Add the OpenFOAM source tree

bin/tools/CleanFunctions

@@ -0,0 +1,136 @@
+#---------------------------------*- sh -*-------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     CleanFunctions
+#
+# Description
+#     Miscellaneous cleanup functions for tutorial cases
+#------------------------------------------------------------------------------
+
+#cleanTimeDirectories()
+#{
+#    echo "Cleaning $PWD case"
+#    for time in $(foamInfoExec -times)
+#    do
+#        # keep 0 and constant directories
+#        [ "$time" = "0" -o "$time" = constant ] || {
+#            echo "Deleting directory $time"
+#            rm -rf $time > /dev/null 2>&1
+#        }
+#    done
+#    rm -rf {log,log.*,log-*,logSummary.*,.fxLock,*.xml,ParaView*,paraFoam*,*.OpenFOAM} > /dev/null 2>&1
+#}
+
+cleanTimeDirectories()
+{
+    echo "Cleaning $PWD case"
+    zeros=""
+    while [ ${#zeros} -lt 8 ]
+    do
+        timeDir="0.${zeros}[1-9]*"
+        rm -rf ./${timeDir} ./-${timeDir} > /dev/null 2>&1
+        zeros="0$zeros"
+    done
+    rm -rf ./[1-9]* ./-[1-9]* ./log ./log.* ./log-* ./logSummary.* ./.fxLock ./*.xml ./ParaView* ./paraFoam* ./*.OpenFOAM ./*.blockMesh ./.setSet > /dev/null 2>&1
+}
+
+
+#
+# Remove dynamicCode subdirectory if it looks appropriate
+#
+cleanDynamicCode()
+{
+    if [ -d system -a -d dynamicCode ]
+    then
+        rm -rf dynamicCode > /dev/null 2>&1
+    fi
+}
+
+
+cleanCase()
+{
+    cleanTimeDirectories
+    cleanDynamicCode
+
+    rm -rf processor* > /dev/null 2>&1
+    rm -rf postProcessing > /dev/null 2>&1
+    rm -rf probes* > /dev/null 2>&1
+    rm -rf forces* > /dev/null 2>&1
+    rm -rf graphs* > /dev/null 2>&1
+    rm -rf sets > /dev/null 2>&1
+    rm -rf surfaceSampling > /dev/null 2>&1
+    rm -rf cuttingPlane > /dev/null 2>&1
+    rm -rf system/machines > /dev/null 2>&1
+
+    if [ -d constant/polyMesh ]
+    then
+        (cd constant/polyMesh && \
+            rm -rf \
+            allOwner* cell* face* meshModifiers* \
+            owner* neighbour* point* edge* \
+            cellLevel* pointLevel* refinementHistory* level0Edge* surfaceIndex* sets \
+            > /dev/null 2>&1 \
+        )
+    fi
+    (cd constant && \
+        rm -rf \
+        cellToRegion cellLevel* pointLevel* \
+        > /dev/null 2>&1 \
+    )
+
+    rm -rf constant/tetDualMesh > /dev/null 2>&1
+
+    rm -rf VTK > /dev/null 2>&1
+    rm -f 0/cellLevel 0/pointLevel 0/cellDist constant/cellDecomposition
+
+    if [ -e constant/polyMesh/blockMeshDict.m4 ]
+    then
+        rm -f constant/polyMesh/blockMeshDict > /dev/null 2>&1
+    fi
+}
+
+removeCase()
+{
+    echo "Removing ${1:-unknown} case"
+    rm -rf $1
+}
+
+cleanSamples()
+{
+    rm -rf ./sets ./samples ./sampleSurfaces > /dev/null 2>&1
+}
+
+cleanUcomponents()
+{
+    rm -rf 0/Ux 0/Uy 0/Uz > /dev/null 2>&1
+}
+
+cleanApplication()
+{
+    echo "Cleaning $PWD application"
+    wclean
+}
+
+
+#------------------------------------------------------------------------------

bin/tools/MakefileDirs

@@ -0,0 +1,42 @@
+#-------------------------------*- makefile -*---------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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
+#     MakefileDirs
+#
+# Description
+#     Makefile used by
+#         foamRunTutorials
+#     to call some script in subdirectories.
+#
+#------------------------------------------------------------------------------
+
+.PHONY: application $(FOAM_TARGETS)
+
+application: $(FOAM_TARGETS)
+
+$(FOAM_TARGETS):
+	+@(cd $@ && $(FOAM_APP) $(FOAM_ARGS))
+
+
+#------------------------------------------------------------------------------

bin/tools/README

@@ -0,0 +1,2 @@
+Misc. tools, scripts, templates that are useful (eg, for building applications)
+but don't need to be in the PATH.

bin/tools/RunFunctions

@@ -0,0 +1,102 @@
+#---------------------------------*- sh -*-------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     RunFunctions
+#
+# Description
+#     Miscellaneous functions for running tutorial cases
+#------------------------------------------------------------------------------
+
+getNumberOfProcessors()
+{
+    sed -ne 's/^numberOfSubdomains *\(.*\);/\1/p' system/decomposeParDict
+}
+
+getApplication()
+{
+    sed -ne 's/^ *application *\([a-zA-Z]*\) *;.*$/\1/p' system/controlDict
+}
+
+runApplication()
+{
+    APP_RUN=$1
+    APP_NAME=${1##*/}
+    shift
+
+    if [ -f log.$APP_NAME ]
+    then
+        echo "$APP_NAME already run on $PWD: remove log file to re-run"
+    else
+        echo "Running $APP_RUN on $PWD"
+        $APP_RUN "$@" > log.$APP_NAME 2>&1
+    fi
+}
+
+runParallel()
+{
+    APP_RUN=$1
+    APP_NAME=${1##*/}
+    shift
+
+    if [ -f log.$APP_NAME ]
+    then
+        echo "$APP_NAME already run on $PWD: remove log file to re-run"
+    else
+        nProcs=$1
+        shift
+        echo "Running $APP_RUN in parallel on $PWD using $nProcs processes"
+
+        #if [ "$WM_SCHEDULER" ]
+        #then
+        #    echo "$PWD: $WM_SCHEDULER -np $nProcs" 1>&2
+        #    $WM_SCHEDULER -np $nProcs "( mpirun -np $nProcs $APP_RUN -parallel "$@" < /dev/null > log.$APP_NAME 2>&1 )"
+        #else
+            ( mpirun -np $nProcs $APP_RUN -parallel "$@" < /dev/null > log.$APP_NAME 2>&1 )
+        #fi
+    fi
+}
+
+compileApplication()
+{
+    echo "Compiling $1 application"
+    wmake $1
+}
+
+cloneCase()
+{
+    if [ -d $2 ]
+    then
+        echo "Case already cloned: remove case directory $2 to clone"
+    else
+        echo "Cloning $2 case from $1"
+        mkdir $2
+        cpfiles="0 system constant"
+        for f in $cpfiles
+        do
+            cp -r $1/$f $2
+        done
+    fi
+}
+
+#------------------------------------------------------------------------------

bin/tools/doxyFilter

@@ -0,0 +1,64 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     doxyFilter
+#
+# Description
+#     pass-through filter for doxygen
+#
+#     Special treatment for applications/{solvers,utilities}/*.C
+#     - only keep the first comment block of the C source file
+#       use @cond / @endcond to suppress documenting all classes/variables
+#
+#     Special treatment for applications/{solvers,utilities}/*.H
+#     - use @cond / @endcond to suppress documenting all classes/variables
+#------------------------------------------------------------------------------
+
+if [ "$#" -gt 0 ]
+then
+    filePath=$(echo $1 | sed -e s@^$WM_PROJECT_DIR@../../..@ )
+    # dirName=$(echo "$filePath" | sed -e 's@/[^/]*$@@' )
+    dirName=${filePath%/[^/]*}
+    fileName=${filePath##*/}
+
+    awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilter.awk
+
+    case "$1" in
+    */applications/solvers/*.C | */applications/utilities/*.C )
+        awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilter-top.awk
+        ;;
+#    */applications/solvers/*.H | */applications/utilities/*.H )
+#        awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilter-ignore.awk
+#        ;;
+    esac
+
+    awk -f $WM_PROJECT_DIR/bin/tools/doxyFilter-table.awk $1 | \
+    awk -f $awkScript  | \
+    sed -f $WM_PROJECT_DIR/bin/tools/doxyFilter.sed \
+        -e s@%filePath%@$filePath@g \
+        -e s@%fileName%@$fileName@g \
+        -e s@%dirName%@$dirName@g
+fi
+#------------------------------------------------------------------------------

bin/tools/doxyFilter-ignore.awk

@@ -0,0 +1,44 @@
+# -----------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     doxyFilter-ignore.awk
+#
+# Description
+#     - Prefix file contents with doxygen @file tag and %filePath% tag
+#       that will be changed in a subsequent sed script
+#     - Surround the contents of an entire file with @cond / @endcond
+#       to skip documenting all classes/variables
+#
+# -----------------------------------------------------------------------------
+BEGIN {
+   print "//! @file %filePath%"
+   print "//! @cond OpenFOAMIgnoreAppDoxygen"
+}
+
+{ print }
+
+END {
+   print "//! @endcond"
+}
+# -----------------------------------------------------------------------------

bin/tools/doxyFilter-table.awk

@@ -0,0 +1,135 @@
+BEGIN {
+    FS = "|";
+    data = "";
+    flag = 0;
+    firstRow = 0;
+}
+
+
+/\\table/ {
+    flag = 1;
+    firstRow = 1;
+    next;
+}
+
+
+/\\endtable/ {
+    if (data != "")
+    {
+        printf "<table class=\"OFTable\">\n";
+        printf data;
+        printf "</table>\n";
+    }
+
+    data = "";
+    flag = 0;
+    next;
+}
+
+
+/\\vartable/ {
+    flag = 2;
+    firstRow = 1;
+    next;
+}
+
+
+/\\endvartable/ {
+    if (data != "")
+    {
+        printf "<table border="0">\n";
+        printf data;
+        printf "</table>\n";
+    }
+
+    data = "";
+    flag = 0;
+    next;
+}
+
+
+/\\plaintable/ {
+    flag = 3;
+    firstRow = 1;
+    next;
+}
+
+
+/\\endplaintable/ {
+    if (data != "")
+    {
+        printf "<table border="0">\n";
+        printf data;
+        printf "</table>\n";
+    }
+
+    data = "";
+    flag = 0;
+    next;
+}
+
+{
+    if (flag > 0)
+    {
+        data = (data "<tr>\n");
+        if (flag == 1)
+        {
+            for (i = 0; i <= NF; i++)
+            {
+                if ((i != 0) && (firstRow == 1))
+                {
+                    data = (data "    <th align=\"center\"><b>"$i"</b></th>\n");
+                }
+                else
+                {
+                    if (i == 1)
+                    {
+                        data = (data "    <td>\\c "$i"</td>\n");
+                    }
+                    else if (i > 1)
+                    {
+                        data = (data "    <td>"$i"</td>\n");
+                    }
+                }
+            }
+        }
+        else if (flag == 2)
+        {
+            for (i = 0; i <= NF; i++)
+            {
+                if (i == 1)
+                {
+                    data = (data "    <td style=\"padding-left: 10px\">\\f$"$i"\\f$</td>\n");
+                    data = (data "    <td style=\"padding-left: 10px; padding-right: 10px;\">=</td>\n");
+                }
+                else if (i > 1)
+                {
+                    data = (data "    <td>"$i"</td>\n");
+                }
+            }
+        }
+        else if (flag == 3)
+        {
+            for (i = 0; i <= NF; i++)
+            {
+                if (i == 1)
+                {
+                    data = (data "    <td style=\"padding-left: 10px\">"$i"</td>\n");
+                    data = (data "    <td style=\"padding-left: 10px; padding-right: 10px;\">:</td>\n");
+                }
+                else if (i > 1)
+                {
+                    data = (data "    <td>"$i"</td>\n");
+                }
+            }
+        }
+        data = (data "</tr>\n");
+        firstRow = 0;
+    }
+    else
+    {
+        print $0
+    }
+}
+
+

bin/tools/doxyFilter-top.awk

@@ -0,0 +1,81 @@
+# -----------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     doxyFilter-top.awk
+#
+# Description
+#     Only output the first /* ... */ comment section found in the file
+#     Use @cond / @endcond to suppress documenting all classes/variables
+#     - This is useful for application files in which only the first
+#       block documents the application itself.
+#
+# -----------------------------------------------------------------------------
+BEGIN {
+    state = 0
+}
+
+# a '/*' at the beginning of a line starts a comment block
+/^ *\/\*/ {
+   state++
+}
+
+# check first line
+# either started with a comment or skip documentation for the whole file
+FNR == 1 {
+   if (!state)
+   {
+      print "//! @cond OpenFOAMIgnoreAppDoxygen"
+      state = 2
+   }
+}
+
+# a '*/' ends the comment block
+# skip documentation for rest of the file
+/\*\// {
+    if (state == 1)
+    {
+        print
+        print "//! @cond OpenFOAMIgnoreAppDoxygen"
+    }
+    state = 2
+    next
+}
+
+# print everything within the first comment block
+{
+    if (state)
+    {
+        print
+    }
+    next
+}
+
+END {
+    if (state == 2)
+    {
+        print "//! @endcond"
+    }
+}
+
+# -----------------------------------------------------------------------------

bin/tools/doxyFilter.awk

@@ -0,0 +1,89 @@
+# -----------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     doxyFilter.awk
+#
+# Description
+#     Converts cocoon style sentinel strings into doxygen style strings
+#
+#     Assumes comment strings are formatted as follows
+#         //- general description
+#         //  more information
+#         //  and even more information
+#     This should be re-formatted as the following
+#         //! general description
+#         /*!
+#         more information
+#         and even more information
+#         */
+#     The intermediate "/*! ... */" block is left-justified to handle
+#     possible verbatim text
+# -----------------------------------------------------------------------------
+
+BEGIN {
+    state = 0
+}
+
+/^ *\/\/-/ {
+    state = 1
+    sub(/\/\/-/, "//!")
+    print
+    next
+}
+
+
+/^ *\/\// {
+    # start comment block
+    if (state == 1)
+    {
+        printf "/*! "
+        state = 2
+    }
+
+    # inside comment block
+    if (state == 2)
+    {
+        if (!sub(/^ *\/\/  /, ""))
+        {
+            sub(/^ *\/\//, "")
+        }
+    }
+
+    print
+    next
+}
+
+
+{
+    # end comment block
+    if (state == 2)
+    {
+        printf "*/ "
+    }
+    state = 0
+    print
+    next
+}
+
+# -----------------------------------------------------------------------------

bin/tools/doxyFilter.sed

@@ -0,0 +1,173 @@
+# -----------------------------------------------------------------------------
+# Script
+#     doxyFilter.sed
+#
+# Description
+#     Transform human-readable tags such as 'Description' into the Doxygen
+#     equivalent
+# -----------------------------------------------------------------------------
+
+# new FSF address
+/^License/,/\*\//{
+/^License/,\%http://www.gnu.org/licenses%{
+s?^License.*?\*\/\
+\/\*! \\file %filePath%\
+<b>Original source file</b> <a href="%filePath%">%fileName%</a>\
+\
+\
+\
+\
+\
+\
+\
+\
+?
+/^    /d
+}
+
+
+# remove entry
+/^Application *$/{
+N
+N
+d
+}
+
+
+# remove entry
+/^Global *$/{
+N
+N
+d
+}
+
+
+# Primitive
+#     typename
+# =>
+# \\relates typename
+#
+/^Primitive *$/,/^[^ ]/{
+s/^Primitive *$//
+s/^    /\\relates /
+}
+
+
+# Class
+#     Foam::className
+# =>
+# \\class Foam::className
+#
+/^Class *$/,/^[^ ]/{
+s/^Class *$//
+s/^    /\\class /
+}
+
+
+# Group
+#     groupName
+# =>
+# \ingroup namespaceName
+#
+/^Group *$/,/^[^ ]/{
+s/^Group//
+s/^    /\\ingroup /
+}
+
+
+# Namespace
+#     namespaceName
+# =>
+# \namespace namespaceName
+#
+/^Namespace *$/,/^[^ ]/{
+s/^Namespace//
+s/^    /\\namespace /
+}
+
+
+# Typedef
+#     Foam::def
+# =>
+# \typedef Foam::def
+/^Typedef *$/,/^[^ ]/{
+s/^Typedef//
+s/^    /\\typedef /
+}
+
+
+# add anchor and use \brief
+# the first paragraph will be 'brief' and the others 'detail'
+/^Description *$/,/^[^ ]/{
+/^Description/c\
+<a class="anchor" name="Description"></a> \\brief
+s/^    //
+}
+
+/^Usage *$/,/^[^ ]/{
+/^Usage/c\
+\\par Usage
+s/^    //
+}
+
+
+/^See *Also *$/,/^[^ ]/{
+/^See *Also/c\
+\\see
+s/^    //
+}
+
+/^Note *$/,/^[^ ]/{
+/^Note/c\
+\\note
+s/^    //
+}
+
+
+# remove ToDo paragraph to avoid them showing on related pages
+/^To[Dd]o *$/,/^[^ ]/{
+s/^To[Dd]o *$//
+s/^    .*//
+}
+
+
+/^Warning *$/,/^[^ ]/{
+/^Warning/c\
+\\warning
+s/^    //
+}
+
+
+/^Deprecated *$/,/^[^ ]/{
+/^Deprecated/c\
+\\deprecated
+s/^    //
+}
+
+
+/^SourceFiles *$/,/^$/{
+s?SourceFiles?\\par Source files\
+<ul><li><a href="%filePath%">%fileName%</a></li>?
+s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?
+s?^$?</ul>?
+}
+
+/fileName%<\/a><\/li>$/{
+N
+s?\n$?</ul>?g
+s/<\/li>\n/<\/li> /
+s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?
+}
+
+s/.*\*\//\*\//
+
+
+# convert /heading in source files to bold font and add some space
+s#\\heading \(.*\)#<br><b>\1</b>#g
+
+# add a linebreak
+s#\\linebreak#<br>#g
+
+}
+
+# -----------------------------------------------------------------------------

bin/tools/foamConfigurePaths

@@ -0,0 +1,214 @@
+#!/bin/sh
+#---------------------------------*- sh -*-------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     foamConfigurePaths
+#
+# Description
+#     hardcode installation directory
+#
+#------------------------------------------------------------------------------
+usage() {
+    exec 1>&2
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    cat<<USAGE
+
+usage: ${0##*/}
+  --foamInstall dir         specify installation directory (e.g. /opt)
+  --projectName name        specify project name (e.g. openfoam220)
+  --projectVersion ver      specify project version (e.g. 2.2.0)
+  --archOption arch         specify architecture option (only 32 or 64 applicable)
+  --paraviewInstall dir     specify ParaView_DIR (e.g. /opt/paraviewopenfoam3120)
+  --paraviewVersion ver     specify ParaView_VERSION (e.g. 3.12.0)
+  --scotchArchPath dir      specify SCOTCH_ARCH_PATH (e.g. /opt/OpenFOAM-scotch-6.0.0/)
+  --scotchVersion ver       specify SCOTCH_VERSION (e.g. 6.0.0)
+
+* hardcode paths to installation
+
+USAGE
+    exit 1
+}
+
+
+# Function to do replacement on file. Checks if any replacement has been done.
+# _inlineSed <file> <regexp> <replacement> <msg>
+_inlineSed()
+{
+    file="$1"
+
+    [ -f "$file" ] || {
+        echo "Missing file: $file"
+        exit 1
+    }
+
+    regexp="$2"
+    replacement="$3"
+    msg="$4"
+
+    cmd='/^[^#]/s@'"$regexp"'@'"$replacement"'@'
+
+    grep -q "$regexp" "$file" && sed -i -e "$cmd" "$file" || \
+        (echo "Failed: $msg in $file" && exit 1)
+
+    echo "Okay: $msg in $file"
+
+    return 0
+}
+
+
+[ -f etc/bashrc ] || usage "Please run from top-level directory of installation"
+
+unset foamInstall projectName projectVersion archOption
+unset paraviewInstall scotchArchPath
+
+# parse options
+while [ "$#" -gt 0 ]
+do
+    case "$1" in
+    -h | -help | --help)
+        usage
+        ;;
+    -foamInstall | --foamInstall)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        foamInstall="$2"
+        # replace foamInstall=...
+        _inlineSed \
+            etc/bashrc \
+            'foamInstall=.*' \
+            'foamInstall='"$foamInstall" \
+            "Replacing foamInstall setting by '$foamInstall'"
+        shift 2
+        ;;
+   -projectName | --projectName)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        projectName="$2"
+        # replace WM_PROJECT_DIR=...
+        _inlineSed \
+            etc/bashrc \
+            'WM_PROJECT_DIR=.*' \
+            'WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/'"$projectName" \
+            "Replacing WM_PROJECT_DIR setting by $projectName"
+        shift 2
+        ;;
+   --projectVersion)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        projectVersion="$2"
+        # replace WM_PROJECT_VERSION=...
+        echo "Replacing WM_PROJECT_VERSION setting by $projectVersion"
+        _inlineSed \
+            etc/bashrc \
+            'WM_PROJECT_VERSION=.*' \
+            'WM_PROJECT_VERSION='"$projectVersion" \
+            "Replacing WM_PROJECT_VERSION setting by $projectVersion"
+
+        shift 2
+        ;;
+    -archOption | --archOption)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        archOption="$2"
+        current_archOption=`grep WM_ARCH_OPTION= etc/bashrc | sed "s/export WM_ARCH_OPTION=//"`
+        if [ "$archOption" != "$current_archOption" ]
+        then
+            # replace WM_ARCH_OPTION=...
+            _inlineSed \
+                etc/bashrc \
+                'WM_ARCH_OPTION=.*' \
+                'WM_ARCH_OPTION='"$archOption" \
+                "Replacing WM_ARCH_OPTION setting by '$archOption'"
+        else
+            echo "WM_ARCH_OPTION already set to $archOption"
+        fi
+        shift 2
+        ;;
+    -paraviewInstall | --paraviewInstall)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        paraviewInstall="$2"
+        # replace ParaView_DIR=...
+        _inlineSed \
+            etc/config/paraview.sh \
+            'ParaView_DIR=.*' \
+            'ParaView_DIR='"$paraviewInstall" \
+            "Replacing ParaView_DIR setting by '$paraviewInstall'"
+        shift 2
+        ;;
+    -paraviewVersion | --paraviewVersion)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        paraviewVersion="$2"
+        # replace ParaView_VERSION=...
+        _inlineSed \
+            etc/config/paraview.sh \
+            'ParaView_VERSION=.*' \
+            'ParaView_VERSION='"$paraviewVersion" \
+            "Replacing ParaView_VERSION setting by '$paraviewVersion'"
+        shift 2
+        ;;
+    -scotchVersion | --scotchVersion)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        scotchVersion="$2"
+        _inlineSed \
+            etc/config/scotch.sh \
+            'SCOTCH_VERSION=.*' \
+            'SCOTCH_VERSION='"$scotchVersion" \
+            "Replacing SCOTCH_VERSION setting by '$scotchVersion'"
+        shift 2
+        ;;
+    -scotchArchPath | --scotchArchPath)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        scotchArchPath="$2"
+        _inlineSed \
+            etc/config/scotch.sh \
+            'SCOTCH_ARCH_PATH=.*' \
+            'SCOTCH_ARCH_PATH='"$scotchArchPath" \
+            "Replacing SCOTCH_ARCH_PATH setting by '$scotchArchPath'"
+        shift 2
+        ;;
+    *)
+        usage "unknown option/argument: '$*'"
+        ;;
+    esac
+done
+
+[ -n "$foamInstall" -o -n "$projectName" -o -n "$projectVersion" -o -n "$archOption" \
+-o -n "$paraviewInstall" -o -n "$paraviewVersion" \
+-o -n "$scotchVersion" -o -n "$scotchArchPath" \
+] || usage "Please specify at least one configure option"
+
+#echo "Replacing WM_PROJECT setting by '$projectName'"
+#sed -i -e 's@WM_PROJECT=.*@WM_PROJECT='"$projectName@" etc/bashrc
+
+# Set WM_MPLIB=SYSTEMOPENMPI always
+_inlineSed \
+    etc/bashrc \
+    'export WM_MPLIB=.*' \
+    'export WM_MPLIB=SYSTEMOPENMPI' \
+    "Replacing WM_MPLIB setting by 'SYSTEMOPENMPI'"
+
+## set foamCompiler=system always
+#_inlineSed \
+#    etc/bashrc \
+#    'foamCompiler=.*' \
+#    'foamCompiler=system' \
+#    "Replacing foamCompiler setting by 'system'"
+
+#------------------------------------------------------------------------------

bin/tools/foamListBinDirs

@@ -0,0 +1,117 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     foamListBinDirs <directory> [archOptions]
+#
+# Description
+#     Lists directories containing binary files of OpenFOAM
+#
+# Note
+#     Not normally called directly by the user.
+#------------------------------------------------------------------------------
+toolsDir="${0%/*}"  # this script is already located in the tools/ directory
+
+[ $# -eq 1 -o $# -eq 2 ] || {
+cat <<USAGE 1>&2
+Usage : ${0##*/} <packDir> [archOptions]
+
+* Lists directories containing binary files for OpenFOAM
+
+    The value of 'archOptions' normally corresponds to \$WM_OPTIONS
+    The current value of \$WM_OPTIONS = $WM_OPTIONS
+
+USAGE
+    exit 1
+}
+
+#------------------------------------------------------------------------------
+packDir="$1"
+
+# default to same as $WM_OPTIONS - eg, 'linux64GccDPOpt'
+archOptions="${2:-$WM_OPTIONS}"
+
+[ -n "$archOptions" ] || {
+    echo "Error: no archOptions specified" 1>&2
+    exit 1
+}
+
+# base arch (w/o precision, optimization, etc)
+# same as "$WM_ARCH$WM_COMPILER"
+archCompiler=$(echo "$archOptions" | sed -e 's@[DS]P.*$@@')
+
+# same as $WM_ARCH - eg, 'linux64'
+# TODO: only works for Gcc, Icc, Clang
+archOS=$(echo "$archOptions" | sed -e 's@[GI]cc.*$@@' -e 's@Clang.*$@@')
+
+# links for 32-bit version, eg convert linux64 -> linux-64
+arch3264=$(echo "$archOS" | sed -e 's@64@-64@')
+
+
+#------------------------------------------------------------------------------
+# check for essential directories
+for dir in \
+    $packDir \
+    $packDir/platforms/$archOptions/bin \
+    $packDir/platforms/$archOptions/lib \
+    ;
+do
+    [ -d $dir ] || {
+        echo "Error: directory $dir does not exist" 1>&2
+        exit 1
+    }
+done
+
+#------------------------------------------------------------------------------
+# list of directories
+dirList=$(
+    for dir in \
+        $packDir/platforms/$archOptions/bin \
+        $packDir/platforms/$archOptions/lib \
+        $packDir/wmake/platforms/$archCompiler \
+        $packDir/wmake/platforms/$archOS \
+        $packDir/wmake/rules/General \
+        $packDir/wmake/rules/$archCompiler \
+        $packDir/wmake/rules/$archOS \
+        ;
+    do
+        [ -d $dir ] && echo $dir
+    done
+)
+
+
+cat <<INFO 1>&2
+-------------------------------------------------------------------------------
+Packing $archOptions ($archCompiler) port of $packDir
+    archOS       = $archOS
+    32bit archOS = $arch3264
+
+dirs:
+    $(echo ${dirList:-NONE})
+
+INFO
+
+echo "$dirList"
+
+#------------------------------------------------------------------------------

bin/tools/foamListSourceFiles

@@ -0,0 +1,91 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     foamListSourceFiles <directory>
+#
+# Description
+#     Lists source files and Make/{files,options} in given directory
+#
+# Note
+#     Not normally called directly by the user.
+#------------------------------------------------------------------------------
+
+[ $# -eq 1 ] || {
+cat <<USAGE 1>&2
+Usage : ${0##*/} directory
+
+* Lists source files and Make/{files,options} in given directory
+
+USAGE
+    exit 1
+}
+
+# canonical form (no double and no trailing dashes)
+packDir=$(echo "$1" | sed -e 's@//*@/@g' -e 's@/$@@')
+
+# check for essential directories
+[ -d "$packDir" ] || {
+    echo "Error: directory $packDir does not exist" 1>&2
+    exit 1
+}
+
+
+#
+# list of files but excluding
+# - dependent files (dep, obj, lib), archives
+# - exclude Doxygen documentation etc
+#
+
+find -H $packDir                                                              \
+    ! -type d                                                                 \
+   \( -type f -o -type l \)                                                   \
+    ! -name "*~"                                                              \
+ -a ! -name ".*~"                                                             \
+ -a ! -name "*.orig"                                                          \
+ -a ! -name "*.dep"                                                           \
+ -a ! -name "*.o"                                                             \
+ -a ! -name "*.so"                                                            \
+ -a ! -name "*.a"                                                             \
+ -a ! -name "*.tar"                                                           \
+ -a ! -name "*.tar.gz"                                                        \
+ -a ! -name "*.tgz"                                                           \
+ -a ! -name "*.tar.bz2"                                                       \
+ -a ! -name "*.tbz"                                                           \
+ -a ! -name "core"                                                            \
+ -a ! -name "core.[1-9]*"                                                     \
+ -a ! -name "libccmio*"                                                       \
+| sed                                                                         \
+ -e '\@/\.git/@d'                                                             \
+ -e '\@/\.tags/@d'                                                            \
+ -e '\@/platforms/@d'                                                         \
+ -e '\@/t/@d'                                                                 \
+ -e '\@/Make[.A-Za-z]*/[^/]*/@d'                                              \
+ -e '\@/[Dd]oxygen/html/@d'                                                   \
+ -e '\@/download/@d'                                                          \
+ -e '\@/libccmio-.*/@d'                                                       \
+ -e '\@/debian/@d'
+
+
+#------------------------------------------------------------------------------

bin/tools/foamListThirdPartyBinDirs

@@ -0,0 +1,123 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     foamListThirdPartyBinDirs <directory> [archOptions]
+#
+# Description
+#     Lists directories containing binary files for OpenFOAM ThirdParty
+#
+# Note
+#     Not normally called directly by the user.
+#------------------------------------------------------------------------------
+toolsDir="${0%/*}"  # this script is already located in the tools/ directory
+
+[ $# -eq 1 -o $# -eq 2 ] || {
+cat <<USAGE 1>&2
+Usage : ${0##*/} <packDir> [archOptions]
+
+* List directories containing binary files for OpenFOAM ThirdParty
+
+    The value of 'archOptions' normally corresponds to \$WM_OPTIONS
+    The current value of \$WM_OPTIONS = $WM_OPTIONS
+
+USAGE
+    exit 1
+}
+
+#------------------------------------------------------------------------------
+packDir="$1"
+
+# default to same as $WM_OPTIONS - eg, 'linux64GccDPOpt'
+archOptions="${2:-$WM_OPTIONS}"
+
+[ -n "$archOptions" ] || {
+    echo "Error: no archOptions specified" 1>&2
+    exit 1
+}
+
+# base arch (w/o precision, optimization, etc)
+# same as "$WM_ARCH$WM_COMPILER"
+archCompiler=$(echo "$archOptions" | sed -e 's@[DS]P.*$@@')
+
+# same as $WM_ARCH - eg, 'linux64'
+# TODO: only works for Gcc, Icc, Clang
+archOS=$(echo "$archOptions" | sed -e 's@[GI]cc.*$@@' -e 's@Clang.*$@@')
+
+# links for 32-bit version, eg convert linux64 -> linux-64
+arch3264=$(echo "$archOS" | sed -e 's@64@-64@')
+
+
+#------------------------------------------------------------------------------
+# check for essential directories
+for dir in \
+    $packDir \
+    $packDir/platforms/$archOptions/lib \
+    ;
+do
+    [ -d $dir ] || {
+        echo "Error: directory $dir does not exist" 1>&2
+        exit 1
+    }
+done
+
+#------------------------------------------------------------------------------
+# list of directories
+dirList=$(
+    for dir in \
+        $packDir/platforms/$archOptions \
+        $packDir/platforms/$archCompiler \
+        $packDir/platforms/$archOS \
+        ;
+    do
+        [ -d $dir ] && echo $dir
+    done
+
+    # add in links for 32-bit version
+    if [ "$archOS" != "$arch3264" ]
+    then
+        for dir in \
+            $packDir/platforms/$arch3264 \
+            ;
+        do
+            [ -d $dir -a -L $dir ] && echo $dir
+        done
+     fi
+)
+
+
+cat <<INFO 1>&2
+-------------------------------------------------------------------------------
+Packing $archOptions ($archCompiler) port of $packDir
+    archOS       = $archOS
+    32bit archOS = $arch3264
+
+dirs:
+    $(echo ${dirList:-NONE})
+
+INFO
+
+echo "$dirList"
+
+#------------------------------------------------------------------------------

bin/tools/foamLog.db

@@ -0,0 +1,55 @@
+#------------------------------------------------------------------------------
+# Query database for Foam Log extraction.
+# Each line stands for one query:
+#
+#    name '/' line selector '/' column selector
+#
+# e.g.
+#    kMin/bounding k,/min:
+#
+# The extraction will select a line using 'bounding k,' and in the line
+# takes the word following 'min:' as the value.
+#
+# A special entry is the 'Separator' entry which delimits one iteration
+# from the other.
+#
+#------------------------------------------------------------------------------
+
+#- String to recognize new iteration by (usually same as 'Time')
+Separator/^[ \t]*Time = /Time = 
+
+#- Time value:
+Time/^[ \t]*Time = /Time = 
+
+#- Continuity errors:
+contLocal/time step continuity errors :/sum local = 
+contGlobal/time step continuity errors :/ global = 
+contCumulative/time step continuity errors :/cumulative = 
+
+#- Special for combustion code:
+minFu/min\(fu\) = /min(fu) = 
+minFt/min\(ft\) = /min(ft) = 
+
+#- Execution time:
+executionTime/ExecutionTime = /ExecutionTime = 
+
+#- Courant no:
+CourantMax/Courant Number /max: 
+CourantMean/Courant Number /mean: 
+
+#- K bounding
+kMin/bounding k,/min: 
+kMax/bounding k,/max: 
+kAvg/bounding k,/average: 
+
+#- epsilon bounding
+epsMin/bounding epsilon,/min: 
+epsMax/bounding epsilon,/max: 
+epsAvg/bounding epsilon,/average: 
+
+#- gamma bounding
+alpha1Min/Min\(alpha1\) =/Min(alpha1) =
+alpha1Max/Max\(alpha1\) =/Max(alpha1) =
+
+# AMI
+AMIMin/AMI: Patch source sum/average = 

bin/tools/gtagsrc

@@ -0,0 +1,62 @@
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Canfiguration file
+#     gtagsrc
+#
+# Description
+#     Configuration file for gtags(1).
+#
+#------------------------------------------------------------------------------
+default:\
+	:tc=gtags:tc=htags:
+#------------------------------------------------------------------------------
+# Configuration for gtags(1)
+# See gtags(1).
+#------------------------------------------------------------------------------
+common:\
+	:skip=GPATH,GTAGS,GRTAGS,GSYMS,HTML/,HTML.pub/,html/,tags,TAGS,ID,.ebrowse,.etags,.etagsDef,.etagsDec,y.tab.c,y.tab.h,.notfunction,cscope.out,cscope.po.out,cscope.in.out,.gdbinit,SCCS/,RCS/,CVS/,CVSROOT/,{arch}/,.svn/,.git/,.cvsrc,.cvsignore,.gitignore,.cvspass,.cvswrappers,.deps/,autom4te.cache/,.snprj/:\
+	:langmap=c\:.c.h,yacc\:.y,asm\:.s.S,java\:.java,cpp\:.c++.cc.cpp.cxx.hxx.hpp.C.H,php\:.php.php3.phtml:
+gtags:\
+	:tc=common:\
+	:GTAGS=gtags-parser %s:\
+	:GRTAGS=gtags-parser -r %s:\
+	:GSYMS=gtags-parser -s %s:\
+	:skip=lnInclude/,tutorials/,wmake/,doc/,lib/,etc/:
+#
+#------------------------------------------------------------------------------
+# Configuration for htags(1)
+#------------------------------------------------------------------------------
+htags:\
+	:body_begin=<body text='#191970' bgcolor='#f5f5dc' vlink='gray'>:body_end=</body>:\
+	:table_begin=<table>:table_end=</table>:\
+	:title_begin=<h1><font color='#cc0000'>:title_end=</font></h1>:\
+	:comment_begin=<i><font color='green'>:comment_end=</font></i>:\
+	:sharp_begin=<font color='darkred'>:sharp_end=</font>:\
+	:brace_begin=<font color='red'>:brace_end=</font>:\
+	:warned_line_begin=<span style='background-color\:yellow'>:warned_line_end=</span>:\
+	:reserved_begin=<b>:reserved_end=</b>:script_alias=/cgi-bin/:\
+	:ncol#4:tabs#8:normal_suffix=html:gzipped_suffix=ghtml:\
+	:definition_header=no:
+
+#------------------------------------------------------------------------------

bin/tools/inlineReplace

@@ -0,0 +1,30 @@
+#!/bin/sh
+
+# $0 oldString newString file1 .. fileN
+#
+if [ $# -lt 3 ]
+then
+    echo "Usage: ${0##*/} <oldString> <newString> <file1> [.. fileN]"
+    echo ""
+    echo "Replaces all occurrences of oldString by newString in files."
+    echo "(replacement for sed -i on systems that don't support it)"
+    exit 1
+fi
+
+oldString="$1"
+newString="$2"
+shift 2
+
+for f
+do
+    if grep "$oldString" "$f" >/dev/null
+    then
+        cp "$f" "${f}_bak"
+        sed -e "s@$oldString@$newString@g" "${f}_bak" > "$f"
+        rm -f "${f}_bak"
+    #else
+    #    echo "String $oldString not present in $f"
+    fi
+done
+
+# ----------------------------------------------------------------- end-of-file

bin/tools/org-batch

@@ -0,0 +1,134 @@
+#!/bin/sh
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     org-batch
+#
+# Description
+#     Batch process emacs org-mode files to create html/LaTeX etc.
+#
+#------------------------------------------------------------------------------
+Script=${0##*/}
+
+usage() {
+    exec 1>&2
+    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+    cat<<USAGE
+
+Usage: $Script [OPTIONS] file1 [.. fileN]
+options:
+  -html      create html (default)
+  -latex     create LaTeX
+  -pdflatex  create pdf via pdflatex
+
+* Batch process emacs org-mode files to create html/LaTeX etc.
+
+USAGE
+    exit 1
+}
+
+
+# default is html export:
+mode=html
+unset makePDF
+
+echo "have $Script"
+case $Script in
+*pdflatex)
+    mode=latex
+    makePDF=pdflatex
+    ;;
+*latex)
+    mode=latex
+    ;;
+*html)
+    mode=html
+    ;;
+esac
+
+# parse options
+while [ "$#" -gt 0 ]
+do
+    case "$1" in
+    -h | -help)
+        usage
+        ;;
+    -html)
+        mode=html
+        shift
+        ;;
+    -latex)
+        mode=latex
+        shift
+        ;;
+    -pdflatex)
+        mode=latex
+        makePDF=pdflatex
+        shift
+        ;;
+    -*)
+        usage "unknown option: '$*'"
+        ;;
+    *)
+        break
+        ;;
+    esac
+done
+
+# default is the current directory
+[ "$#" -gt 0 ] || usage "No files specified"
+
+type emacs >/dev/null 2>&1 || usage "No emacs found in PATH"
+
+
+for org
+do
+    echo "Processing: $org"
+    echo "----------"
+    if [ -f "$org" ]
+    then
+        emacs --batch -l org --visit=$org \
+              --funcall org-export-as-$mode-batch
+
+        # post-processing step to create pdf
+        case "$makePDF" in
+        pdflatex)
+            input="${org%.org}.tex"
+
+            if [ -f "$input" ]
+            then
+                pdflatex "$input"
+            else
+                echo "No $input to convert to pdf"
+            fi
+            ;;
+        esac
+
+    else
+        echo "File not found"
+    fi
+    echo "----------"
+done
+
+#------------------------------------------------------------------------------

bin/tools/pre-commit-hook

@@ -0,0 +1,328 @@
+#!/bin/bash
+#---------------------------------*- sh -*-------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     pre-commit-hook
+#
+# Description
+#     pre-commit hook for git.
+#     Copy or link this file as ".git/hooks/pre-commit"
+#
+#     Eg,
+#     (
+#         cd $WM_PROJECT_DIR/.git/hooks &&
+#         ln -sf ../../bin/tools/pre-commit-hook pre-commit
+#     )
+#
+#     Hook receives: empty
+#
+#     Checks for
+#     - illegal code, e.g. <TAB>
+#     - columns greater than 80 for *.[CH] files
+#
+# Note
+#     Using "git commit --no-verify" it is possible to override the hook.
+#
+#     By supplying arguments to the hook, it can also be used to manually
+#     test the specified files/directories for standards conformance.
+#
+#------------------------------------------------------------------------------
+hookName="pre-commit"
+die()
+{
+    echo "$hookName hook failure" 1>&2
+    echo '-----------------------------------' 1>&2
+    echo '' 1>&2
+    echo "$@" 1>&2
+    echo '' 1>&2
+    exit 1
+}
+
+#-----------------------------------------------------------------------------
+# Check content that will be added by this commit.
+
+if git rev-parse --verify HEAD > /dev/null 2>&1
+then
+    against=HEAD
+else
+    # Initial commit: diff against an empty tree object
+    against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# called manually with arguments for the files/directories to be tested?
+if [ "$#" -gt 0 ]
+then
+    case "$1" in
+    -h | -help)
+        die "interactive usage: supply list of files/directories to check"
+        ;;
+    esac
+
+    # obtain list of all specified files/directories
+    fileList=$(git ls-files -- $@ 2>/dev/null)
+else
+    # list of all files to be committed
+    fileList=$(git diff-index --cached --name-only $against --)
+fi
+
+#
+# no files changed: can skip all the checks
+# this usage can correspond to a 'git commit --amend'
+#
+[ -n "$fileList" ] || exit 0
+
+
+unset badFiles
+# join list of files with this amount of space
+Indent="    "
+
+#
+# report bad files and die if there are any
+#
+dieOnBadFiles()
+{
+    if [ -n "$badFiles" ]
+    then
+        echo "$hookName hook failure" 1>&2
+        echo '-----------------------------------' 1>&2
+        echo "$@" 1>&2
+        echo '' 1>&2
+        echo "File(s):" 1>&2
+        echo "$badFiles" 1>&2
+        echo ''  1>&2
+        exit 1
+    fi
+}
+
+
+#
+# qualify 'git grep' to check cached value or from a specific commit
+#
+gitScope()
+{
+    if [ "$#" -gt 0 ]
+    then
+        echo "$1:"
+    else
+        echo "--cached -- "
+    fi
+}
+
+
+#
+# check for bad strings, characters, etc
+#
+checkIllegalCode()
+{
+    echo "$hookName: check bad strings/characters etc ..." 1>&2
+
+    reBad="("$'\t'")"
+    msgBad="<TAB>"
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        case "$f" in
+        # exclude potential makefiles
+        (*[Mm]akefile* | wmake/rules/* | *.f* | *.v[cf]proj | *.pdf | *.png | *.html | *.gif | *.css | *.gz)
+        ;;
+        (*)
+            fileType=`file -b $f`
+            if [ "$fileType" != "data" ]
+            then
+                # parse line numbers from grep output:
+                #        <lineNr>:   contents
+                lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
+                    sed -e 's@:.*@@' |
+                    tr '\n' ' '
+                )
+                [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+            fi
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Remove/correct bad '$msgBad' references"
+}
+
+
+#
+# limit line length to 80-columns
+#
+checkLineLength()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#
+# limit line length to 80-columns, except C++ comment lines
+#
+checkLineLengthNonComments()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' \
+                --and --not -e '^ *//' \
+                $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#
+# limit line length to 80-columns, except #directive lines
+#
+checkLineLengthNonDirective()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' \
+                --and --not -e '^ *#' \
+                $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#
+# check that OpenFOAM Foundation copyright is current
+#
+checkCopyright()
+{
+    year=$(date +%Y)
+    echo "$hookName: check copyright ..." 1>&2
+
+    badFiles=$(
+    for f in $fileList
+    do
+        startYear=`grep "Copyright.*OpenFOAM" $f | sed 's/[^0-9]*\([0-9]*\).*/\1/g'`
+        endYear=`grep "Copyright.*-.*OpenFOAM" $f | sed 's/[^-]*-\([0-9]*\).*/\1/g'`
+        #echo "startYear=$startYear endYear=$endYear"
+        if [ "$startYear" != "" ]
+        then
+            if [ "$endYear" != "" ]
+            then
+                # Date is of type 2011-2012 OpenFOAM Foundation
+                if [ "$year" != "$endYear" ]
+                then
+                    echo "Updated copyright for: $f" 1>&2
+                    echo "$f"
+                    sed -i "s/$startYear-$endYear OpenFOAM/$startYear-$year OpenFOAM/g" $f
+                fi
+            else
+                # Date is of type 2011 OpenFOAM Foundation
+                if [ "$year" != "$startYear" ]
+                then
+                    echo "$f"
+                    echo "Updated copyright for: $f" 1>&2
+                    sed -i "s/$startYear OpenFOAM/$startYear-$year OpenFOAM/g" $f
+                fi
+            fi
+        fi
+    done
+    )
+
+    dieOnBadFiles "Some copyright dates were automatically updated; Please check these before pushing"
+}
+
+
+#------------------------------------------------------------------------------
+# Main code : do all checks
+#
+
+# builtin whitespace check to avoid trailing space, including CR-LF endings
+bad=$(git diff-index --cached --check $against --) || die "$bad"
+
+# check for illegal code, e.g. <TAB>, etc
+checkIllegalCode
+
+# ensure code conforms to 80 columns max
+checkLineLengthNonDirective
+
+checkCopyright
+
+exit 0
+#------------------------------------------------------------------------------

bin/tools/pre-receive-hook

@@ -0,0 +1,272 @@
+#!/bin/bash
+#---------------------------------*- sh -*-------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+#    \\/     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/>.
+#
+# Script
+#     pre-receive-hook
+#
+# Description
+#     pre-receive hook for git.
+#     Copy or link this file as ".git/hooks/pre-receive"
+#
+#     Eg,
+#     (
+#         cd $WM_PROJECT_DIR/.git/hooks &&
+#         ln -sf ../../bin/tools/pre-receive-hook pre-receive
+#     )
+#
+#     Hook receives: <old-sha1> <new-sha1> <ref-name>
+#
+#     Checks for
+#     - illegal code, e.g. <TAB>
+#     - columns greater than 80 for *.[CH] files
+#
+#------------------------------------------------------------------------------
+hookName="pre-receive"
+die()
+{
+    echo "$hookName hook failure" 1>&2
+    echo '-----------------------------------' 1>&2
+    echo '' 1>&2
+    echo "$@" 1>&2
+    echo '' 1>&2
+    exit 1
+}
+
+#-----------------------------------------------------------------------------
+
+unset fileList
+unset badFiles
+# join list of files with this amount of space
+Indent="    "
+
+#
+# report bad files and die if there are any
+#
+dieOnBadFiles()
+{
+    if [ -n "$badFiles" ]
+    then
+        echo "$hookName hook failure" 1>&2
+        echo '-----------------------------------' 1>&2
+        echo "$@" 1>&2
+        echo '' 1>&2
+        echo "File(s):" 1>&2
+        echo "$badFiles" 1>&2
+        echo ''  1>&2
+        exit 1
+    fi
+}
+
+
+#
+# qualify 'git grep' to check cached value or from a specific commit
+#
+gitScope()
+{
+    if [ "$#" -gt 0 ]
+    then
+        echo "$1:"
+    else
+        echo "--cached -- "
+    fi
+}
+
+
+#
+# check for bad strings, characters, etc
+#
+checkIllegalCode()
+{
+    echo "$hookName: check bad strings/characters etc ..." 1>&2
+
+    reBad="("$'\t'"|"$'\r\n'")"
+    msgBad="<TAB> or DOS-line-endings"
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        case "$f" in
+        # exclude potential makefiles
+        (*[Mm]akefile* | wmake/rules/*)
+        ;;
+        (*)
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Remove/correct bad '$msgBad' references"
+}
+
+
+#
+# limit line length to 80-columns
+#
+checkLineLength()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#
+# limit line length to 80-columns, except C++ comment lines
+#
+checkLineLengthNonComments()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' \
+                --and --not -e '^ *//' \
+                $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#
+# limit line length to 80-columns, except #directive lines
+#
+checkLineLengthNonDirective()
+{
+    echo "$hookName: check line lengths ..." 1>&2
+
+    scope=$(gitScope $@)
+
+    badFiles=$(
+    for f in $fileList
+    do
+        # limit to *.[CH] files
+        case "$f" in
+        (*.[CH])
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -hn -e '^.\{81,\}' \
+                --and --not -e '^ *#' \
+                $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
+    done
+    )
+
+    dieOnBadFiles "Limit code to 80 columns before pushing"
+}
+
+
+#------------------------------------------------------------------------------
+# Main code : do all checks
+#
+
+while read oldSHA1 newSHA1 refName
+do
+    unset fileList rawFileList
+
+    if [ "$newSHA1" = 0 ]
+    then
+        # ref to be deleted
+        continue
+    elif [ "$oldSHA1" = 0 ]
+    then
+        # ref to be created
+        rawFileList=$(git diff-tree --root $newSHA1)
+    else
+        # normal changes
+        rawFileList=$(git diff --name-only $oldSHA1..$newSHA1)
+    fi
+
+    #
+    # no files changed: can skip all the checks
+    #
+    [ -n "$rawFileList" ] || continue
+
+    fileList=$(
+    for f in $rawFileList
+    do
+        git cat-file -e $newSHA1:$f > /dev/null 2>&1 && echo "$f"
+    done
+    )
+
+    # check for illegal code, e.g. <TAB>, etc
+    checkIllegalCode $newSHA1
+
+    # ensure code conforms to 80 columns max
+    checkLineLengthNonDirective $newSHA1
+
+done
+
+
+exit 0
+#------------------------------------------------------------------------------

bin/tools/replaceAllShellSun

@@ -0,0 +1,17 @@
+#!/usr/xpg4/bin/sh
+
+# Replace all shell script headers with 
+if [ $# -ne 1 -o ! -d "$1" ]
+then
+    echo "Usage: ${0##*/} <dir>"
+    echo ""
+    echo "Replaces all occurrences of #!/bin/sh with #!/usr/xpg4/bin/sh inside a directory tree."
+    exit 1
+fi
+
+#- note that below does not work since {} does not get replaced
+#find $1 -type f -exec /usr/xpg4/bin/sh -c "grep '^#\!/bin/sh' {} >/dev/null && echo {} && mv {} {}_bak && sed -e 's@^#\!/bin/sh@#\!/usr/xpg4/bin/sh@' {}_bak > {}" ';'
+
+find $1 -exec $WM_PROJECT_DIR/bin/tools/inlineReplace '^#\!/bin/sh' '#\!/usr/xpg4/bin/sh' {} \; -print
+
+# ----------------------------------------------------------------- end-of-file

bin/tools/scanpackages

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# Generate Packages file on debian repositories.
+
+for D in `find . -mindepth 4 -type d`
+do
+    dpkg-scanpackages $D | gzip -9c > ${D}/Packages.gz
+done