Merge branch 'master' of ssh://noisy/home/noisy2/OpenFOAM/OpenFOAM-dev

applications/utilities/postProcessing/stressField/stressComponents/stressComponents.C

@@ -23,10 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    turbFoam
+    stressComponents
 
 Description
-    Calculates and writes the scalar fields of the six components of the stress 
+    Calculates and writes the scalar fields of the six components of the stress
     tensor sigma for each time.
 
 \*---------------------------------------------------------------------------*/

bin/doxyFilt

@@ -29,9 +29,12 @@
 # Description
 #     pass-through filter for doxygen
 #
-#     Filter has special treatment for applications/{solvers,utilities}/*.C
-#       - only keep the first comment block of the C source file
-#       - the corresponding H files are ignored in Doxyfile EXCLUDE_PATTERNS
+#     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 [ "$#" -gt 0 ]
@@ -41,16 +44,19 @@ then
    dirName=${filePath%/[^/]*}
    fileName=${filePath##*/}
 
-   awkScript=$WM_PROJECT_DIR/bin/doxyAwk
+   awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilt.awk
 
    case "$1" in
    */applications/solvers/*.C | */applications/utilities/*.C )
-      awkScript=$WM_PROJECT_DIR/bin/doxyAwkTop
+      awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilt-top.awk
+      ;;
+   */applications/solvers/*.H | */applications/utilities/*.H )
+      awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilt-ignore.awk
       ;;
    esac
 
    awk -f $awkScript $1 | \
-   sed -f $WM_PROJECT_DIR/bin/doxyScr \
+   sed -f $WM_PROJECT_DIR/bin/tools/doxyFilt.sed \
        -e s@%filePath%@$filePath@g \
        -e s@%fileName%@$fileName@g \
        -e s@%dirName%@$dirName@g

bin/doxyAwkTop → bin/tools/doxyFilt-ignore.awk

@@ -4,7 +4,7 @@
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
 #    \\/     M anipulation  |
-# ------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
 #
@@ -23,41 +23,23 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     doxyAwkTop
+#     doxyFilt-ignore.awk
 #
 # Description
-#     Output only the first /* ... */ comment section found in the file
-#       - This is useful for application files in which only the first
-#         block documents the application itself and all other files simply
-#         pollute our documentation
+#     - 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 {
-    state = 0
-}
-
-# a '/*' at the beginning of a line starts a block
-/^ *\/\*/ {
-    state++
+   print "//! @file %filePath%"
+   print "//! @cond OpenFOAMIgnoreAppDoxygen"
 }
 
-# a '*/' ends the block
-/\*\// {
-    if (state == 1)
-    {
-        print
-    }
-    state = 2
-    next
+{ print }
+        
+END {
+   print "//! @endcond OpenFOAMIgnoreAppDoxygen"
 }
-
-# end block
-{
-    if (state == 1)
-    {
-        print
-    }
-    next
-}
-
 # -----------------------------------------------------------------------------

tutorials/runAll → bin/tools/doxyFilt-top.awk

-#!/bin/sh
-#------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
@@ -24,50 +23,60 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     runAll
+#     doxyFilt-top.awk
 #
 # Description
-#       Run either Allrun or blockMesh/application in current directory
-#       and all its subdirectories.
+#     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
+}
 
-unset WM_COLOURS
+# a '/*' at the beginning of a line starts a comment block
+/^ *\/\*/ {
+   state++
+}
 
-tutorialsDir=$PWD
-while [ ! -f $tutorialsDir/RunFunctions ]
-do
-    tutorialsDir="$tutorialsDir/.."
-done
-. $tutorialsDir/RunFunctions
+# check first line
+# either started with a comment or skip documentation for the whole file
+FNR == 1 {
+   if (!state)
+   {
+      print "//! @cond OpenFOAMIgnoreAppDoxygen"
+      state = 2
+   }
+}
 
-thisScript=$0
-if [ "/${thisScript#/}" != "$thisScript" ]
-then
-    thisScript="$PWD/$thisScript"
-fi
+# a '*/' ends the comment block
+# skip documentation for rest of the file
+/\*\// {
+    if (state == 1)
+    {
+        print
+        print "//! @cond OpenFOAMIgnoreAppDoxygen"
+    }
+    state = 2
+    next
+}
 
-if [ -f "./Allrun" ] 
-then
-    # Specialised script.
-    ./Allrun
-elif [ -d "./system" ]
-then
-    # Normal case. 
-    parentDir=`dirname $PWD`
-    application=`basename $parentDir`
-    runApplication blockMesh
-    runApplication $application
-else
-    # Recurse to subdirectories
-    for case in *
-    do
-        if [ -d $case ]
-        then
-            #(cd $case && $thisScript)
-            $WM_SCHEDULER "cd $PWD/$case && $thisScript"
-        fi
-    done
-fi
+# print everything within the first comment block
+{
+    if (state)
+    {
+        print
+    }
+    next
+}
 
-#------------------------------------------------------------------------------
+END {
+    if (state == 2)
+    {
+        print "//! @endcond OpenFOAMIgnoreAppDoxygen"
+    }
+}
+
+# -----------------------------------------------------------------------------

bin/doxyAwk → bin/tools/doxyFilt.awk

@@ -4,7 +4,7 @@
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
 #    \\/     M anipulation  |
-# ------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
 #
@@ -23,23 +23,23 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     doxyAwk
+#     doxyFilt.awk
 #
 # Description
 #     Converts cocoon style sentinel strings into doxygen style strings
 #
-#     - assume the 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
+#     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 {
@@ -55,14 +55,14 @@ BEGIN {
 
 
 /^ *\/\// {
-    # start block
+    # start comment block
     if (state == 1)
     {
         printf "/*!\n"
         state = 2
     }
 
-    # inside block
+    # inside comment block
     if (state == 2)
     {
         if (!sub(/^ *\/\/  /, ""))
@@ -77,7 +77,7 @@ BEGIN {
 
 
 {
-    # end block
+    # end comment block
     if (state == 2)
     {
         printf "*/\n"

bin/doxyScr → bin/tools/doxyFilt.sed

+# -----------------------------------------------------------------------------
+# Script
+#     doxyFilt.sed
+#
+# Description
+#     Transform human-readable tags such as 'Description' into the Doxygen
+#     equivalent
+# -----------------------------------------------------------------------------
+
 /^License/,/\*\//{
 /^License/,/MA 0211.-130. USA/{
 s?^License.*?\*\/\
@@ -141,3 +150,5 @@ s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?
 s/.*\*\//\*\//
 
 }
+
+# -----------------------------------------------------------------------------

doc/Doxygen/Doxyfile

@@ -522,9 +522,7 @@ EXCLUDE_SYMLINKS       = NO
 # for example use the pattern */test/*
 
 EXCLUDE_PATTERNS       = */lnInclude/*  \
-                         */t/* \
-                         */applications/utilities/*.H \
-                         */applications/solvers/*.H
+                         */t/*
 
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names

etc/controlDict

@@ -16,44 +16,6 @@ FoamFile
 // NB: the #functions do not work here
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-hosts
-(
-);
-
-caseRoots
-(
-    "."
-    "$FOAM_RUN/tutorials/bubbleFoam"
-    "$FOAM_RUN/tutorials/buoyantFoam"
-    "$FOAM_RUN/tutorials/buoyantSimpleFoam"
-    "$FOAM_RUN/tutorials/channelOodles"
-    "$FOAM_RUN/tutorials/coodles"
-    "$FOAM_RUN/tutorials/dnsFoam"
-    "$FOAM_RUN/tutorials/electrostaticFoam"
-    "$FOAM_RUN/tutorials/engineFoam"
-    "$FOAM_RUN/tutorials/icoFoam"
-    "$FOAM_RUN/tutorials/interFoam"
-    "$FOAM_RUN/tutorials/laplacianFoam"
-    "$FOAM_RUN/tutorials/lesInterFoam"
-    "$FOAM_RUN/tutorials/mhdFoam"
-    "$FOAM_RUN/tutorials/oodles"
-    "$FOAM_RUN/tutorials/potentialFoam"
-    "$FOAM_RUN/tutorials/rasInterFoam"
-    "$FOAM_RUN/tutorials/rhoSonicFoam"
-    "$FOAM_RUN/tutorials/rhoTurbFoam"
-    "$FOAM_RUN/tutorials/scalarTransportFoam"
-    "$FOAM_RUN/tutorials/settlingFoam"
-    "$FOAM_RUN/tutorials/simpleFoam"
-    "$FOAM_RUN/tutorials/solidDisplacementFoam"
-    "$FOAM_RUN/tutorials/sonicFoam"
-    "$FOAM_RUN/tutorials/sonicLiquidFoam"
-    "$FOAM_RUN/tutorials/sonicTurbFoam"
-    "$FOAM_RUN/tutorials/turbFoam"
-    "$FOAM_RUN/tutorials/twoPhaseEulerFoam"
-    "$FOAM_RUN/tutorials/XiFoam"
-    "$FOAM_RUN/tutorials/Xoodles"
-);
-
 Documentation
 {
     docBrowser      "kde-open %f";

src/OpenFOAM/primitives/Tensor/TensorI.H

@@ -719,7 +719,7 @@ operator+(const Tensor<Cmpt>& t1, const SymmTensor<Cmpt>& st2)
     return Tensor<Cmpt>
     (
         t1.xx() + st2.xx(), t1.xy() + st2.xy(), t1.xz() + st2.xz(),
-        t1.yx() + st2.xy(), t1.yy() + st2.yy(), t1.yz() + st2.yy(),
+        t1.yx() + st2.xy(), t1.yy() + st2.yy(), t1.yz() + st2.yz(),
         t1.zx() + st2.xz(), t1.zy() + st2.yz(), t1.zz() + st2.zz()
     );
 }
@@ -745,7 +745,7 @@ operator-(const Tensor<Cmpt>& t1, const SymmTensor<Cmpt>& st2)
     return Tensor<Cmpt>
     (
         t1.xx() - st2.xx(), t1.xy() - st2.xy(), t1.xz() - st2.xz(),
-        t1.yx() - st2.xy(), t1.yy() - st2.yy(), t1.yz() - st2.yy(),
+        t1.yx() - st2.xy(), t1.yy() - st2.yy(), t1.yz() - st2.yz(),
         t1.zx() - st2.xz(), t1.zy() - st2.yz(), t1.zz() - st2.zz()
     );
 }

tutorials/Allclean

-#!/bin/sh
-#------------------------------------------------------------------------------
-# =========                 |
-# \\      /  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
-#     Allclean
-#
-# Description
-#     
-#------------------------------------------------------------------------------
-
-. ./CleanFunctions
-
-echo "Cleaning backup files"
-find . -type f \( -name "*~" -o -name "*.bak" \) -exec rm {} \; 
-find . \( -name 'core' -o -name 'core.[1-9]*' \) -exec rm {} \;
-find . \( -name '*.pvs' -o -name '*.foam' \) -exec rm {} \;
-rm logs > /dev/null 2>&1
-rm testLoopReport > /dev/null 2>&1
-
-echo ""
-
-for application in *
-do
-    if [ -d $application ]
-    then
-        (cd $application && ../cleanAll)
-    fi
-done
-
-#------------------------------------------------------------------------------

tutorials/Allrun

-#!/bin/sh
-#------------------------------------------------------------------------------
-# =========                 |
-# \\      /  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
-#     Allrun
-#
-# Description
-#     
-#------------------------------------------------------------------------------
-
-. RunFunctions
-
-
-# logReport <logfile>
-# Extracts useful info from log file.
-logReport () {
-    case=`dirname $1 | sed s/"\(.*\)\.\/"/""/g`
-    app=`echo $1 | sed s/"\(.*\)\."/""/g`
-    appAndCase="Application $app - case $case"
-
-    fatalError=`grep "FOAM FATAL" $1`
-    UxSS=`grep -E "Ux[:| ]*solution singularity" $1`
-    UySS=`grep -E "Uy[:| ]*solution singularity" $1`
-    UzSS=`grep -E "Uz[:| ]*solution singularity" $1`
-    completed=`grep -E "^[\t ]*[eE]nd" $1`
-
-    if [ "$fatalError" ] ; then
-        echo "$appAndCase: ** FOAM FATAL ERROR **"
-        return
-    elif [ "$UxSS" -a "$UySS" -a "$UzSS" ] ; then
-        echo "$appAndCase: ** Solution singularity **"
-        return
-    elif [ "$completed" ] ; then
-        completionTime=`tail -10 $log | grep Execution | cut -d= -f2 | sed 's/^[ \t]*//'` 
-        if [ "$completionTime" ] ; then
-            completionTime="in $completionTime"
-        fi
-        echo "$appAndCase: completed $completionTime"
-        return
-    else
-        echo "$appAndCase: unconfirmed completion"
-    fi
-}
-
-
-# Recursively run all tutorials
-for application in *
-do
-    if [ -d $application ]
-    then
-        #(cd $application && ../runAll)
-        $WM_SCHEDULER "cd $PWD/$application && ../runAll"
-    fi
-done
-
-# Analyse all log files
-rm testLoopReport > /dev/null 2>&1 &
-touch testLoopReport
-for application in *
-do
-    if [ -d $application ]
-    then
-        cd $application
-        for log in `find . -name "log.*" | xargs ls -rt`
-        do
-            logReport $log >> ../testLoopReport
-        done
-        echo "" >> ../testLoopReport
-        cd ..
-    fi
-done
-
-find . -name "log.*" -exec cat {} \; >> logs
-
-#------------------------------------------------------------------------------

tutorials/Alltest

-#!/bin/sh
-
-#
-# FUNCTIONS
-#
-printUsage () {
-cat <<EOF
-Usage: $0
-Quickly tests the tutorials and writes out the scheme/solver information
-
-Options are:
--d         sets up a default scheme on all schemes
--h         help
-EOF
-}
-
-newRunApplication () {
-cat<<EOF
-runApplication ()
-{
-    if [ -f \$2/log.\$1 ] ; then
-        echo "$1 already run on $2: remove log file to run"
-    else
-        mv \$2/system/controlDict \$2/system/controlDict.org
-        sed \\
-        -e s/"\(startFrom[ \t]*\)\([0-9a-zA-Z.-]*\);"/"\1 latestTime;"/g \\
-        -e s/"\(stopAt[ \t]*\)\([a-zA-Z]*\);"/"\1 nextWrite;"/g \\
-        -e s/"\(writeControl[ \t]*\)\([a-zA-Z]*\);"/"\1 timeStep;"/g \\
-        -e s/"\(writeInterval[ \t]*\)\([0-9a-zA-Z.-]*\);"/"\1 1;"/g \\
-        \$2/system/controlDict.org > \$2/system/controlDict
-        echo "Running \$1 on \$2"
-        \$1 . \$2 > \$2/log.\$1 2>&1
-    fi
-}
-EOF
-}
-
-setDefaultFvSchemes () {
-cat<<EOF
-gradSchemes { default Gauss linear; }
-divSchemes 
-{ 
-    default Gauss linear;
-    div(phi,fu_ft_h) Gauss multivariateSelection
-    {
-        fu upwind;
-        ft upwind;
-        h  upwind;
-    };
-    div(phi,ft_b_h_hu) Gauss multivariateSelection
-    {
-        fu upwind;
-        ft upwind;
-        b  upwind;
-        h  upwind;
-        hu upwind;
-    };    
-}
-laplacianSchemes { default Gauss linear corrected; }
-interpolationSchemes { default linear; }
-snGradSchemes { default corrected; }
-fluxRequired { default yes; }
-EOF
-}
-#
-# VARIABLE
-#
-MAIN_CONTROL_DICT=
-: ${FOAM_DOT_DIR:=.$WM_PROJECT-$WM_PROJECT_VERSION}
-
-for i in \
-  $HOME/$FOAM_DOT_DIR \
-  $HOME/.$WM_PROJECT/$WM_PROJECT_VERSION \
-  $HOME/.$WM_PROJECT \
-  $WM_PROJECT_DIR/etc \
-  $WM_PROJECT_DIR/$FOAM_DOT_DIR \
-  ;
-do
-  if [ -f "$i/controlDict" ]; then
-     MAIN_CONTROL_DICT="$i/controlDict"
-     break
-  fi
-done
-TUTORIALS_DIR=.
-TEST_RUN_DIR=../tutorialsTest
-FV_SCHEMES=\
-" \
-    gradScheme \
-    divScheme \
-    laplacianScheme \
-    interpolationScheme \
-    snGradScheme \
-    fluxRequired \
-"
-SCHEMES_FILE="FvSchemes"
-SCHEMES_TEMP="FvSchemes.temp"
-SOLVERS_FILE="FvSolution"
-SOLVERS_TEMP="FvSolution.temp"
-DEFAULT_SCHEMES=0
-
-#