg, called from makeCGAL):
+#         - boost_version / cgal_version variables are retained.
+#         - the LD_LIBRARY_PATH is not adjusted.
 #------------------------------------------------------------------------------
 
 boost_version=boost-system
-cgal_version=CGAL-4.7
+cgal_version=CGAL-4.8
 
-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ]
+export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version
+export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version
+
+#------------------------------------------------------------------------------
+if [ "$FOAM_VERBOSE" -a "$PS1" ]
+then
+    echo "Using boost ($boost_version)  ->  $BOOST_ARCH_PATH" 1>&2
+    echo "Using CGAL ($cgal_version)  ->  $CGAL_ARCH_PATH" 1>&2
+fi
+
+if type _foamAddLib > /dev/null 2>&1    # normal sourcing
 then
 
-    common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER
+    # If BOOST_ARCH_PATH, CGAL_ARCH_PATH do not end with '-system' or '-none',
+    # they are either located within ThirdParty, or a central installation
+    # outside of ThirdParty and must be added to the lib-path.
 
-    export BOOST_ARCH_PATH=$common_path/$boost_version
+    ending="${BOOST_ARCH_PATH##*-}"
-    export CGAL_ARCH_PATH=$common_path/$cgal_version
+    if [ "$ending" != none -a "$ending" != system ]
-
-    if [ "$FOAM_VERBOSE" -a "$PS1" ]
-    then
-        echo "Using CGAL and boost" 1>&2
-        echo "    $cgal_version at $CGAL_ARCH_PATH" 1>&2
-        echo "    $boost_version at $BOOST_ARCH_PATH" 1>&2
-    fi
-
-    if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ]
-    then
-        _foamAddLib $CGAL_ARCH_PATH/lib
-    fi
-
-    if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ]
     then
         _foamAddLib $BOOST_ARCH_PATH/lib
     fi
 
-    unset boost_version cgal_version common_path
+    ending="${CGAL_ARCH_PATH##*-}"
+    if [ "$ending" != none -a "$ending" != system ]
+    then
+        _foamAddLib $CGAL_ARCH_PATH/lib
+    fi
+
+    unset boost_version cgal_version ending
 
 fi
 

etc/config.sh/aliases

@@ -55,7 +55,7 @@ alias wmSchedOFF='unset WM_SCHEDULER'
 unset foamPV
 foamPV()
 {
-    . $WM_PROJECT_DIR/etc/config.sh/paraview ParaView_VERSION=$1
+    . $WM_PROJECT_DIR/etc/config.sh/paraview ParaView_VERSION=${1:-none}
     echo "paraview-$ParaView_VERSION  (major: $ParaView_MAJOR)" 1>&2
 }
 

etc/config.sh/compiler

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -32,11 +32,10 @@
 
 case "$WM_COMPILER_TYPE" in
 OpenFOAM | ThirdParty)
-
     # Default versions of GMP, MPFR and MPC, override as necessary
-    gmp_version=gmp-5.1.2
+    gmp_version=gmp-system
-    mpfr_version=mpfr-3.1.2
+    mpfr_version=mpfr-system
-    mpc_version=mpc-1.0.1
+    mpc_version=mpc-system
 
     case "$WM_COMPILER" in
     Gcc | Gcc48)
@@ -63,11 +62,18 @@ OpenFOAM | ThirdParty)
     Gcc53)
         gcc_version=gcc-5.3.0
         ;;
+    Gcc54)
+        gcc_version=gcc-5.4.0
+        ;;
+    Gcc61)
+        gcc_version=gcc-6.1.0
+        ;;
     Clang)
         # Using clang - not gcc
         export WM_CC='clang'
         export WM_CXX='clang++'
         clang_version=llvm-3.7.0
+        # clang_version=llvm-3.8.0
         ;;
     *)
         echo 1>&2
@@ -80,3 +86,5 @@ OpenFOAM | ThirdParty)
     ;;
 
 esac
+
+#------------------------------------------------------------------------------

etc/config.sh/libccmio

@@ -0,0 +1,42 @@
+#----------------------------------*-sh-*--------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM.
+#
+#     OpenFOAM is free software: you can redistribute it and/or modify it
+#     under the terms of the GNU General Public License as published by
+#     the Free Software Foundation, either version 3 of the License, or
+#     (at your option) any later version.
+#
+#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#     for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#
+# File
+#     etc/config.sh/libccmio
+#
+# Description
+#     Setup file for libccmio include/libraries.
+#     Sourced during wmake process only.
+#
+#     Dynamic libraries are found under the FOAM_EXT_LIBBIN path.
+#     Static libraries  are found under the CCMIO_ARCH_PATH/lib path.
+#
+# Note
+#     A csh version is not needed, since the values here are only sourced
+#     during the wmake process
+#------------------------------------------------------------------------------
+
+ccmio_version=libccmio-2.6.1
+export CCMIO_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$ccmio_version
+
+#------------------------------------------------------------------------------

etc/config.sh/mpi

@@ -58,11 +58,7 @@ OPENMPI)
     export OPAL_PREFIX=$MPI_ARCH_PATH
 
     _foamAddPath    $MPI_ARCH_PATH/bin
-
-    # 64-bit on OpenSuSE 12.1 uses lib64 others use lib
     _foamAddLib     $MPI_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH
-    _foamAddLib     $MPI_ARCH_PATH/lib
-
     _foamAddMan     $MPI_ARCH_PATH/share/man
     ;;
 
@@ -256,7 +252,6 @@ then
 fi
 
 
-
 # Set the minimum MPI buffer size (used by all platforms except SGI MPI)
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 : ${minBufferSize:=20000000}

etc/config.sh/paraview

@@ -25,7 +25,7 @@
 #     etc/config.sh/paraview
 #
 # Description
-#     Setup file for paraview-[3-5].x
+#     Setup file for paraview
 #     Sourced from OpenFOAM-<VERSION>/etc/bashrc or from foamPV alias
 #
 # Note
@@ -57,12 +57,8 @@ done
 
 
 #- ParaView version, automatically determine major version
-#export ParaView_VERSION=3.12.0
-#export ParaView_VERSION=4.0.1
-#export ParaView_VERSION=4.1.0
-#export ParaView_VERSION=4.3.1
 #export ParaView_VERSION=4.4.0
-export ParaView_VERSION=5.0.0
+export ParaView_VERSION=5.0.1
 export ParaView_MAJOR=detect
 
 

etc/config.sh/settings

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -198,7 +198,7 @@ _foamAddLib  $FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN:$FOAM_LIBBIN:$FOAM_EXT_LIBBIN:$
 # Compiler settings
 # ~~~~~~~~~~~~~~~~~
 unset gcc_version gmp_version mpfr_version mpc_version
-unset MPFR_ARCH_PATH GMP_ARCH_PATH
+unset GMP_ARCH_PATH MPFR_ARCH_PATH
 
 # Location of compiler installation
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -214,14 +214,16 @@ fi
 _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/compiler`
 
 case "$WM_COMPILER_TYPE" in
+system)
+    # Use system compiler
+    ;;
 OpenFOAM | ThirdParty)
-
     if [ -n "$gcc_version" ]
     then
         gccDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$gcc_version
-        gmpDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$gmp_version
+        gmpDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/${gmp_version:-gmp-system}
-        mpfrDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpfr_version
+        mpfrDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/${mpfr_version:-mpfr-system}
-        mpcDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpc_version
+        mpcDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/${mpc_version:-mpc-system}
 
         # Check that the compiler directory can be found
         [ -d "$gccDir" ] || {
@@ -237,22 +239,32 @@ OpenFOAM | ThirdParty)
         _foamAddMan     $gccDir/man
         _foamAddPath    $gccDir/bin
 
-        # Add compiler libraries to run-time environment
+        # Add ThirdParty compiler libraries to run-time environment
         _foamAddLib     $gccDir/lib$WM_COMPILER_LIB_ARCH
 
-        # Add gmp/mpfr libraries to run-time environment
+        # Add ThirdParty gmp/mpfr/mpc libraries to run-time environment
-        _foamAddLib     $gmpDir/lib
+        if [ "${gmpDir##*-}" != system ]
-        _foamAddLib     $mpfrDir/lib
-
-        # Add mpc libraries (not need for older gcc) to run-time environment
-        if [ -n "$mpc_version" ]
         then
-            _foamAddLib     $mpcDir/lib
+            _foamAddLib $gmpDir/lib$WM_COMPILER_LIB_ARCH
+        fi
+        if [ "${mpfrDir##*-}" != system ]
+        then
+            _foamAddLib $mpfrDir/lib$WM_COMPILER_LIB_ARCH
+        fi
+        if [ "${mpcDir##*-}" != system ]
+        then
+            _foamAddLib $mpcDir/lib$WM_COMPILER_LIB_ARCH
         fi
 
         # Used by boost/CGAL:
-        export MPFR_ARCH_PATH=$mpfrDir
         export GMP_ARCH_PATH=$gmpDir
+        export MPFR_ARCH_PATH=$mpfrDir
+
+        if [ "$FOAM_VERBOSE" -a "$PS1" ]
+        then
+            echo "Using ThirdParty compiler"
+            echo "    ${gccDir##*/}  (${gmpDir##*/}  $${mpfrDir##*/}  ${mpcDir##*/})"
+        fi
     fi
     unset gcc_version gccDir
     unset gmp_version gmpDir  mpfr_version mpfrDir  mpc_version mpcDir
@@ -274,12 +286,15 @@ OpenFOAM | ThirdParty)
 
         _foamAddMan     $clangDir/share/man
         _foamAddPath    $clangDir/bin
+
+        if [ "$FOAM_VERBOSE" -a "$PS1" ]
+        then
+            echo "Using ThirdParty compiler"
+            echo "    ${clangDir##*/}"
+        fi
     fi
     unset clang_version clangDir
     ;;
-system)
-    # Use system compiler
-    ;;
 *)
     echo "Warn: WM_COMPILER_TYPE='$WM_COMPILER_TYPE' is unsupported" 1>&2
     echo "   treating as 'system' instead" 1>&2

etc/config.sh/unset

@@ -145,6 +145,7 @@ unalias wm32
 unalias wmSP
 unalias wmDP
 
+unalias wmREFRESH
 unalias wmUNSET
 
 unalias wmSchedON

etc/cshrc

@@ -61,7 +61,7 @@ if ( ! $?FOAM_INST_DIR ) setenv FOAM_INST_DIR $foamInstall
 setenv WM_COMPILER_TYPE system
 
 #- Compiler:
-#    WM_COMPILER = Gcc | Gcc45 | Gcc46 | Gcc47 | Gcc48 | Gcc49 | Clang | Icc
+#    WM_COMPILER = Gcc | Gcc4[5-9] | Gcc5[1-4] | Gcc61 | Clang | Icc
 setenv WM_COMPILER Gcc
 setenv WM_COMPILER_ARCH # defined but empty
 unsetenv WM_COMPILER_LIB_ARCH

src/OpenFOAM/global/profiling/profiling.C

@@ -90,8 +90,6 @@ bool Foam::profiling::writeNow()
 {
     if (pool_)
     {
-        Info<<"profiling::writeNow() at time = "
-            << pool_->owner().timeName() << endl;
         return pool_->write();
     }
     else

src/mesh/snappyHexMesh/meshRefinement/meshRefinement.H

@@ -678,12 +678,14 @@ private:
             ) const;
 
             //- Finds zone per cell. Uses topological walk with all faces
-            //  marked in namedSurfaceIndex regarded as blocked.
+            //  marked in unnamedSurfaceRegion (intersections with unnamed
+            //  surfaces) and namedSurfaceIndex (intersections with named
+            //  surfaces) regarded as blocked.
             void findCellZoneTopo
             (
                 const label backgroundZoneID,
                 const pointField& locationsInMesh,
-                const labelList& allSurfaceIndex,
+                const labelList& unnamedSurfaceRegion,
                 const labelList& namedSurfaceIndex,
                 const labelList& surfaceToCellZone,
                 labelList& cellToZone

src/mesh/snappyHexMesh/meshRefinement/meshRefinementBaffles.C

@@ -1833,7 +1833,15 @@ bool Foam::meshRefinement::calcRegionToZone
 
         if (regionToCellZone[ownRegion] == -2)
         {
-            if (regionToCellZone[neiRegion] == surfZoneI)
+            if (surfZoneI == -1)
+            {
+                // Special: face is -on faceZone  -not real boundary
+                //          -not on cellZone
+                // so make regions same on either side
+                regionToCellZone[ownRegion] = regionToCellZone[neiRegion];
+                changed = true;
+            }
+            else if (regionToCellZone[neiRegion] == surfZoneI)
             {
                 // Face between unset and my region. Put unset
                 // region into keepRegion
@@ -1854,7 +1862,15 @@ bool Foam::meshRefinement::calcRegionToZone
         }
         else if (regionToCellZone[neiRegion] == -2)
         {
-            if (regionToCellZone[ownRegion] == surfZoneI)
+            if (surfZoneI == -1)
+            {
+                // Special: face is -on faceZone  -not real boundary
+                //          -not on cellZone
+                // so make regions same on either side
+                regionToCellZone[neiRegion] = regionToCellZone[ownRegion];
+                changed = true;
+            }
+            else if (regionToCellZone[ownRegion] == surfZoneI)
             {
                 // Face between unset and my region. Put unset
                 // region into keepRegion
@@ -1881,7 +1897,7 @@ void Foam::meshRefinement::findCellZoneTopo
 (
     const label backgroundZoneID,
     const pointField& locationsInMesh,
-    const labelList& allSurfaceIndex,
+    const labelList& unnamedSurfaceRegion,
     const labelList& namedSurfaceIndex,
     const labelList& surfaceToCellZone,
     labelList& cellToZone
@@ -1914,9 +1930,9 @@ void Foam::meshRefinement::findCellZoneTopo
     // Analyse regions. Reuse regionsplit
     boolList blockedFace(mesh_.nFaces());
 
-    forAll(allSurfaceIndex, faceI)
+    forAll(unnamedSurfaceRegion, faceI)
     {
-        if (allSurfaceIndex[faceI] == -1)
+        if (unnamedSurfaceRegion[faceI] == -1 && namedSurfaceIndex[faceI] == -1)
         {
             blockedFace[faceI] = false;
         }
@@ -2018,7 +2034,7 @@ void Foam::meshRefinement::findCellZoneTopo
             label surfI = namedSurfaceIndex[faceI];
 
             // Connected even if no cellZone defined for surface
-            if (surfI != -1)
+            if (unnamedSurfaceRegion[faceI] == -1 && surfI != -1)
             {
                 // Calculate region to zone from cellRegions on either side
                 // of internal face.
@@ -2058,7 +2074,7 @@ void Foam::meshRefinement::findCellZoneTopo
                     label surfI = namedSurfaceIndex[faceI];
 
                     // Connected even if no cellZone defined for surface
-                    if (surfI != -1)
+                    if (unnamedSurfaceRegion[faceI] == -1 && surfI != -1)
                     {
                         bool changedCell = calcRegionToZone
                         (
@@ -2353,6 +2369,7 @@ void Foam::meshRefinement::zonify
 
 
     labelList namedSurfaces(surfaceZonesInfo::getNamedSurfaces(surfZones));
+    labelList unnamedSurfaces(surfaceZonesInfo::getUnnamedSurfaces(surfZones));
 
     // Get map from surface to cellZone (or -1)
     labelList surfaceToCellZone;
@@ -2379,15 +2396,17 @@ void Foam::meshRefinement::zonify
     // 1. Test all (unnamed & named) surfaces
 
     labelList globalRegion1;
-    labelList globalRegion2;
+    {
-    getIntersections
+        labelList globalRegion2;
-    (
+        getIntersections
-        identity(surfaces_.surfaces().size()),  // surfacesToTest,
+        (
-        neiCc,
+            identity(surfaces_.surfaces().size()),  // surfacesToTest,
-        intersectedFaces(),     // testFaces
+            neiCc,
-        globalRegion1,
+            intersectedFaces(),     // testFaces
-        globalRegion2
+            globalRegion1,
-    );
+            globalRegion2
+        );
+    }
 
     if (namedSurfaces.size())
     {
@@ -2555,12 +2574,25 @@ void Foam::meshRefinement::zonify
         Info<< "Walking from known cellZones; crossing a faceZone "
             << "face changes cellZone" << nl << endl;
 
+        labelList unnamedRegion1;
+        {
+            labelList unnamedRegion2;
+            getIntersections
+            (
+                unnamedSurfaces,
+                neiCc,
+                intersectedFaces(),
+                unnamedRegion1,
+                unnamedRegion2
+            );
+        }
+
         findCellZoneTopo
         (
             backgroundZoneID,
             pointField(0),
-            globalRegion1,      // To split up cells
+            unnamedRegion1,      // Intersections with unnamed surfaces
-            namedSurfaceIndex,  // Step across named surfaces to propagate
+            namedSurfaceIndex,   // Intersections with named surfaces
             surfaceToCellZone,
             cellToZone
         );

src/postProcessing/functionObjects/graphics/runTimePostProcessing/Allwclean

@@ -4,9 +4,8 @@ cd ${0%/*} || exit 1    # Run from this directory
 # Source the wmake functions
 . $WM_DIR/scripts/wmakeFunctions
 
-(
+# Where are the generated files stored?
-    # Where are the generated files stored?
+findObjectDir $PWD
-    findObjectDir dummy.C
+rm -rf "$objectsDir" > /dev/null 2>&1
-    depDir="$objectsDir"
+
-    rm -rf "$depDir" > /dev/null 2>&1
+#------------------------------------------------------------------------------
-)

src/postProcessing/functionObjects/graphics/runTimePostProcessing/Allwmake

@@ -4,25 +4,45 @@ cd ${0%/*} || exit 1    # Run from this directory
 # Source the wmake functions
 . $WM_DIR/scripts/wmakeFunctions
 
-# Store current directory
+# The source directory
 sourceDir=$PWD
 
 # Where are any generated files stored?
-findObjectDir dummy.C
+findObjectDir $sourceDir
 depDir="$objectsDir"
 
-if [ -d "$VTK_DIR" -o  -d "$ParaView_DIR" ]
+echo
+echo "======================================================================"
+echo "${PWD##*/} : $PWD"
+echo
+
+if [ -d "$VTK_DIR" -o -d "$ParaView_DIR" ]
 then
     # ensure CMake gets the correct C++ compiler
     [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
     [ -n "$WM_CC" ] && export CC="$WM_CC"
 
-    (mkdir -p $depDir && cd $depDir && cmake $sourceDir && make)
+    if type cmake > /dev/null 2>&1
+    then
+    (
+        mkdir -p $depDir \
+        && cd $depDir \
+        && cmake $sourceDir \
+        && make
+    ) || {
+        echo
+        echo "WARNING: incomplete build of VTK-based post-processing"
+    }
+    else
+        echo "WARNING: skipped - needs cmake"
+    fi
 else
-    echo "ERROR: Build of $PWD requires a valid VTK installation which"
+    echo "WARNING: skipped - needs a VTK or a ParaView installation"
-    echo "       can be supplied either by ParaView by VTK. In case of"
+    echo "    - For ParaView  : export the 'ParaView_DIR' variable"
-    echo "       - ParaView : export the ParaView_DIR environment variable"
+    echo "    - For VTK       : export the 'VTK_DIR'      variable"
-    echo "       - VTK      : export the VTK_DIR variable"
 fi
 
+echo "======================================================================"
+echo
+
 # ----------------------------------------------------------------- end-of-file

src/renumber/Allwmake

@@ -5,11 +5,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 targetType=libso
 . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
 
-# Get CGAL and scotch versions
-. $WM_PROJECT_DIR/etc/config.sh/functions
-_foamEval SOURCE_CGAL_VERSIONS_ONLY=yes \
-          $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/CGAL)
-
 ## Get ZOLTAN_ARCH_PATH
 #if settings=`$WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan`
 #then
@@ -21,22 +16,21 @@ _foamEval SOURCE_CGAL_VERSIONS_ONLY=yes \
 #    echo
 #fi
 
-
 set -x
 
 wmake $targetType renumberMethods
 
-if [ -n "$BOOST_ARCH_PATH" -o "$boost_version" = "boost-system" ]
+if [ -d "$BOOST_ARCH_PATH/include/boost" ] || \
+   [ "${BOOST_ARCH_PATH##*-}" = system -a -d /usr/include/boost ]
 then
     wmake $targetType SloanRenumber
 else
     echo
-    echo "Skipping SloanRenumber"
+    echo "Skipping SloanRenumber (no boost)"
     echo
 fi
 
-
+if [ -d "$ZOLTAN_ARCH_PATH" ]
-if [ -n "$ZOLTAN_ARCH_PATH" ]
 then
     wmake $targetType zoltanRenumber
 else

tutorials/lagrangian/reactingParcelFoam/verticalChannelLTS/0.org/U

@@ -33,12 +33,14 @@ boundaryField
     {
         type            flowRateInletVelocity;
         massFlowRate    constant 0.00379;
+        rhoInlet        1.22;
         value           uniform (0 14.68 0);
     }
     inletSides
     {
         type            flowRateInletVelocity;
         massFlowRate    constant 0.00832;
+        rhoInlet        1.22;
         value           uniform (0 17.79 0);
     }
     outlet

tutorials/lagrangian/reactingParcelFoam/verticalChannelLTS/system/fvSolution

@@ -59,6 +59,12 @@ solvers
         relTol          0.1;
         maxIter         20;
     }
+
+    Phi
+    {
+        $p;
+    }
+
 }
 
 PIMPLE
@@ -76,5 +82,9 @@ PIMPLE
     maxDeltaT       1;
 }
 
+potentialFlow
+{
+    nNonOrthogonalCorrectors 3;
+}
 
 // ************************************************************************* //

wmake/wclean

@@ -157,8 +157,15 @@ then
         # For all the sub-directories containing a 'Make' directory
         for dir in `find . \( -type d -a -name Make \)`
         do
+            dir=${dir%/Make}  # Parent directory - trim /Make from the end
             echo $dir
-            $0 ${dir%/Make}   # Parent directory - trim /Make from the end
+            # If Allwclean exists execute otherwise wclean
+            if [ -e "$dir/Allwclean" ]
+            then
+                $dir/Allwclean
+            else
+                $0 $dir
+            fi
         done
     fi
 fi