More cleanup on headers/source for doxygen

- it also found things like size_t instead of size_type in fileName class

applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C

@@ -28,7 +28,8 @@ Description
     Work in progress! Handles ascii multiblock (and optionally singleBlock)
     format.
     By default expects blanking. Use -noBlank if none.
-    Use -2D <thickness> if 2D.
+    Use -2D @a thickness if 2D.
+
     Niklas Nordin has experienced a problem with lefthandedness of the blocks.
     The code should detect this automatically - see hexBlock::readPoints but
     if this goes wrong just set the blockHandedness_ variable to 'right'

src/OpenFOAM/db/functionObject/functionObject.H

@@ -28,6 +28,9 @@ Class
 Description
     Abstract base-class for Time/database function objects.
 
+See Also
+    Foam::OutputFilterFunctionObject
+
 SourceFiles
     functionObject.C
 

src/OpenFOAM/db/functionObjectList/functionObjectList.H

@@ -29,6 +29,9 @@ Description
     List of function objects with execute function which is called for
     each object.
 
+See Also
+    Foam::functionObject and Foam::OutputFilterFunctionObject
+
 SourceFiles
     functionObjectList.C
 

src/OpenFOAM/fields/FieldFields/FieldField/FieldField.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::FieldField\<T\>
+    Foam::FieldField
 
 Description
     Generic field type.
@@ -134,7 +134,7 @@ public:
             );
 
             forAll(*nffPtr, i)
-            { 
+            {
                 nffPtr->set(i, Field<Type>::NewCalculatedType(ff[i]).ptr());
             }
 

src/OpenFOAM/meshes/polyMesh/polyPatches/basic/generic/genericPolyPatch.H

@@ -23,14 +23,15 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::genericPolyPatch.C
+    Foam::genericPolyPatch
 
 Description
     Determines a mapping between patch face centres and mesh cell centres and
     processors they're on.
 
-    Note: storage is not optimal. It stores all face centres and cells on
+Note
-    all processors to keep the addressing calculation simple.
+    Storage is not optimal. It stores all face centres and cells on all
+    processors to keep the addressing calculation simple.
 
 SourceFiles
     genericPolyPatch.C

src/OpenFOAM/primitives/Scalar/doubleFloat.H

@@ -22,9 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Typedef
-    Foam::double and float
-
 \*---------------------------------------------------------------------------*/
 
 #ifndef doubleFloat_H

src/OpenFOAM/primitives/strings/fileName/fileName.H

@@ -147,7 +147,7 @@ public:
             wordList components(const char delimiter='/') const;
 
             //- Return a component of the path
-            word component(const size_t, const char delimiter='/') const;
+            word component(const size_type, const char delimiter='/') const;
 
 
         // Interogation

src/autoMesh/autoHexMesh/shellSurfaces/shellSurfaces.H

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    shellSurfaces
+    Foam::shellSurfaces
 
 Description
     Encapsulates queries for volume refinement ('refine all cells within

src/conversion/ensight/part/ensightPart.H

@@ -137,7 +137,7 @@ protected:
         (
             ensightFile& os,
             const List<scalar>& field,
-            const labelList& idList
+            const List<label>& idList
         ) const;
 
         //- track points used

src/dynamicMesh/boundaryMesh/octreeDataFaceList.C

@@ -501,7 +501,7 @@ Foam::scalar Foam::octreeDataFaceList::calcSign
 (
     const label index,
     const point& sample,
-    point&
+    vector&
 ) const
 {
     label faceI = faceLabels_[index];

src/dynamicMesh/motionSmoother/motionSmoother.H

@@ -27,18 +27,18 @@ Class
 
 Description
     Given a displacement moves the mesh by scaling the displacement back
-    until there are no more mesh errors. Holds displacement field
+    until there are no more mesh errors.
-    (read upon construction since need boundary conditions) and scaling factor
-    and optional patch number on which to scale back displacement.
 
-    E.g.
+    Holds displacement field (read upon construction since need boundary
+    conditions) and scaling factor and optional patch number on which to
+    scale back displacement.
 
     E.g.
     @verbatim
         // Construct iterative mesh mover.
         motionSmoother meshMover(mesh, labelList(1, patchI));
 
-        // Set wanted displacement:
+        // Set desired displacement:
         meshMover.displacement() = ..
 
         for (label iter = 0; iter < maxIter; iter++)
@@ -49,19 +49,20 @@ Description
                 return true;
             }
         }
-    @envverbatim
+    @endverbatim
 
+Note
+    Shared points (parallel): a processor can have points which are part of
+    pp on another processor but have no pp itself (i.e. it has points
+    and/or edges but no faces of pp). Hence we have to be careful when e.g.
+    synchronising displacements that the value from the processor which has
+    faces of pp get priority. This is currently handled in setDisplacement
+    by resetting the internal displacement to zero before doing anything
+    else. The combine operator used will give preference to non-zero
+    values.
 
-    Note: shared points (parallel). A processor can have points which are
+    Various routines take baffles. These are sets of boundary faces that
-    part of pp on another processor but have no pp itself (i.e. it has points
+    are treated as a single internal face. This is a hack used to apply
-    and/or edges but no faces of pp). Hence we have to be careful when
-    e.g. synchronising displacements that the value from the processor which
-    has faces of pp get priority. This is currently handled in setDisplacement
-    by resetting the internal displacement to zero before doing anything else.
-    The combine operator used will give preference to non-zero values.
-
-    Note: various routines take baffles. These are sets of boundary faces
-    that are treated as a single internal face. This is a hack used to apply
     movement to internal faces.
 
 SourceFiles
@@ -420,7 +421,7 @@ public:
                 labelHashSet& wrongFaces
             );
 
-            //- Check (subset of mesh including baffles) with mesh settings 
+            //- Check (subset of mesh including baffles) with mesh settings
             //  in dict. Collects incorrect faces in set. Returns true if one
             //  or more faces in error. Parallel ok.
             static bool checkMesh

src/fvMotionSolver/fvMotionSolvers/displacement/interpolation/displacementInterpolationFvMotionSolver.H

@@ -35,7 +35,7 @@ Description
     - interpolates the displacement of all points based on the
       faceZone motion.
 
-    Tables are in the <verbatim>constant/tables</verbatim> directory.
+    Tables are in the @a constant/tables directory.
 
 Note
     could be a motionSolver - does not use any fvMesh structure.

src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ManualInjection/ManualInjection.H

@@ -27,15 +27,17 @@ Class
 
 Description
     Manual injection
+
     - User specifies
       - Total mass to inject
-      - Parcel positions in file <positionsFile>
+      - Parcel positions in file @c positionsFile
       - Initial parcel velocity
     - Parcel diameters obtained by PDF model
     - All parcels introduced at the start of the calculation
 
-    NOTE - not suitable for 2-D slab/wedge simulations unless the positions
+Note
-           file describes 2-D data!
+    Not suitable for 2-D slab/wedge simulations unless the @c positionsFile
+    describes 2-D data.
 
 SourceFiles
     ManualInjection.C

src/lagrangian/molecularDynamics/molecule/molecule/molecule.H

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    molecule
+    Foam::molecule
 
 Description
+    Foam::molecule
 
 SourceFiles
     moleculeI.H
@@ -59,12 +60,12 @@ class molecule
 {
     // Private data
 
-        //- Be careful with the ordering of data.  It has an impact on binary
+        //- Be careful with the ordering of data.
-        //  transfer:
+        //  It has an impact on binary transfer:
-        //  1) Put the largest data members 1st
+        //    -# Put the largest data members 1st
-        //  2) Pair up labels,
+        //    -# Pair up labels,
-        //  3) Don't go scalar-label, scalar-label, becasue in 64bit mode,
+        //    -# Don't go scalar-label, scalar-label, because in 64bit mode,
-        //     the labels will be padded by 4bytes.
+        //       the labels will be padded by 4bytes.
 
         // - mass of molecule
         scalar mass_;
@@ -200,16 +201,15 @@ public:
 
     // Member Operators
 
-        //- Overridable function to handle the particle hitting a
+        //- Overridable function to handle the particle hitting a processorPatch
-        //  processorPatch
         void hitProcessorPatch
         (
             const processorPolyPatch&,
             molecule::trackData& td
         );
 
-        //- Overridable function to handle the particle hitting a
+        //- Overridable function to handle the particle hitting a processorPatch
-        //  processorPatch without trackData
+        //  without trackData
         void hitProcessorPatch
         (
             const processorPolyPatch&,
@@ -224,7 +224,7 @@ public:
         );
 
         //- Overridable function to handle the particle hitting a wallPatch
-        //- without trackData
+        //  without trackData
         void hitWallPatch
         (
             const wallPolyPatch&,
@@ -239,7 +239,7 @@ public:
         );
 
         //- Overridable function to handle the particle hitting a polyPatch
-        //- without trackData
+        //  without trackData
         void hitPatch
         (
             const polyPatch&,

src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C

@@ -22,11 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Class
-    moleculeCloud
-
-Description
-
 \*----------------------------------------------------------------------------*/
 
 #include "moleculeCloud.H"

src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C

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

src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C

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

src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C

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

src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C

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

src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H

@@ -26,22 +26,24 @@ Class
     Foam::pairPotentials::azizChen
 
 Description
+    Foam::pairPotentials::azizChen
 
     From:
-
+    @verbatim
-    @article{MA_Aziz_Chen,
+        @article{MA_Aziz_Chen,
-    author = {R. A. Aziz and H. H. Chen},
+        author = {R. A. Aziz and H. H. Chen},
-    collaboration = {},
+        collaboration = {},
-    title = {An accurate intermolecular potential for argon},
+        title = {An accurate intermolecular potential for argon},
-    publisher = {AIP},
+        publisher = {AIP},
-    year = {1977},
+        year = {1977},
-    journal = {The Journal of Chemical Physics},
+        journal = {The Journal of Chemical Physics},
-    volume = {67},
+        volume = {67},
-    number = {12},
+        number = {12},
-    pages = {5719-5726},
+        pages = {5719-5726},
-    url = {http://link.aip.org/link/?JCP/67/5719/1},
+        url = {http://link.aip.org/link/?JCP/67/5719/1},
-    doi = {10.1063/1.434827}
+        doi = {10.1063/1.434827}
-    }
+        }
+    @endverbatim
 
 SourceFiles
     azizChen.C

src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H

@@ -26,28 +26,32 @@ Class
     Foam::pairPotentials::maitlandSmith
 
 Description
+    Foam::pairPotentials::maitlandSmith
 
     From:
-
+    @verbatim
-    @ARTICLE{MA_Maitland_Smith,
+        @ARTICLE{MA_Maitland_Smith,
-    author = {{Maitland}, G.~C. and {Smith}, E.~B.},
+        author = {{Maitland}, G.~C. and {Smith}, E.~B.},
-    title = {A simplified representation of intermolecular potential energy},
+        title = {A simplified representation of intermolecular potential energy},
-    journal = {Chemical Physics Letters},
+        journal = {Chemical Physics Letters},
-    year = 1973,
+        year = 1973,
-    month = oct,
+        month = oct,
-    volume = 22,
+        volume = 22,
-    pages = {443-446},
+        pages = {443-446},
-    adsurl = {http://adsabs.harvard.edu/abs/1973CPL....22..443M},
+        adsurl = {http://adsabs.harvard.edu/abs/1973CPL....22..443M},
-    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-    }
+        }
+    @endverbatim
 
     Parameters for other monoatomics from:
-    @BOOK{MD_Maitland_Rigby_Smith_Wakeham,
+    @verbatim
-    AUTHOR =       {Geoffrey C. Maitland and Maurice Rigby and E. Brian Smith and William A. Wakeham},
+        @BOOK{MD_Maitland_Rigby_Smith_Wakeham,
-    TITLE =        {Intermolecular Forces: Their Origin and Determination},
+        AUTHOR =       {Geoffrey C. Maitland and Maurice Rigby and E. Brian Smith and William A. Wakeham},
-    PUBLISHER =    {Oxford University Press},
+        TITLE =        {Intermolecular Forces: Their Origin and Determination},
-    YEAR =         {1981}
+        PUBLISHER =    {Oxford University Press},
-    }
+        YEAR =         {1981}
+        }
+    @endverbatim
 
 SourceFiles
     maitlandSmith.C

src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C

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

src/meshTools/directMapped/directMappedPolyPatch/directMappedPolyPatch.H

@@ -23,14 +23,15 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Class
-    Foam::directMappedPolyPatch.C
+    Foam::directMappedPolyPatch
 
 Description
     Determines a mapping between patch face centres and mesh cell centres and
     processors they're on.
 
-    Note: storage is not optimal. It stores all face centres and cells on
+Note
-    all processors to keep the addressing calculation simple.
+    Storage is not optimal. It stores all face centres and cells on all
+    processors to keep the addressing calculation simple.
 
 SourceFiles
     directMappedPolyPatch.C

src/postProcessing/fieldAverage/fieldAverage/fieldAverage.H

@@ -66,7 +66,7 @@ Description
 
     Information regarding the number of averaging steps, and total averaging
     time are written on a (base) per-field basis to the
-    fieldAveragingProperties dictionary, located in <time>/uniform
+    fieldAveragingProperties dictionary, located in \<time\>/uniform
 
 SourceFiles
     fieldAverage.C

src/postProcessing/forces/forces/forces.H

@@ -33,7 +33,7 @@ Description
     moments.
 
     Member function forces::write() calls calcForcesMoment() and writes the
-    forces and moments into the file <time dir>/forces.dat
+    forces and moments into the file \<timeDir\>/forces.dat
 
 SourceFiles
     forces.C

src/sampling/outputFilters/OutputFilterFunctionObject/OutputFilterFunctionObject.H

@@ -26,8 +26,14 @@ Class
     Foam::OutputFilterFunctionObject
 
 Description
-    FunctionObject wrapper around OutputFilter to allow them to be created
+    A functionObject wrapper around OutputFilter to allow them to be
-    via the functions list within controlDict.
+    created via the functions list within controlDict.
+
+Note
+    Since the timeIndex is used directly from Foam::Time, it is unaffected
+    by user-time conversions. For example, Foam::engineTime might cause @a
+    writeInterval to be degrees crank angle, but the functionObject
+    execution @a interval would still be in timestep.
 
 SourceFiles
     OutputFilterFunctionObject.C

src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinLexer.L

@@ -37,6 +37,7 @@ License
 int Foam::chemkinReader::yyBufSize = YY_BUF_SIZE;
 
 // Dummy yyFlexLexer::yylex() to keep the linker happy. It is not called
+//! @cond dummy
 int yyFlexLexer::yylex()
 {
     Foam::FatalErrorIn("yyFlexLexer::yylex()")
@@ -45,11 +46,13 @@ int yyFlexLexer::yylex()
 
     return 0;
 }
+//! @endcond dummy
 
 
 // Dummy yywrap to keep yylex happy at compile time.
 // It is called by yylex but is not used as the mechanism to change file.
 // See <<EOF>>
+//! @cond dummy
 #if YY_FLEX_SUBMINOR_VERSION < 34
 extern "C" int yywrap()
 #else
@@ -58,6 +61,8 @@ int yyFlexLexer::yywrap()
 {
     return 1;
 }
+//! @endcond dummy
+
 
 Foam::string foamSpecieString(const char* YYText)
 {

src/triSurface/triSurface/interfaces/STL/readSTLASCII.L

@@ -40,6 +40,7 @@ License
 using namespace Foam;
 
 // Dummy yyFlexLexer::yylex() to keep the linker happy. It is not called
+//! @cond dummy
 int yyFlexLexer::yylex()
 {
     FatalErrorIn("yyFlexLexer::yylex()")
@@ -47,10 +48,12 @@ int yyFlexLexer::yylex()
         << abort(FatalError);
     return 0;
 }
+//! @endcond dummy
 
 // Dummy yywrap to keep yylex happy at compile time.
 // It is called by yylex but is not used as the mechanism to change file.
 // See <<EOF>>
+//! @cond dummy
 #if YY_FLEX_SUBMINOR_VERSION < 34
 extern "C" int yywrap()
 #else
@@ -59,6 +62,7 @@ int yyFlexLexer::yywrap()
 {
     return 1;
 }
+//! @endcond dummy
 
 
 class STLLexer

src/turbulenceModels/LES/incompressible/dynOneEqEddy/dynOneEqEddy.H

@@ -47,7 +47,7 @@ Description
         D = symm(grad(U));
         nuSgs = ck*sqrt(k)*delta
         nuEff = nuSgs + nu
-    @endverabtim
+    @endverbatim
 
 SourceFiles
     dynOneEqEddy.C

src/turbulenceModels/RAS/incompressible/LienCubicKELowRe/LienCubicKELowRe.H

@@ -41,7 +41,7 @@ Description
         Etemad, S., et al.,
         "Turbulent flow and heat transfer in a square-sectioned U bend"
         Progress in compuational fluid dynamics 6, 89-100. 2006.
-    @verbatim
+    @endverbatim
 
 SourceFiles
     LienCubicKELowRe.C