Merge branch 'master' of /home/noisy2/OpenFOAM/OpenFOAM-dev

.gitignore

@@ -38,13 +38,9 @@ doc/[Dd]oxygen/latex
 doc/[Dd]oxygen/man
 
 # source packages - anywhere
+*.tar.bz2
 *.tar.gz
 *.tgz
 
-# specific locations
-applications/utilities/preProcessing/FoamX/Java/Make/classes
-
-# other 3rd party sources
-src/other
 
 # end-of-file

Allwmake

@@ -1,9 +1,10 @@
 #!/bin/sh
 set -x
 
-(cd $WM_PROJECT_INST_DIR/ThirdParty && ./Allwmake)
+# wmake is required for subsequent targets
+(cd wmake/src && make)
 
-(cd wmake && ./makeWmake)
+(cd $WM_PROJECT_INST_DIR/ThirdParty && ./Allwmake)
 
 (cd src && ./Allwmake)
 

README

@@ -23,20 +23,19 @@
   7.  Documentation
   8.  Help
   9.  Reporting Bugs
-  A.  Network settings
+  A.  Running OpenFOAM in 32-bit mode
-  B.  Running OpenFOAM in 32-bit mode
 
 
 2. System requirements
 ~~~~~~~~~~~~~~~~~~~~~~
-  OpenFOAM generally requires that the host machine operates a basic level
+  OpenFOAM is developed and tested on Linux, but should work with other
-  of networking.  To check your system setup, execute the foamSystemCheck
+  Unix style system.  To check your system setup, execute the foamSystemCheck
   script in the bin directory of the OpenFOAM installation. If no problems
-  are reported, proceed to "3. Installation"; otherwise see the
+  are reported, proceed to "3. Installation"; otherwise contact your
-  appendix "A. Network settings" and/or contact your system administrator.
+  system administrator.
 
   If the user wishes to run OpenFOAM in 32/64-bit mode they should consult
-  the appendix "B. Running OpenFOAM in 32-bit mode".
+  the appendix "A. Running OpenFOAM in 32-bit mode".
 
 
 3. Installation
@@ -48,14 +47,16 @@
   The environment variable settings are contained in files in an etc/
   directory in the OpenFOAM release. e.g. in
 
-      $HOME/OpenFOAM/OpenFOAM-dev/etc/
+      $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/
+
+      where <VERSION> corresponds to the version 1.4, 1.5, ...
 
   a)
     EITHER, if running bash or ksh (if in doubt type 'echo $SHELL'),
     source the etc/bashrc file by adding the following line to the end
     of your $HOME/.bashrc file:
 
-        . $HOME/OpenFOAM/OpenFOAM-dev/etc/bashrc
+        . $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/bashrc
 
     Then update the environment variables by sourcing the $HOME/.bashrc file
     by typing in the terminal:
@@ -66,7 +67,7 @@
     OR, if running tcsh or csh, source the etc/cshrc file by adding the
     following line to the end of your $HOME/.cshrc file:
 
-        source $HOME/OpenFOAM/OpenFOAM-dev/etc/cshrc
+        source $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/cshrc
 
     Then update the environment variables by sourcing the $HOME/.cshrc file
     by typing in the terminal:
@@ -85,39 +86,42 @@
     the appropriate resource file. Here is a bash/ksh/sh example:
 
         export FOAM_INST_DIR=/data/app/OpenFOAM
-        foamDotFile=$FOAM_INST_DIR/OpenFOAM-dev/etc/bashrc
+        foamDotFile=$FOAM_INST_DIR/OpenFOAM-<VERSION>/etc/bashrc
         [ -f $foamDotFile ] && . $foamDotFile
 
     and a csh example:
 
         setenv FOAM_INST_DIR /data/app/OpenFOAM
-        foamDotFile=$FOAM_INST_DIR/OpenFOAM-dev/etc/bashrc
+        foamDotFile=$FOAM_INST_DIR/OpenFOAM-<VERSION>/etc/bashrc
         if ( -f $foamDotFile ) source $foamDotFile
 
 
-    The value set in '$FOAM_INST_DIR' will be used to locate the rest
+    The value set in '$FOAM_INST_DIR' will be used to locate the remaining
-    of the OpenFOAM installation.
+    parts of the OpenFOAM installation.
-
 
 
 4. Building from Sources (Optional)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  If you cannot find an appropriate binary pack for your platform you can
+
+  If you cannot find an appropriate binary pack for your platform, you can
   build the complete OpenFOAM from the source-pack.  First you will need to
-  compile or obtain a recent version of gcc (we recommend gcc-4.2.?) for
+  compile or obtain a recent version of gcc (we recomend gcc-4.2.?) for
-  your platform which may be obtained from http://gcc.gnu.org/.  Install the
+  your platform, which may be obtained from http://gcc.gnu.org/.
-  compiler in $WM_PROJECT_INST_DIR/$WM_ARCH/gcc-4.2.? and change the gcc
+
-  version number in $WM_PROJECT_DIR/.bashrc and $WM_PROJECT_DIR/.cshrc as
+  Install the compiler in
-  appropriate and update the environment variables as in section 3.
+  $WM_PROJECT_INST_DIR/ThirdParty/gcc-<GCC_VERSION>/platforms/$WM_ARCH$WM_COMPILER_ARCH/
+  and change the gcc version number in $WM_PROJECT_DIR/etc/settings.sh and
+  $WM_PROJECT_DIR/etc/settings.csh appropriately and finally update the
+  environment variables as in section 3.
 
   Now go to the top-level source directory $WM_PROJECT_DIR and type
   ./Allwmake, which is the name of the top-level build script for building
-  the whole of OpenFOAM.  In principle this will build everything but
+  the whole of OpenFOAM.  In principle this will build everything, but
   sometimes problems occur with the build order and it is necessary to
   update the environment variables and re-execute Allwmake.  If you
   experience difficulties with building the source-pack or your platform is
-  not currently supported please contact enquiries@OpenCFD.co.uk to
+  not currently supported please contact <enquiries@OpenCFD.co.uk> to
-  negotiate a support contract and we will do the port and maintiain it in
+  negotiate a support contract and we will do the port and maintain it in
   future releases.
 
 
@@ -132,21 +136,22 @@
 
 6. Getting Started
 ~~~~~~~~~~~~~~~~~~
-  Create a project directory within the $HOME/OpenFOAM directory named
-  <userName>-dev (e.g. 'chris-dev' for user chris) and create a
-  directory named 'run' within it, e.g. by typing:
 
-      mkdir -p $HOME/OpenFOAM/${LOGNAME}-dev/run
+  Create a project directory within the $HOME/OpenFOAM directory named
+  <USER>-<VERSION> (e.g. 'chris-1.5' for user chris and OpenFOAM version 1.5)
+  and create a directory named 'run' within it, e.g. by typing:
+
+      mkdir -p $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run
 
   Copy the 'tutorial' examples directory in the OpenFOAM distribution to the
   'run' directory.  If OpenFOAM environment variables are set correctly,
   then the following command will be correct:
 
-      cp -r $WM_PROJECT_DIR/tutorials $HOME/OpenFOAM/${LOGNAME}-dev/run
+      cp -r $WM_PROJECT_DIR/tutorials $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run
 
   Run the first example case of incompressible laminar flow in a cavity:
 
-      cd $HOME/OpenFOAM/${LOGNAME}-dev/run/tutorials/icoFoam/cavity
+      cd $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run/tutorials/icoFoam/cavity
       blockMesh
       icoFoam
 
@@ -176,3 +181,4 @@ A. Running OpenFOAM in 32-bit mode on 64-bit machines
   variable $WM_32 (to anything, e.g. "on") before sourcing the etc/bashrc
   (or etc/cshrc) file.  Unsetting $WM_32 and sourcing the bashrc file will
   set up the user to run in 64-bit mode.
+

applications/utilities/mesh/conversion/Optional/Allwmake

@@ -0,0 +1,11 @@
+#!/bin/sh
+# Build optional components (eg, may depend on third-party libraries)
+set -x
+
+# if the library exists, assume there are headers too
+if [ -e $FOAM_LIBBIN/libccmio.so ]
+then
+   wmake ccm26ToFoam
+fi
+
+# end

applications/utilities/mesh/conversion/Optional/ccm26ToFoam/Allwmake

@@ -1,4 +0,0 @@
-#!/bin/sh
-set -x
-
-wmake ccm26ToFoam

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

@@ -1,11 +1,10 @@
 EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(LIB_SRC)/other/libccmio \
+    -I$(THIRD_PARTY)/libccmio \
-    -I$(LIB_SRC)/other/libccmio/libccmio/lnInclude
+    -I$(THIRD_PARTY)/libccmio/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \
     -lmeshTools \
-    -lccmio \
+    -lccmio
-    -ladf

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

@@ -63,7 +63,7 @@
 
 <!-- Include sets check box -->
         <IntVectorProperty
-            name="IncludeSets / Zones"
+            name="IncludeSets"
             command="SetIncludeSets"
             number_of_elements="1"
             default_values="0">

bin/foamDiffSourceList

@@ -85,10 +85,6 @@ find -H $newDir                \
 | sed                          \
  -e "\@$newDir/.git/@d"        \
  -e "\@$newDir/lib/@d"         \
- -e "\@$newDir/src/other/mpich-*/platforms@d" \
- -e "\@$newDir/src/other/mpich-*/lib@d"       \
- -e "\@$newDir/src/other/lam-*/platforms@d"   \
- -e "\@$newDir/src/other/openmpi-*/platforms@d"   \
  -e '\@applications/bin/@d'      \
  -e '\@/t/@d'                    \
  -e '\@Make[.A-Za-z]*/[^/]*/@d'  \

bin/foamInstallationTest

@@ -532,8 +532,7 @@ reportEnv '$WM_DIR'           '$PATH' "yes"
 reportEnv '$CEI_HOME'         '$PATH' "no"
 echo ""
 reportEnv '$JAVA_PATH'        '$PATH' "no"
-reportEnv '$LAM_ARCH_PATH'    '$PATH' "yes"
+reportEnv '$MPI_ARCH_PATH'    '$PATH' "yes"
-reportEnv '$MPICH_ARCH_PATH'  '$PATH' "no"
 hline #--------------------
 #
 heading "Checking the FOAM env variables set on the LD_LIBRARY_PATH..."
@@ -543,7 +542,7 @@ echo "$COL1 $COL2 $COL3 $COL4 $COL5"
 hline #--------------------
 reportEnv '$FOAM_LIBBIN'      '$LD_LIBRARY_PATH' "yes"
 reportEnv '$FOAM_USER_LIBBIN' '$LD_LIBRARY_PATH' "no"
-reportEnv '$LAM_ARCH_PATH'    '$LD_LIBRARY_PATH' "yes"
+reportEnv '$MPI_ARCH_PATH'    '$LD_LIBRARY_PATH' "yes"
 hline #--------------------
 #
 heading "Software versions"

bin/foamPack

@@ -87,10 +87,6 @@ find -H $packDir               \
 | sed                          \
  -e "\@$packDir/.git/@d"       \
  -e "\@$packDir/lib/@d"        \
- -e "\@$packDir/src/other/mpich-*/platforms@d" \
- -e "\@$packDir/src/other/mpich-*/lib@d"       \
- -e "\@$packDir/src/other/lam-*/platforms@d"   \
- -e "\@$packDir/src/other/openmpi-*/platforms@d"   \
  -e '\@applications/bin/@d'       \
  -e '\@/t/@d'                     \
  -e '\@Make[.A-Za-z]*/[^/]*/@d'   \

bin/foamPackBin

@@ -73,7 +73,6 @@ dirList=$(
       $packDir/lib/$arch \
       $packDir/applications/bin/$arch \
       $packDir/wmake/rules \
-      $packDir/src/other/{mpich,lam,openmpi}-*/platforms/$arch \
       ;
    do
       [ -d $dir ] && echo $dir

bin/foamPackChanged

@@ -61,10 +61,6 @@ find -H $packDir               \
     -name "*.orig"             \
 | sed                          \
  -e "\@$packDir/lib/@d"        \
- -e "\@$packDir/src/other/mpich-*/platforms@d" \
- -e "\@$packDir/src/other/mpich-*/lib@d"       \
- -e "\@$packDir/src/other/lam-*/platforms@d"   \
- -e "\@$packDir/src/other/openmpi-*/platforms@d"   \
  -e '\@applications/bin/@d'      \
  -e '\@/t/@d'                    \
  -e '\@Make[.A-Za-z]*/[^/]*/@d'  \

bin/foamPackSource

@@ -76,10 +76,6 @@ find -H $packDir               \
 | sed                          \
  -e "\@$packDir/.git/@d"       \
  -e "\@$packDir/lib/@d"        \
- -e "\@$packDir/src/other/mpich-*/platforms@d" \
- -e "\@$packDir/src/other/mpich-*/lib@d"       \
- -e "\@$packDir/src/other/lam-*/platforms@d"   \
- -e "\@$packDir/src/other/openmpi-*/platforms@d"   \
  -e '\@applications/bin/@d'       \
  -e '\@/t/@d'                     \
  -e '\@Make[.A-Za-z]*/[^/]*/@d'   \

bin/tools/buildParaView3.2.1

@@ -1,87 +1,57 @@
 #!/bin/sh
-set -x
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM.
+#
+#     OpenFOAM is free software; you can redistribute it and/or modify it
+#     under the terms of the GNU General Public License as published by the
+#     Free Software Foundation; either version 2 of the License, or (at your
+#     option) any later version.
+#
+#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#     for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with OpenFOAM; if not, write to the Free Software Foundation,
+#     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+#
+# Script
+#     buildParaView
+#
+# Description
+#     Build and install ParaView
+#     - run from folder above ParaView source folder or place the
+#       ParaView source under $WM_PROJECT_INST_DIR
+#
+#------------------------------------------------------------------------------
+. $WM_PROJECT_DIR/bin/tools/buildParaViewFunctions
+
+# set -x
 
-# ParaView 3.x build script
-# - run from folder above source folder
 PARAVIEW_SRC="ParaView3.2.1"
+PARAVIEW_MAJOR_VERSION="3.2"
 
-VERBOSE="OFF"
+VERBOSE=OFF
-INCLUDE_MPI="ON"
+INCLUDE_MPI=ON
 MPI_MAX_PROCS=32
-INCLUDE_PYTHON="ON"
+INCLUDE_PYTHON=ON
-INCLUDE_MESA="OFF"
+PYTHON_LIBRARY=""
+INCLUDE_MESA=OFF
 
-# initialisation
+set +x
-CMAKE_VARIABLES=""
-PWD=`pwd`
-OBJ_ADD=""
 
-# set general options
+# provide a shortcut for repeated builds - use with caution
-CMAKE_VARIABLES="$CMAKE_VARIABLES -DBUILD_SHARED_LIBS:BOOL=ON"
+if [ "$#" -gt 0 ]
-
+then
-if [ "$VERBOSE" = "ON" ]; then
+   CMAKE_SKIP=YES
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DCMAKE_VERBOSE_MAKEFILE=TRUE"
-fi
-
-# set MPI specific options
-if [ "$INCLUDE_MPI" = "ON" ]; then
-    OBJ_ADD="$OBJ_ADD-mpi"
-
-    if [ "$WM_MPLIB" = "OPENMPI" ]; then
-        MPI_INCLUDE_PATH=$OPENMPI_ARCH_PATH/include
-        MPI_LIBRARY=$OPENMPI_ARCH_PATH/lib/libmpi.so
-        MPI_RUN=$OPENMPI_ARCH_PATH/bin/mpirun
-    elif [ "$WM_MPLIB" = "LAM" ]; then
-        MPI_INCLUDE_PATH=$LAM_ARCH_PATH/include
-        MPI_LIBRARY=$LAM_ARCH_PATH/lib/libmpi.so
-        MPI_RUN=$LAM_ARCH_PATH/bin/mpirun
-    elif [ "$WM_MPLIB" = "MPICH" ]; then
-        MPI_INCLUDE_PATH=$MPICH_ARCH_PATH/include
-        MPI_LIBRARY=$MPICH_ARCH_PATH/lib/libmpich.so
-        MPI_RUN=$MPICH_ARCH_PATH/bin/mpirun
-    fi
-
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DVTK_USE_MPI=ON"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DPARAVIEW_USE_MPI=ON"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DMPI_INCLUDE_PATH=$MPI_INCLUDE_PATH"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DMPI_LIBRARY=$MPI_LIBRARY"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DVTK_MPIRUN_EXE=$MPI_RUN"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DVTK_MPI_MAX_NUMPROCS=$MPI_MAX_PROCS"
-fi
-
-# set python specific options
-if [ "$INCLUDE_PYTHON" = "ON" ]; then
-    WHICH_PYTHON=`which python`
-    if [ "$WHICH_PYTHON" != "" ]; then
-        OBJ_ADD="$OBJ_ADD-py"
-
-        PYTHON_LIBRARY=`ldd $WHICH_PYTHON | grep libpython | \
-            sed 's/.* => \(.*\) (.*/\1/'`
-        PYTHON_MAJOR_VERSION=`echo $PYTHON_LIBRARY | \
-            sed 's/.*libpython\(.*\).so.*/\1/'`
-        PYTHON_INCLUDE_DIR=/usr/include/python$PYTHON_MAJOR_VERSION
-
-        CMAKE_VARIABLES="$CMAKE_VARIABLES -DPARAVIEW_ENABLE_PYTHON=ON"
-        CMAKE_VARIABLES= \
-            "$CMAKE_VARIABLES -DPYTHON_INCLUDE_PATH=$PYTHON_INCLUDE_DIR"
-        CMAKE_VARIABLES="$CMAKE_VARIABLES -DPYTHON_LIBRARY=$PYTHON_LIBRARY"
-    else
-        echo "*** Warning: Unable to determine python libray"
-        echo "***          De-activating python support"
-        INCLUDE_PYTHON="OFF"
-    fi
-fi
-
-# set MESA specific options
-if [ "$INCLUDE_MESA" = "ON" ]; then
-    OBJ_ADD="$OBJ_ADD-mesa"
-
-    MESA_INCLUDE_DIR=/usr/include/GL
-    MESA_LIBRARY=/usr/lib$WM_COMPILER_LIB_ARCH/libOSMesa.so
-
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DVTK_OPENGL_HAS_OSMESA=ON"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DOSMESA_INCLUDE_DIR=$MESA_INCLUDE_DIR"
-    CMAKE_VARIABLES="$CMAKE_VARIABLES -DOSMESA_LIBRARY=$MESA_LIBRARY"
 fi
 
 # set paraview environment
@@ -89,68 +59,13 @@ PARAVIEW_SRC_DIR=$PWD/$PARAVIEW_SRC
 #PARAVIEW_OBJ_DIR=$PARAVIEW_SRC_DIR/platforms/$WM_OPTIONS/obj$OBJ_ADD
 PARAVIEW_OBJ_DIR=$PARAVIEW_SRC_DIR/platforms/$WM_ARCH$WM_COMPILER
 
-# remove existing build folder if present
+addMpiSupport       # set MPI specific options
-if [ -e "$PARAVIEW_OBJ_DIR" ]; then
+addPythonSupport    # set python specific options
-    rm -rf $PARAVIEW_OBJ_DIR
+addMesaSupport      # set MESA specific options
-fi
 
-# create paraview build folder
+buildParaView
-mkdir -p $PARAVIEW_OBJ_DIR
+installParaView
-cd $PARAVIEW_OBJ_DIR
-
-echo "Building $PARAVIEW_SRC"
-echo "    MPI support    : $INCLUDE_MPI"
-echo "    Python support : $INCLUDE_PYTHON"
-echo "    MESA support   : $INCLUDE_MESA"
-echo "    Source         : $PARAVIEW_SRC_DIR"
-echo "    Target         : $PARAVIEW_OBJ_DIR"
-
-# make paraview
-cmake \
-    -DCMAKE_INSTALL_PREFIX=$PARAVIEW_APP_DIR \
-    $CMAKE_VARIABLES \
-    $PARAVIEW_SRC_DIR
-
-if [ -r /proc/cpuinfo ]; then
-    WM_NCOMPPROCS=`egrep "^processor" /proc/cpuinfo | wc -l`
-
-    if [ $WM_NCOMPPROCS -gt 8 ]; then
-        WM_NCOMPPROCS=8
-    fi
-
-    make -j $WM_NCOMPPROCS
-else
-    make
-fi
-
-if [ -e "$PARAVIEW_OBJ_DIR/bin/paraview" ]; then
-    echo "    Build complete"
-
-    # replace local links with ParaView_INST_DIR environment variables
-    echo "    Replacing path hard links"
-    find . -iname \*.cmake -execdir sed -i \
-        "s,$PARAVIEW_SRC_DIR,\$ENV{ParaView_INST_DIR},g" {} ';' \
-        -print
-
-    # create a softlink to the $PARAVIEW_OBJ_DIR/bin folder
-    echo "    Creating paraview 3.2 soft link to /bin"
-    ( mkdir lib && cd lib && ln -s ../bin paraview-3.2 )
-
-    # info on symlinks to screen
-    echo ""
-    echo "    ---"
-    echo "    Installation complete"
-    echo "    Set environment variables:"
-    echo "    - ParaView_INST_DIR to $PARAVIEW_SRC_DIR"
-    echo "    - ParaView_DIR to $PARAVIEW_OBJ_DIR"
-    echo "    - PV_PLUGIN_PATH to $FOAM_LIBBIN"
-    echo "    Add $PARAVIEW_OBJ_DIR/bin to PATH"
-    #echo "   Add $ParaView_INST_DIR/lib to LD_LIBRARY_PATH"
-    echo "    ---"
-    echo "done."
-fi
-
-# finalisation
-cd $PWD
 
+echo "done"
 
+#------------------------------------------------------------------------------

doc/Doxygen/Doxyfile

@@ -477,40 +477,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = $(WM_PROJECT_DIR)/src/OpenFOAM \
+INPUT                  = $(WM_PROJECT_DIR)/src \
-                         $(WM_PROJECT_DIR)/src/Pstream \
-                         $(WM_PROJECT_DIR)/src/finiteVolume \
-                         $(WM_PROJECT_DIR)/src/transportModels/incompressible \
-                         $(WM_PROJECT_DIR)/src/transportModels/interfaceProperties \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/thermophysicalFunctions \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/specie \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/liquids \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/liquidMixture \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/basic \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/combustion \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/pdfs \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/chemistryModel \
-                         $(WM_PROJECT_DIR)/src/thermophysicalModels/laminarFlameSpeed \
-                         $(WM_PROJECT_DIR)/src/turbulenceModels/incompressible \
-                         $(WM_PROJECT_DIR)/src/turbulenceModels/compressible \
-                         $(WM_PROJECT_DIR)/src/LESmodels/LESfilters \
-                         $(WM_PROJECT_DIR)/src/LESmodels/incompressible \
-                         $(WM_PROJECT_DIR)/src/LESmodels/compressible \
-                         $(WM_PROJECT_DIR)/src/errorEstimation \
-                         $(WM_PROJECT_DIR)/src/dynamicMesh \
-                         $(WM_PROJECT_DIR)/src/triSurface \
-                         $(WM_PROJECT_DIR)/src/edgeMesh \
-                         $(WM_PROJECT_DIR)/src/lagrangian/basic \
-                         $(WM_PROJECT_DIR)/src/lagrangian/solidParticle \
-                         $(WM_PROJECT_DIR)/src/lagrangian/dieselSpray \
-                         $(WM_PROJECT_DIR)/src/engine \
-                         $(WM_PROJECT_DIR)/src/ODE \
-                         $(WM_PROJECT_DIR)/src/randomProcesses \
-                         $(WM_PROJECT_DIR)/src/sampling \
-                         $(WM_PROJECT_DIR)/src/meshTools \
-                         $(WM_PROJECT_DIR)/src/dynamicFvMesh \
-                         $(WM_PROJECT_DIR)/src/topoChangerFvMesh \
-                         $(WM_PROJECT_DIR)/src/fvMotionSolver \
                          $(WM_PROJECT_DIR)/applications/utilities \
                          $(WM_PROJECT_DIR)/applications/solvers
 

etc/settings.csh

@@ -137,10 +137,10 @@ case OPENMPI:
     set mpi_version=openmpi-1.2.6
     setenv MPI_ARCH_PATH $thirdParty/$mpi_version/platforms/$WM_OPTIONS
 
-    # Tell OpenMPI where to find it's install directory
+    # Tell OpenMPI where to find its install directory
     setenv OPAL_PREFIX $MPI_ARCH_PATH
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
     AddPath $MPI_ARCH_PATH/bin
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
@@ -151,8 +151,9 @@ case LAM:
     set mpi_version=lam-7.1.4
     setenv MPI_ARCH_PATH $thirdParty/$mpi_version/platforms/$WM_OPTIONS
     setenv LAMHOME $thirdParty/$mpi_version
+    # note: LAMHOME is deprecated, should probably point to MPI_ARCH_PATH too
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
     AddPath $MPI_ARCH_PATH/bin
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
@@ -164,7 +165,7 @@ case MPICH:
     setenv MPI_ARCH_PATH $thirdParty/$mpi_version/platforms/$WM_OPTIONS
     setenv MPICH_ROOT $MPI_ARCH_PATH
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
     AddPath $MPI_ARCH_PATH/bin
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
@@ -172,20 +173,20 @@ case MPICH:
     breaksw
 
 case MPICH-GM:
-    setenv MPICH_PATH /opt/mpi
+    setenv MPI_ARCH_PATH /opt/mpi
-    setenv MPICH_ROOT $MPICH_ARCH_PATH
+    setenv MPICH_PATH $MPI_ARCH_PATH
-    setenv MPI_ARCH_PATH $MPICH_PATH
+    setenv MPICH_ROOT $MPI_ARCH_PATH
     setenv GM_LIB_PATH /opt/gm/lib64
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
-    AddLib $GM_LIB_PATH
+    AddLib  $GM_LIB_PATH
     AddPath $MPI_ARCH_PATH/bin
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/mpich-gm
     breaksw
 
 case GAMMA:
-    setenv GAMMA_ARCH_PATH /usr
+    setenv MPI_ARCH_PATH /usr
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/gamma
     breaksw
 
@@ -220,5 +221,4 @@ endif
 #    setenv LD_PRELOAD $FOAM_LIBBIN/libhoard.so:${LD_PRELOAD}
 #endif
 
-
 # -----------------------------------------------------------------------------

etc/settings.sh

@@ -95,7 +95,6 @@ export FOAM_RUN=$WM_PROJECT_USER_DIR/run
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 thirdParty=$WM_PROJECT_INST_DIR/ThirdParty
 
-
 # Compiler settings
 # ~~~~~~~~~~~~~~~~~
 WM_COMPILER_BIN=
@@ -152,7 +151,7 @@ OPENMPI)
     # Tell OpenMPI where to find its install directory
     export OPAL_PREFIX=$MPI_ARCH_PATH
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
     AddPath $MPI_ARCH_PATH/bin
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/$mpi_version
@@ -175,7 +174,7 @@ LAM)
 MPICH)
     mpi_version=mpich-1.2.4
     export MPI_ARCH_PATH=$thirdParty/$mpi_version/platforms/$WM_OPTIONS
-    export MPICH_ROOT=$MPICH_ARCH_PATH
+    export MPICH_ROOT=$MPI_ARCH_PATH
 
     AddLib  $MPI_ARCH_PATH/lib
     AddPath $MPI_ARCH_PATH/bin
@@ -185,20 +184,20 @@ MPICH)
     ;;
 
 MPICH-GM)
-    export MPICH_PATH=/opt/mpi
+    export MPI_ARCH_PATH=/opt/mpi
-    export MPICH_ROOT=$MPICH_PATH
+    export MPICH_PATH=$MPI_ARCH_PATH
-    export MPI_ARCH_PATH=$MPICH_PATH
+    export MPICH_ROOT=$MPI_ARCH_PATH
     export GM_LIB_PATH=/opt/gm/lib64
 
-    AddLib $MPI_ARCH_PATH/lib
+    AddLib  $MPI_ARCH_PATH/lib
-    AddLib $GM_LIB_PATH
+    AddLib  $GM_LIB_PATH
     AddPath $MPI_ARCH_PATH/bin
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/mpich-gm
     ;;
 
 GAMMA)
-    export GAMMA_ARCH_PATH=/usr
+    export MPI_ARCH_PATH=/usr
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/gamma
     ;;
 
@@ -231,5 +230,4 @@ export MPI_BUFFER_SIZE=20000000
 #    export LD_PRELOAD=$FOAM_LIBBIN/libhoard.so:$LD_PRELOAD
 #fi
 
-
 # -----------------------------------------------------------------------------

src/OpenFOAM/containers/HashTables/HashSet/HashSet.H

@@ -28,6 +28,11 @@ Class
 Description
     A HashTable with word keys but without contents.
 
+Class
+    Foam::wordHashSet
+
+Description
+    A HashSet with (the default) word keys.
 \*---------------------------------------------------------------------------*/
 
 #ifndef HashSet_H

src/OpenFOAM/global/foamVersion.H

@@ -30,7 +30,7 @@ Description
 
 
 Global
-    foamVersion
+    Foam::FOAMversion
 
 Description
     OpenFOAM version number static string.

src/OpenFOAM/meshes/polyMesh/polyPatches/basic/coupled/coupledPolyPatch.H

@@ -23,11 +23,12 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    coupledPolyPatch
+    Foam::coupledPolyPatch
 
 Description
-    coupledPolyPatch is an abstract base class for patches that couple regions
+    The coupledPolyPatch is an abstract base class for patches that couple
-    of the computational domain e.g. cyclic and processor-processor links.
+    regions of the computational domain e.g. cyclic and processor-processor
+    links.
 
 SourceFiles
     coupledPolyPatch.C

src/autoMesh/autoHexMesh/autoHexMeshDriver/autoHexMeshDriver.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    autoHexMeshDriver
-
 \*----------------------------------------------------------------------------*/
 
 #include "autoHexMeshDriver.H"

src/autoMesh/autoHexMesh/autoHexMeshDriver/autoHexMeshDriver.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    autoHexMeshDriver
+    Foam::autoHexMeshDriver
 
 Description
     main meshing driver.
@@ -85,9 +85,9 @@ class autoHexMeshDriver
         //- Extrusion controls
         enum extrudeMode
         {
-            NOEXTRUDE,      // Do not extrude. No layers added.
+            NOEXTRUDE,      /*!< Do not extrude. No layers added. */
-            EXTRUDE,        // Extrude
+            EXTRUDE,        /*!< Extrude */
-            EXTRUDEREMOVE   // Extrude but afterwards remove added faces locally
+            EXTRUDEREMOVE   /*!< Extrude but afterwards remove added faces locally */
         };
 
 
@@ -107,7 +107,7 @@ class autoHexMeshDriver
             }
         };
 
-        // Combine operator class to combine normal with other normal.
+        //- Combine operator class to combine normal with other normal.
         class nomalsCombine
         {
         public:

src/autoMesh/autoHexMesh/autoHexMeshDriver/pointData/pointData.H

@@ -23,11 +23,12 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    pointData
+    Foam::pointData
 
 Description
     Holds information regarding nearest wall point. Used in pointEdgeWave.
     (so not standard meshWave)
+
     To be used in wall distance calculation.
 
 SourceFiles

src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    meshRefinement
-
 \*----------------------------------------------------------------------------*/
 
 #include "Pstream.H"

src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H

@@ -23,11 +23,12 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    meshRefinement
+    Foam::meshRefinement
 
 Description
     Helper class which maintains intersections of (changing) mesh with
     (static) surfaces.
+
     Maintains
     - per face any intersections of this edge with any of the surfaces
 
@@ -90,9 +91,9 @@ public:
         //- Enumeration for how the userdata is to be mapped upon refinement.
         enum mapType
         {
-            MASTERONLY = 1, // maintain master only
+            MASTERONLY = 1, /*!< maintain master only */
-            KEEPALL = 2,    // have slaves (upon refinement) from master
+            KEEPALL = 2,    /*!< have slaves (upon refinement) from master */
-            REMOVE = 4      // set value to -1 any face that has been refined
+            REMOVE = 4      /*!< set value to -1 any face that has been refined */
         };
 
 

src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    meshRefinement
-
 \*----------------------------------------------------------------------------*/
 
 #include "meshRefinement.H"

src/autoMesh/autoHexMesh/meshRefinement/meshRefinementMerge.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    meshRefinement
-
 \*----------------------------------------------------------------------------*/
 
 #include "meshRefinement.H"

src/autoMesh/autoHexMesh/meshRefinement/meshRefinementRefine.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    meshRefinement
-
 \*----------------------------------------------------------------------------*/
 
 #include "meshRefinement.H"

src/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.C

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    refinementSurfaces
-
 \*----------------------------------------------------------------------------*/
 
 #include "refinementSurfaces.H"
@@ -261,7 +258,7 @@ Foam::refinementSurfaces::refinementSurfaces
                     << " which has regions " << regionNames
                     << abort(FatalError);
             }
-            
+
             label globalRegionI = regionOffset_[surfI] + regionI;
 
             minLevel_[globalRegionI] = iter();

src/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    refinementSurfaces
+    Foam::refinementSurfaces
 
 Description
     Container for triSurfaces used for surface-driven refinement.

src/autoMesh/autoHexMesh/trackedParticle/ExactParticle.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    ExactParticle
+    Foam::ExactParticle
 
 Description
     Special version of Particle to do tracking on non-convex cells.

src/autoMesh/autoHexMesh/trackedParticle/trackedParticle.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    trackedParticle
+    Foam::trackedParticle
 
 Description
     Particle class that marks cells it passes through. Used to mark cells

src/decompositionAgglomeration/Allwmake

@@ -3,12 +3,11 @@ set -x
 
 wmake libso decompositionMethods
 
-if [ -d $FOAM_MPI_LIBBIN ]
+if [ -d "$FOAM_MPI_LIBBIN" ]
 then
     wmake libso parMetisDecomp
 fi
 
-( cd MGridGenGamgAgglomeration && ./Allwmake )
+wmake libso MGridGenGamgAgglomeration
-
 
 # ----------------------------------------------------------------- end-of-file

src/decompositionAgglomeration/MGridGenGamgAgglomeration/Allwmake

@@ -1 +0,0 @@
-wmake libso MGridGenGAMGAgglomeration

src/decompositionAgglomeration/MGridGenGamgAgglomeration/Make/options

@@ -1,4 +1,4 @@
-ParMGridGen = ${WM_PROJECT_INST_DIR}/ThirdParty/ParMGridGen-1.0
+ParMGridGen = $(THIRD_PARTY)/ParMGridGen-1.0
 
 TYPE_REAL=
 #if defined(SP)

src/decompositionAgglomeration/decompositionMethods/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I${WM_PROJECT_INST_DIR}/ThirdParty/metis-5.0pre2/include
+    -I$(THIRD_PARTY)/metis-5.0pre2/include
 
 LIB_LIBS = \
     -lmetis \

src/decompositionAgglomeration/parMetisDecomp/Make/options

@@ -2,8 +2,8 @@ include $(RULES)/mplib$(WM_MPLIB)
 
 EXE_INC = \
     $(PFLAGS) $(PINC) \
-    -I${WM_PROJECT_INST_DIR}/ThirdParty/ParMetis-3.1/ParMETISLib \
+    -I$(THIRD_PARTY)/ParMetis-3.1/ParMETISLib \
-    -I${WM_PROJECT_INST_DIR}/ThirdParty/ParMetis-3.1 \
+    -I$(THIRD_PARTY)/ParMetis-3.1 \
     -I../decompositionMethods/lnInclude
 
 LIB_LIBS = \

src/dynamicFvMesh/dynamicRefineFvMesh/dynamicRefineFvMesh.H

@@ -23,11 +23,12 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    dynamicRefineFvMesh
+    Foam::dynamicRefineFvMesh
 
 Description
-    fvMesh with built-in refinement. Determines which cells to refine/unrefine
+    A fvMesh with built-in refinement.
-    and does all in update().
+
+    Determines which cells to refine/unrefine and does all in update().
 
 SourceFiles
     dynamicRefineFvMesh.C

src/dynamicMesh/polyTopoChange/polyTopoChange/addPatchCellLayer.H

@@ -23,27 +23,29 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    addPatchCellLayer
+    Foam::addPatchCellLayer
 
 Description
-    Adds layers of cells to outside of polyPatch. Call setRefinement with
+    Adds layers of cells to outside of polyPatch.
-    offset vector for every patch point and number of layers per patch face
+
-    and number of layers per patch point.
+    Call setRefinement with offset vector for every patch point and number
+    of layers per patch face and number of layers per patch point.
     - offset vector should be zero for any non-manifold point and synchronised
-    on coupled points before calling this.
+      on coupled points before calling this.
     - offset vector of zero will not add any points.
     - gets supplied the number of extruded layers both per face and per
       point. Usually the point nlayers is the max of surrounding face nlayers.
 
-        point nlayers:
+      point nlayers:
-         0 : no extrusion. Any surrounding face being extruded becomes 'prism'
+       -  0 : no extrusion. Any surrounding face being extruded becomes 'prism'
-        >0 : should be max of surrounding face nlayers.
+       - >0 : should be max of surrounding face nlayers.
 
     - differing face nlayers: 'termination' : (e.g. from 2 to 4 layers) match
       at original patch face side.
 
         E.g. 2 boundary faces on patches a,b. 2 layers for a, 3 for b.
 
+    @verbatim
         Was:
 
            a      b         <- patch of boundary face
@@ -51,7 +53,6 @@ Description
         |      |      |     <- original cells
         +------+------+
 
-
         Becomes:
 
            a      b         <- patch of boundary face
@@ -61,6 +62,7 @@ Description
         +------+------+
         |      |      |     <- original cells
         +------+------+
+    @endverbatim
 
 
     - added faces get same patchID as face they are extruded from
@@ -70,24 +72,26 @@ Description
 
     E.g. 3 boundary faces on patches a,b. b gets extruded, a doesn't.
 
-       a      b      b          <- patch of boundary face
+    @verbatim
-    +------+------+------+
+           a      b      b          <- patch of boundary face
-    |      |      |      |      <- cells
+        +------+------+------+
-    +------+------+------+
+        |      |      |      |      <- cells
+        +------+------+------+
 
 
-           ^      ^             <- wanted extrusion vector (none at far right)
+               ^      ^             <- wanted extrusion vector (none at far right)
-       a   |  b   |  b          <- patch of boundary face
+           a   |  b   |  b          <- patch of boundary face
-    +------+------+------+
+        +------+------+------+
-    |      |      |      |      <- cells
+        |      |      |      |      <- cells
-    +------+------+------+
+        +------+------+------+
 
-              b
+                  b
-           +------+\ b          1. prism cell added onto second b face since
+               +------+\ b          1. prism cell added onto second b face since
-       a  a|      | ----\          only one side gets extruded.
+           a  a|      | ----\          only one side gets extruded.
-    +------+------+------+      2. side-face gets patch a, not b.
+        +------+------+------+      2. side-face gets patch a, not b.
-    |      |      |      |
+        |      |      |      |
-    +------+------+------+
+        +------+------+------+
+    @endverbatim
 
 
 SourceFiles

src/dynamicMesh/polyTopoChange/polyTopoChange/combineFaces.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    combineFaces
+    Foam::combineFaces
 
 Description
     Combines boundary faces into single face. The faces get the patch

src/finiteVolume/finiteVolume/fvc/fvc.H

@@ -22,7 +22,7 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-InNamespace
+Namespace
     Foam::fvc
 
 Description

src/finiteVolume/finiteVolume/fvm/fvm.H

@@ -27,7 +27,9 @@ Namespace
 
 Description
     Namespace of functions to calculate implicit derivatives returning a
-    matrix. Time derivatives are calculated using Euler-implicit, backward
+    matrix.
+
+    Temporal derivatives are calculated using Euler-implicit, backward
     differencing or Crank-Nicholson. Spatial derivatives are calculated
     using Gauss' Theorem.
 

src/finiteVolume/interpolation/surfaceInterpolation/limitedSchemes/LimitedScheme/LimitFuncs.C

@@ -22,20 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Description
-    Class to create the weighting-factors based on the NVD
-    (Normalised Variable Diagram).
-    The particular differencing scheme class is supplied as a template argument,
-    the weight function of which is called by the weight function of this class
-    for the internal faces as well as faces of coupled patches
-    (e.g. processor-processor patches). The weight function is supplied the
-    central-differencing weighting factor, the face-flux, the cell and face
-    gradients (from which the normalised variable distribution may be created)
-    and the cell centre distance.
-
-    This code organisation is both neat and efficient, allowing for convenient
-    implementation of new schemes to run on parallelised cases.
-
 \*---------------------------------------------------------------------------*/
 
 #include "volFields.H"

src/finiteVolume/interpolation/surfaceInterpolation/limitedSchemes/LimitedScheme/LimitFuncs.H

@@ -22,12 +22,19 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
+Namespace
+    Foam::limitFuncs
+
+Description
+    Namespace for limiting functions
+
+
 Class
     Foam::limitFuncs::LimitFuncs
 
 Description
     Class to create NVD/TVD limited weighting-factors.
- 
+
     The particular differencing scheme class is supplied as a template
     argument, the weight function of which is called by the weight function
     of this class for the internal faces as well as faces of coupled

src/lagrangian/intermediate/clouds/Templates/ReactingCloud/ReactingCloudThermoTypes.H

@@ -22,7 +22,7 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+Typedefs
     Foam::cloudThermoTypes
 
 Description

src/lagrangian/intermediate/submodels/addOns/radiation/absorptionEmission/cloudAbsorptionEmission/cloudAbsorptionEmission.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::cloudAbsorptionEmission
+    Foam::radiation::cloudAbsorptionEmission
 
 Description
     Retrieves absorption/emission data from a cloud object

src/lagrangian/intermediate/submodels/addOns/radiation/scatter/cloudScatter/cloudScatter.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::scatterModel
+    Foam::radiation::cloudScatter
 
 Description
     Cloud radiation scatter model

src/lagrangian/molecule/molecule/molecule.H

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    molecule
+    Foam::molecule
 
 Description
+    Foam::molecule
 
 SourceFiles
     moleculeI.H

src/meshTools/triSurface/searchableSurface/triSurfaceMesh.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    triSurfaceMesh
+    Foam::triSurfaceMesh
 
 Description
     IOoject and searching on triSurface

src/postProcessing/foamCalcFunctions/calcType/calcType.H

@@ -22,6 +22,13 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
+Namespace
+    Foam::calcTypes
+
+Description
+    Namespace for post-processing calculation functions
+
+
 Class
     Foam::calcType
 

src/postProcessing/foamCalcFunctions/field/components/components.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::components
+    Foam::calcTypes::components
 
 Description
     Writes scalar fields corresponding to each component of the supplied

src/postProcessing/foamCalcFunctions/field/div/div.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::div
+    Foam::calcTypes::div
 
 Description
     Writes scalar fields corresponding to the divergence of the supplied

src/postProcessing/foamCalcFunctions/field/mag/mag.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::mag
+    Foam::calcTypes::mag
 
 Description
     Calculates and writes the magnitude of a field for each time

src/postProcessing/foamCalcFunctions/field/magGrad/magGrad.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::magGrad
+    Foam::calcTypes::magGrad
 
 Description
     Writes scalar fields corresponding to the magnitude ot the gradient

src/postProcessing/foamCalcFunctions/field/magSqr/magSqr.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::magSqr
+    Foam::calcTypes::magSqr
 
 Description
     Calculates and writes the magnitude-sqaured of a field for each time

src/postProcessing/forces/forceCoeffs/forceCoeffs.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    forceCoeffs
+    Foam::forceCoeffs
 
 Description
     Derived from the forces function object, creates a specialisation to

src/postProcessing/forces/forces/forces.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    forces
+    Foam::forces
 
 Description
     Calculates the forces and moments by integrating the pressure and
@@ -77,8 +77,7 @@ public:
     // pressure/viscous forces Tuples.
     typedef Tuple2<pressureViscous, pressureViscous> forcesMoments;
 
-    // Sum operation class used to accumulate the pressure and viscous
+    //- Sum operation class to accumulate the pressure, viscous forces and moments
-    // forces and moments
     class sumOp
     {
     public:

src/sampling/sampledSurface/writers/dx/dxWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    dxWriters
+    Foam::dxWriters
 
 Description
 

src/sampling/sampledSurface/writers/foamFile/foamFile.H

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    foamFile
+    Foam::foamFile
 
 Description
+    A surfaceWriter for foamFiles
 
 SourceFiles
     foamFile.C

src/sampling/sampledSurface/writers/foamFile/foamFileWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    foamFileWriters
+    Foam::foamFileWriters
 
 Description
 

src/sampling/sampledSurface/writers/null/nullWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    nullWriters
+    Foam::nullWriters
 
 Description
 

src/sampling/sampledSurface/writers/raw/rawSurfaceWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    rawSurfaceWriters
+    Foam::rawSurfaceWriters
 
 Description
 

src/sampling/sampledSurface/writers/stl/stlWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    stlWriters
+    Foam::stlWriters
 
 Description
 

src/sampling/sampledSurface/writers/surfaceWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    surfaceWriter
+    Foam::surfaceWriters
 
 Description
 

src/sampling/sampledSurface/writers/vtk/vtkWriters.H

@@ -22,8 +22,8 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
-    vtkWriters
+    Foam::vtkWriters
 
 Description
 

src/thermophysicalModels/barotropicCompressibilityModel/barotropicCompressibilityModel/barotropicCompressibilityModel.H

@@ -22,10 +22,18 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
+Namespace
+    Foam::compressibilityModels
+
+Description
+    Namespace for compressibility models.
+
+
 Class
     Foam::barotropicCompressibilityModel
 
 Description
+    Abstract class for barotropic compressibility models
 
 SourceFiles
     barotropicCompressibilityModel.C

src/triSurface/triSurfaceFields/triSurfaceFields.H

@@ -22,7 +22,7 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
+InClass
     Foam::triSurfaceFields
 
 Description

wmake/Makefile

@@ -59,6 +59,7 @@ LIB_DIR            = $(WM_PROJECT_DIR)/lib
 LIB_WM_OPTIONS_DIR = $(LIB_DIR)/$(WM_OPTIONS)
 OBJECTS_DIR        = $(MAKE_DIR)/$(WM_OPTIONS)
 CLASSES_DIR        = $(MAKE_DIR)/classes
+THIRD_PARTY        = $(WM_PROJECT_INST_DIR)/ThirdParty
 
 SYS_INC            =
 SYS_LIBS           =

wmake/rules/General/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linux64Gcc/mplibGAMMA

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(GAMMA_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(GAMMA_ARCH_PATH)/lib -lgamma
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lgamma

wmake/rules/linux64Gcc/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linux64Gcc/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linux64Gcc/mplibMPICH-GM

@@ -1,3 +1,3 @@
 PFLAGS     =
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm

wmake/rules/linux64Gcc/mplibOPENMPI

@@ -1,3 +1,3 @@
 PFLAGS     = -DOMPI_SKIP_MPICXX
-PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi

wmake/rules/linux64Gcc43/mplibGAMMA

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(GAMMA_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(GAMMA_ARCH_PATH)/lib -lgamma
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lgamma

wmake/rules/linux64Gcc43/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linux64Gcc43/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linux64Gcc43/mplibMPICH-GM

@@ -1,3 +1,3 @@
 PFLAGS     =
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm

wmake/rules/linux64Gcc43/mplibOPENMPI

@@ -1,3 +1,3 @@
 PFLAGS     = -DOMPI_SKIP_MPICXX
-PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi

wmake/rules/linux64Icc/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lutil

wmake/rules/linux64Icc/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linux64Icc/mplibOPENMPI

@@ -1,3 +1,3 @@
 PFLAGS     = -DOMPI_SKIP_MPICXX
-PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi

wmake/rules/linuxGcc/mplibGAMMA

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(GAMMA_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(GAMMA_ARCH_PATH)/lib -lgamma
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lgamma

wmake/rules/linuxGcc/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linuxGcc/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linuxGcc/mplibMPICH-GM

@@ -1,3 +1,3 @@
 PFLAGS     =
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm

wmake/rules/linuxGcc/mplibOPENMPI

@@ -1,3 +1,3 @@
 PFLAGS     = -DOMPI_SKIP_MPICXX
-PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi

wmake/rules/linuxGcc43/mplibGAMMA

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(GAMMA_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(GAMMA_ARCH_PATH)/lib -lgamma
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lgamma

wmake/rules/linuxGcc43/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linuxGcc43/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linuxGcc43/mplibMPICH-GM

@@ -1,3 +1,3 @@
 PFLAGS     =
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm

wmake/rules/linuxGcc43/mplibOPENMPI

@@ -1,3 +1,3 @@
 PFLAGS     = -DOMPI_SKIP_MPICXX
-PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi

wmake/rules/linuxIA64Gcc/mplibLAM

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(LAM_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linuxIA64Gcc/mplibMPICH

@@ -1,3 +1,3 @@
 PFLAGS     = 
-PINC       = -I$(MPICH_ARCH_PATH)/include
+PINC       = -I$(MPI_ARCH_PATH)/include
-PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpich -lrt