Doxygen docs: Corrected doxyFilter to preserve line numbers

Also corrected many formatting errors in the comments in C and H files

applications/solvers/multiphase/interPhaseChangeFoam/phaseChangeTwoPhaseMixtures/Kunz/Kunz.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -39,7 +39,7 @@ Description
          to Cavitation Prediction,”
         Computers and Fluids,
         29(8):849-875, 2000.
-    @verbatim
+    @endverbatim
 
 SourceFiles
     Kunz.C

applications/solvers/multiphase/interPhaseChangeFoam/phaseChangeTwoPhaseMixtures/Merkle/Merkle.H

@@ -2,7 +2,7 @@
   ========Merkle=                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -33,7 +33,7 @@ Description
         "Computational modeling of the dynamics of sheet cavitation",
         in Proceedings Third International Symposium on Cavitation
         Grenoble, France 1998.
-   @verbatim
+   @endverbatim
 
 SourceFiles
     Merkle.C

applications/solvers/multiphase/interPhaseChangeFoam/phaseChangeTwoPhaseMixtures/SchnerrSauer/SchnerrSauer.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -33,7 +33,7 @@ Description
         "Physical and Numerical Modeling of Unsteady Cavitation Dynamics",
         Proc. 4th International Conference on Multiphase Flow,
         New Orleans, U.S.A., 2001.
-    @verbatim
+    @endverbatim
 
 SourceFiles
     SchnerrSauer.C

applications/utilities/mesh/generation/extrude/extrudeToRegionMesh/extrudeToRegionMesh.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -30,9 +30,9 @@ Description
         - create baffles in original mesh with directMappedWall patches
     - if extruding boundary faces:
         - convert boundary faces to directMappedWall patches
-    - extrude edges of faceZone as a <zone>_sidePatch
+    - extrude edges of faceZone as a \<zone\>_sidePatch
     - extrude edges inbetween different faceZones as a
-      (nonuniformTransform)cyclic <zoneA>_<zoneB>
+      (nonuniformTransform)cyclic \<zoneA\>_\<zoneB\>
     - extrudes into master direction (i.e. away from the owner cell
       if flipMap is false)
     - not parallel
@@ -106,7 +106,7 @@ becomes
 
 Usage
 
-    - extrudeToRegionMesh <regionName> <faceZones> <thickness>
+    - extrudeToRegionMesh \<regionName\> \<faceZones\> \<thickness\>
 
     @param \<regionName\> \n
     Name of mesh to create.

bin/tools/doxyFilter

@@ -3,7 +3,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+#   \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
 #    \\/     M anipulation  |
 #-------------------------------------------------------------------------------
 # License
@@ -52,7 +52,7 @@ then
 #    */applications/solvers/*.H | */applications/utilities/*.H )
 #        awkScript=$WM_PROJECT_DIR/bin/tools/doxyFilter-ignore.awk
 #        ;;
-   esac
+    esac
 
     awk -f $awkScript $1 | \
     sed -f $WM_PROJECT_DIR/bin/tools/doxyFilter.sed \

bin/tools/doxyFilter.awk

@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+#   \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
 #    \\/     M anipulation  |
 # -----------------------------------------------------------------------------
 # License
@@ -57,7 +57,7 @@ BEGIN {
     # start comment block
     if (state == 1)
     {
-        printf "/*!\n"
+        printf "/*! "
         state = 2
     }
 
@@ -79,7 +79,7 @@ BEGIN {
     # end comment block
     if (state == 2)
     {
-        printf "*/\n"
+        printf "*/ "
     }
     state = 0
     print

bin/tools/doxyFilter.sed

@@ -11,147 +11,140 @@
 /^License/,/\*\//{
 /^License/,\%http://www.gnu.org/licenses%{
 s?^License.*?\*\/\
-\/\*! @file %filePath%\
+\/\*! \\file %filePath%\
 <b>Original source file</b> <a href="%filePath%">%fileName%</a>\
+\
+\
+\
+\
+\
+\
+\
+\
 ?
 /^    /d
 }
 
-# old FSF address
-/^License/,/MA 0211.-130. USA/{
-s?^License.*?\*\/\
-\/\*! @file %filePath%\
-<b>Original source file</b> <a href="%filePath%">%fileName%</a>\
-?
-/^    /d
-}
 
 # remove entry
-/^Primitive *$/{
+/^Application *$/{
 N
 N
 d
 }
 
-# remove entry
-/^Implementation *$/{
-N
-N
-d
-}
 
 # remove entry
-/^Application *$/{
+/^Global *$/{
 N
 N
 d
 }
 
-# remove entry
-/^Type *$/{
-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 Foam::className
 #
 /^Class *$/,/^[^ ]/{
-/^Class/d
-s/^    /@class /
+s/^Class *$//
+s/^    /\\class /
 }
 
 
 # Namespace
 #     namespaceName
 # =>
-# @namespace namespaceName
+# \namespace namespaceName
 #
 /^Namespace *$/,/^[^ ]/{
-/^Namespace/d
-s/^    /@namespace /
+s/^Namespace//
+s/^    /\\namespace /
 }
 
 
 # Typedef
 #     Foam::def
 # =>
-# @class Foam::def
-# This is not strictly correct, but makes it easier to find the typedefs
+# \typedef Foam::def
 /^Typedef *$/,/^[^ ]/{
-/^Typedef/d
-s/^    /@class /
+s/^Typedef//
+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\
-<a class="anchor" name="Description"></a>\
-@brief
+<a class="anchor" name="Description"></a> \\brief
 s/^    //
 }
 
 /^Usage *$/,/^[^ ]/{
 /^Usage/c\
-@par Usage
+\\par Usage
 s/^    //
 }
 
 
 /^See *Also *$/,/^[^ ]/{
 /^See *Also/c\
-@see
-s/^    //
-}
-
-/^Author *$/,/^[^ ]/{
-/^Author/c\
-@author
+\\see
 s/^    //
 }
 
 /^Note *$/,/^[^ ]/{
 /^Note/c\
-@note
+\\note
 s/^    //
 }
 
 
 # remove ToDo paragraph to avoid them showing on related pages
-/^To[Dd]o *$/,/^ *$/d
+/^To[Dd]o *$/,/^[^ ]/{
+s/^To[Dd]o *$//
+s/^    .*//
+}
 
 
 /^Warning *$/,/^[^ ]/{
 /^Warning/c\
-@warning
+\\warning
 s/^    //
 }
 
+
 /^Deprecated *$/,/^[^ ]/{
 /^Deprecated/c\
-@deprecated
+\\deprecated
 s/^    //
 }
 
-/SourceFiles/,/^[ ]*$/{
-s?SourceFiles?@par Source files\
-<ul>\
-  <li><a href="%filePath%">%fileName%</a></li>?
-s?^[ ]*$?</ul>\
-?
+
+/^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>?
 }
 

doc/Doxygen/Doxyfile

@@ -1104,7 +1104,7 @@ TAGFILES               =
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.
 
-GENERATE_TAGFILE       =
+GENERATE_TAGFILE       = DTAGS
 
 # If the ALLEXTERNALS tag is set to YES all external classes will be listed
 # in the class index. If set to NO only the inherited external classes
@@ -1254,7 +1254,7 @@ DOTFILE_DIRS           =
 # MAX_DOT_GRAPH_NOTES then the graph will not be shown at all. Also note
 # that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
 
-DOT_GRAPH_MAX_NODES    = 50
+DOT_GRAPH_MAX_NODES    = 10
 
 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
 # graphs generated by dot. A depth value of 3 means that only nodes reachable
@@ -1264,7 +1264,7 @@ DOT_GRAPH_MAX_NODES    = 50
 # code bases. Also note that the size of a graph can be further restricted by
 # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
 
-MAX_DOT_GRAPH_DEPTH    = 3
+MAX_DOT_GRAPH_DEPTH    = 1
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
 # background. This is disabled by default, which results in a white background.

doc/doxygen/Doxyfile

@@ -581,7 +581,8 @@ WARN_LOGFILE           =
 # limit input for testing purposes
 INPUT                  = $(WM_PROJECT_DIR)/src/OpenFOAM/global \
                          $(WM_PROJECT_DIR)/src/OpenFOAM/containers \
-                         $(WM_PROJECT_DIR)/src/OpenFOAM/primitives
+                         $(WM_PROJECT_DIR)/src/OpenFOAM/primitives \
+                         $(WM_PROJECT_DIR)/src/finiteVolume/fvMesh
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -1353,7 +1354,7 @@ TAGFILES               =
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.
 
-GENERATE_TAGFILE       =
+GENERATE_TAGFILE       = DTAGS
 
 # If the ALLEXTERNALS tag is set to YES all external classes will be listed
 # in the class index. If set to NO only the inherited external classes

src/OSspecific/POSIX/fileMonitor.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -109,8 +109,7 @@ namespace Foam
 
 
 
-    //! @cond internalClass
-    //- Internal tracking via stat(3p) or inotify(7)
+    //-  Internal tracking via stat(3p) or inotify(7)
     class fileMonitorWatcher
     {
     public:
@@ -140,7 +139,7 @@ namespace Foam
         {
             if (useInotify_)
             {
-#ifdef FOAM_USE_INOTIFY
+                #ifdef FOAM_USE_INOTIFY
                 inotifyFd_ = inotify_init();
                 dirWatches_.setCapacity(sz);
                 dirFiles_.setCapacity(sz);
@@ -167,13 +166,13 @@ namespace Foam
                             << endl;
                     }
                 }
-#else
+                #else
                     FatalErrorIn("fileMonitorWatcher(const bool, const label)")
                         << "You selected inotify but this file was compiled"
                         << " without FOAM_USE_INOTIFY"
                         << "Please select another fileModification test method"
                         << exit(FatalError);
-#endif
+                #endif
             }
             else
             {
@@ -184,7 +183,7 @@ namespace Foam
         //- remove all watches
         inline ~fileMonitorWatcher()
         {
-#ifdef FOAM_USE_INOTIFY
+            #ifdef FOAM_USE_INOTIFY
             if (useInotify_ && inotifyFd_ >= 0)
             {
                 forAll(dirWatches_, i)
@@ -200,7 +199,7 @@ namespace Foam
                     }
                 }
             }
-#endif
+            #endif
         }
 
         inline bool addWatch(const label watchFd, const fileName& fName)
@@ -212,7 +211,7 @@ namespace Foam
                     return false;
                 }
 
-#ifdef FOAM_USE_INOTIFY
+                #ifdef FOAM_USE_INOTIFY
                 // Add/retrieve watch on directory containing file.
                 // Note that fName might be non-existing in special situations
                 // (master-only reading for IODictionaries)
@@ -250,7 +249,7 @@ namespace Foam
 
                 dirWatches_(watchFd) = dirWatchID;
                 dirFiles_(watchFd) = fName.name();
-#endif
+                #endif
             }
             else
             {
@@ -288,7 +287,6 @@ namespace Foam
         }
 
     };
-    //! @endcond
 }
 
 
@@ -298,7 +296,7 @@ void Foam::fileMonitor::checkFiles() const
 {
     if (useInotify_)
     {
-#ifdef FOAM_USE_INOTIFY
+        #ifdef FOAM_USE_INOTIFY
         // Large buffer for lots of events
         char buffer[EVENT_BUF_LEN];
 
@@ -392,7 +390,7 @@ void Foam::fileMonitor::checkFiles() const
                 return;
             }
         }
-#endif
+        #endif
     }
     else
     {

src/OpenFOAM/db/runTimeSelection/globalFunctions/addToGlobalFunctionSelectionTable.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,7 +21,8 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-@file Foam::addToGlobalFunctionSelectionTable
+Global
+    Foam::addToGlobalFunctionSelectionTable
 
 Description
     Macros for easy insertion into global function selection tables
@@ -33,20 +34,18 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 // add to hash-table of functions with 'lookup' as the key
 #define addNamedToGlobalFunctionSelectionTable\
 (memberFunction,argNames,lookup,functionPtr)                                  \
                                                                               \
     /* Add to the table, find by lookup name */                               \
     add##memberFunction##argNames##GlobalMemberFunctionToTable                \
-    add_##lookup##_##memberFunction##argNames##GlobalMemberFunctionTo##Table_\
+    add_##lookup##_##memberFunction##argNames##GlobalMemberFunctionTo##Table_ \
     (#lookup, functionPtr)
 
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 #endif
 
 // ************************************************************************* //

src/OpenFOAM/db/runTimeSelection/globalFunctions/globalFunctionSelectionTables.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,7 +21,8 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-@file Foam::globalFunctionSelectionTables
+Global
+    Foam::globalFunctionSelectionTables
 
 Description
     Macros to enable the easy declaration of global function selection tables.
@@ -35,7 +36,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 // external use:
 // ~~~~~~~~~~~~~
 // declare a run-time selection:
@@ -138,7 +138,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 #endif
 
 // ************************************************************************* //

src/OpenFOAM/db/runTimeSelection/staticMemberFunctions/addToStaticMemberFunctionSelectionTable.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,7 +21,8 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-@file Foam::addToStaticMemberFunctionSelectionTable
+Global
+    Foam::addToStaticMemberFunctionSelectionTable
 
 Description
     Macros for easy insertion into member function selection tables
@@ -47,7 +48,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 #endif
 
 // ************************************************************************* //

src/OpenFOAM/db/runTimeSelection/staticMemberFunctions/staticMemberFunctionSelectionTables.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,7 +21,8 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-@file Foam::staticMemberFunctionSelectionTables
+Global
+    Foam::staticMemberFunctionSelectionTables
 
 Description
     Macros to enable the easy declaration of member function selection tables.
@@ -35,7 +36,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 // external use:
 // ~~~~~~~~~~~~~
 // declare a run-time selection:
@@ -140,7 +140,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-
 #endif
 
 // ************************************************************************* //

src/OpenFOAM/interpolations/interpolationTable/interpolationTable.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.