GIT: Initial state after latest Foundation merge

bin/tools/CleanFunctions

@@ -26,22 +26,9 @@
 #
 # 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"
@@ -59,9 +46,6 @@ cleanTimeDirectories()
 }
 
 
-#
-# Remove dynamicCode subdirectory if it looks appropriate
-#
 cleanDynamicCode()
 {
     if [ -d system -a -d dynamicCode ]
@@ -105,6 +89,7 @@ cleanCase()
 
     rm -rf processor* > /dev/null 2>&1
     rm -rf postProcessing > /dev/null 2>&1
+    rm -rf TDAC > /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
@@ -148,22 +133,26 @@ cleanCase()
     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"

bin/tools/RunFunctions

@@ -41,10 +41,7 @@ isTest()
 
 getNumberOfProcessors()
 {
-    if [ -f "$1" ]
-    then
-        expandDictionary $1 | sed -ne 's/^numberOfSubdomains\s*\(.*\);/\1/p'
-    fi
+    foamDictionary -entry numberOfSubdomains -value system/decomposeParDict
 }
 
 getApplication()

bin/tools/doxyFilter

@@ -3,7 +3,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -47,7 +47,6 @@ then
         filePath=$realFilePath
     fi
 
-    # dirName=$(echo "$filePath" | sed -e 's@/[^/]*$@@' )
     dirName=${filePath%/[^/]*}
     fileName=${filePath##*/}
 
@@ -57,9 +56,6 @@ then
     */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 $1 | \
@@ -70,4 +66,5 @@ then
         -e s@%fileName%@$fileName@g \
         -e s@%dirName%@$dirName@g
 fi
+
 #------------------------------------------------------------------------------

bin/tools/doxyFilter-ignore.awk

@@ -31,6 +31,7 @@
 #       to skip documenting all classes/variables
 #
 #------------------------------------------------------------------------------
+
 BEGIN {
    print "//! @file %filePath%"
    print "//! @cond OpenFOAMIgnoreAppDoxygen"
@@ -41,4 +42,5 @@ BEGIN {
 END {
    print "//! @endcond"
 }
+
 #------------------------------------------------------------------------------

bin/tools/doxyFilter-table.awk

@@ -131,5 +131,3 @@ BEGIN {
         print $0
     }
 }
-
-

bin/tools/doxyFilter-top.awk

@@ -31,16 +31,17 @@
 #       block documents the application itself.
 #
 #------------------------------------------------------------------------------
+
 BEGIN {
     state = 0
 }
 
-# a '/*' at the beginning of a line starts a comment block
+# A '/*' at the beginning of a line starts a comment block
 /^ *\/\*/ {
    state++
 }
 
-# check first line
+# Check first line
 # either started with a comment or skip documentation for the whole file
 FNR == 1 {
    if (!state)
@@ -50,7 +51,7 @@ FNR == 1 {
    }
 }
 
-# a '*/' ends the comment block
+# A '*/' ends the comment block
 # skip documentation for rest of the file
 /\*\// {
     if (state == 1)
@@ -62,7 +63,7 @@ FNR == 1 {
     next
 }
 
-# print everything within the first comment block
+# Print everything within the first comment block
 {
     if (state)
     {

bin/tools/doxyFilter.awk

@@ -52,16 +52,15 @@ BEGIN {
     next
 }
 
-
 /^ *\/\// {
-    # start comment block
+    # Start comment block
     if (state == 1)
     {
         printf "/*! "
         state = 2
     }
 
-    # inside comment block
+    # Inside comment block
     if (state == 2)
     {
         if (!sub(/^ *\/\/  /, ""))
@@ -74,9 +73,8 @@ BEGIN {
     next
 }
 
-
 {
-    # end comment block
+    # End comment block
     if (state == 2)
     {
         printf "*/ "

bin/tools/doxyFilter.sed

@@ -7,7 +7,7 @@
 #     equivalent
 #------------------------------------------------------------------------------
 
-# new FSF address
+# New FSF address
 /^License/,/\*\//{
 /^License/,\%http://www.gnu.org/licenses%{
 s?^License.*?\*\/\
@@ -26,7 +26,7 @@ s?^License.*?\*\/\
 }
 
 
-# remove entry
+# Remove entry
 /^Application *$/{
 N
 N
@@ -34,7 +34,7 @@ d
 }
 
 
-# remove entry
+# Remove entry
 /^Global *$/{
 N
 N
@@ -79,7 +79,7 @@ s/Class *\n *\(.*\) */\\class \1/
 # Group
 #     groupName
 # =>
-# \ingroup namespaceName
+# \ingroup groupName
 #
 /^Group *$/,/^[^ ]/{
 s/^Group//
@@ -108,7 +108,7 @@ s/^    /\\typedef /
 }
 
 
-# add anchor and use \brief
+# Add anchor and use \brief
 # the first paragraph will be 'brief' and the others 'detail'
 /^Description *$/,/^[^ ]/{
 /^Description/c\
@@ -123,8 +123,8 @@ s/^    //
 }
 
 
-/^See *Also *$/,/^[^ ]/{
-/^See *Also/c\
+/^See *[Aa]lso *$/,/^[^ ]/{
+/^See *[Aa]lso/c\
 \\see
 s/^    //
 }
@@ -136,13 +136,6 @@ s/^    //
 }
 
 
-# remove ToDo paragraph to avoid them showing on related pages
-/^To[Dd]o *$/,/^[^ ]/{
-s/^To[Dd]o *$//
-s/^    .*//
-}
-
-
 /^Warning *$/,/^[^ ]/{
 /^Warning/c\
 \\warning
@@ -150,13 +143,6 @@ s/^    //
 }
 
 
-/^Deprecated *$/,/^[^ ]/{
-/^Deprecated/c\
-\\deprecated
-s/^    //
-}
-
-
 /^SourceFiles *$/,/^$/{
 s?SourceFiles?\\par Source files\
 <ul><li><a href="%filePath%">%fileName%</a></li>?
@@ -164,6 +150,7 @@ 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
@@ -174,12 +161,13 @@ 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><br>#g
+# 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

@@ -79,10 +79,10 @@ _inlineSed()
 
 [ -f etc/bashrc ] || usage "Please run from top-level directory of installation"
 
-unset foamInstall projectName projectVersion archOption
+unset foamInstDir projectName projectVersion archOption
 unset paraviewInstall scotchArchPath
 
-# parse options
+# Parse options
 while [ "$#" -gt 0 ]
 do
     case "$1" in
@@ -91,13 +91,18 @@ do
         ;;
     -foamInstall | --foamInstall)
         [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
-        foamInstall="$2"
-        # replace foamInstall=...
+        foamInstDir="$2"
+        # Replace FOAM_INST_DIR=...
         _inlineSed \
             etc/bashrc \
-            'foamInstall=.*' \
-            'foamInstall='"$foamInstall" \
-            "Replacing foamInstall setting by '$foamInstall'"
+            '\(.*BASH_SOURCE.*\)' \
+            '#\1' \
+            "Removing default FOAM_INST_DIR setting"
+        _inlineSed \
+            etc/bashrc \
+            '^export FOAM_INST_DIR=.*' \
+            'export FOAM_INST_DIR='"$foamInstDir" \
+            "Setting FOAM_INST_DIR to '$foamInstDir'"
         shift 2
         ;;
    -projectName | --projectName)
@@ -189,7 +194,7 @@ do
     esac
 done
 
-[ -n "$foamInstall" -o -n "$projectName" -o -n "$projectVersion" -o -n "$archOption" \
+[ -n "$foamInstDir" -o -n "$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"

bin/tools/foamListSourceFiles

@@ -63,7 +63,6 @@ find -H $packDir                                                               \
    \( -type f -o -type l \)                                                    \
     ! -name "*~"                                                               \
  -a ! -name ".*~"                                                              \
- -a ! -name "*.orig"                                                           \
  -a ! -name "*.dep"                                                            \
  -a ! -name "*.o"                                                              \
  -a ! -name "*.so"                                                             \