From b42e13583a2e76c05fef7152e46515a0787062c7 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 22 Jul 2008 11:12:40 +0200
Subject: [PATCH] More cleanup on headers/source for doxygen

 - it also found things like size_t instead of size_type in fileName class
---
 .../conversion/plot3dToFoam/plot3dToFoam.C    |  3 +-
 .../db/functionObject/functionObject.H        |  3 ++
 .../functionObjectList/functionObjectList.H   |  3 ++
 .../FieldFields/FieldField/FieldField.H       |  4 +-
 .../basic/generic/genericPolyPatch.H          |  7 ++--
 src/OpenFOAM/primitives/Scalar/doubleFloat.H  |  3 --
 .../primitives/strings/fileName/fileName.H    |  2 +-
 .../autoHexMesh/shellSurfaces/shellSurfaces.H |  2 +-
 src/conversion/ensight/part/ensightPart.H     |  2 +-
 .../boundaryMesh/octreeDataFaceList.C         |  2 +-
 .../motionSmoother/motionSmoother.H           | 35 ++++++++--------
 .../displacementInterpolationFvMotionSolver.H |  2 +-
 .../ManualInjection/ManualInjection.H         |  8 ++--
 .../molecule/molecule/molecule.H              | 26 ++++++------
 .../moleculeCloudBuildCellOccupancy.C         |  5 ---
 .../basic/energyScalingFunction.C             |  3 --
 .../basic/newEnergyScalingFunction.C          |  3 --
 .../pairPotential/basic/newPairPotential.C    |  3 --
 .../pairPotential/basic/pairPotential.C       |  3 --
 .../pairPotential/derived/azizChen/azizChen.H | 30 +++++++-------
 .../derived/maitlandSmith/maitlandSmith.H     | 40 ++++++++++---------
 .../basic/newTetherPotential.C                |  3 --
 .../directMappedPolyPatch.H                   |  7 ++--
 .../fieldAverage/fieldAverage/fieldAverage.H  |  2 +-
 src/postProcessing/forces/forces/forces.H     |  2 +-
 .../OutputFilterFunctionObject.H              | 10 ++++-
 .../chemkinReader/chemkinLexer.L              |  5 +++
 .../triSurface/interfaces/STL/readSTLASCII.L  |  4 ++
 .../dynOneEqEddy/dynOneEqEddy.H               |  2 +-
 .../LienCubicKELowRe/LienCubicKELowRe.H       |  2 +-
 30 files changed, 118 insertions(+), 108 deletions(-)

diff --git a/applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C b/applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C
index f686180195..6e81ff9f0b 100644
--- a/applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C
+++ b/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'
diff --git a/src/OpenFOAM/db/functionObject/functionObject.H b/src/OpenFOAM/db/functionObject/functionObject.H
index d729c1c8cb..4761636613 100644
--- a/src/OpenFOAM/db/functionObject/functionObject.H
+++ b/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
 
diff --git a/src/OpenFOAM/db/functionObjectList/functionObjectList.H b/src/OpenFOAM/db/functionObjectList/functionObjectList.H
index 752c6d8a0d..bd71c1578c 100644
--- a/src/OpenFOAM/db/functionObjectList/functionObjectList.H
+++ b/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
 
diff --git a/src/OpenFOAM/fields/FieldFields/FieldField/FieldField.H b/src/OpenFOAM/fields/FieldFields/FieldField/FieldField.H
index 20b41f17b8..958e2f259b 100644
--- a/src/OpenFOAM/fields/FieldFields/FieldField/FieldField.H
+++ b/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());
             }
 
diff --git a/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/generic/genericPolyPatch.H b/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/generic/genericPolyPatch.H
index a5a0614b99..6ab6354a08 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/generic/genericPolyPatch.H
+++ b/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
-    all processors to keep the addressing calculation simple.
+Note
+    Storage is not optimal. It stores all face centres and cells on all
+    processors to keep the addressing calculation simple.
 
 SourceFiles
     genericPolyPatch.C
diff --git a/src/OpenFOAM/primitives/Scalar/doubleFloat.H b/src/OpenFOAM/primitives/Scalar/doubleFloat.H
index 58e8f65002..40ccb27279 100644
--- a/src/OpenFOAM/primitives/Scalar/doubleFloat.H
+++ b/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
diff --git a/src/OpenFOAM/primitives/strings/fileName/fileName.H b/src/OpenFOAM/primitives/strings/fileName/fileName.H
index 71cdfbdb46..1ef3839ea5 100644
--- a/src/OpenFOAM/primitives/strings/fileName/fileName.H
+++ b/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
diff --git a/src/autoMesh/autoHexMesh/shellSurfaces/shellSurfaces.H b/src/autoMesh/autoHexMesh/shellSurfaces/shellSurfaces.H
index b996e98e89..0ec93cbeb1 100644
--- a/src/autoMesh/autoHexMesh/shellSurfaces/shellSurfaces.H
+++ b/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
diff --git a/src/conversion/ensight/part/ensightPart.H b/src/conversion/ensight/part/ensightPart.H
index b511c6d095..5df840ea01 100644
--- a/src/conversion/ensight/part/ensightPart.H
+++ b/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
diff --git a/src/dynamicMesh/boundaryMesh/octreeDataFaceList.C b/src/dynamicMesh/boundaryMesh/octreeDataFaceList.C
index 27028e0df6..2249bc006e 100644
--- a/src/dynamicMesh/boundaryMesh/octreeDataFaceList.C
+++ b/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];
diff --git a/src/dynamicMesh/motionSmoother/motionSmoother.H b/src/dynamicMesh/motionSmoother/motionSmoother.H
index 92cee05637..c9e20f6a55 100644
--- a/src/dynamicMesh/motionSmoother/motionSmoother.H
+++ b/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
-    (read upon construction since need boundary conditions) and scaling factor
-    and optional patch number on which to scale back displacement.
+    until there are no more mesh errors.
 
-    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
-    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: 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
+    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
diff --git a/src/fvMotionSolver/fvMotionSolvers/displacement/interpolation/displacementInterpolationFvMotionSolver.H b/src/fvMotionSolver/fvMotionSolvers/displacement/interpolation/displacementInterpolationFvMotionSolver.H
index b146fe8c8e..04f3eda5cc 100644
--- a/src/fvMotionSolver/fvMotionSolvers/displacement/interpolation/displacementInterpolationFvMotionSolver.H
+++ b/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.
diff --git a/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ManualInjection/ManualInjection.H b/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ManualInjection/ManualInjection.H
index a3a6d0dd78..3aba7306e7 100644
--- a/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ManualInjection/ManualInjection.H
+++ b/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
-           file describes 2-D data!
+Note
+    Not suitable for 2-D slab/wedge simulations unless the @c positionsFile
+    describes 2-D data.
 
 SourceFiles
     ManualInjection.C
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
index 4f180cdec1..f0104963ac 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
+++ b/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
-        //  transfer:
-        //  1) Put the largest data members 1st
-        //  2) Pair up labels,
-        //  3) Don't go scalar-label, scalar-label, becasue in 64bit mode,
-        //     the labels will be padded by 4bytes.
+        //- Be careful with the ordering of data.
+        //  It has an impact on binary transfer:
+        //    -# Put the largest data members 1st
+        //    -# Pair up labels,
+        //    -# Don't go scalar-label, scalar-label, because in 64bit mode,
+        //       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
-        //  processorPatch
+        //- Overridable function to handle the particle hitting a processorPatch
         void hitProcessorPatch
         (
             const processorPolyPatch&,
             molecule::trackData& td
         );
 
-        //- Overridable function to handle the particle hitting a
-        //  processorPatch without trackData
+        //- Overridable function to handle the particle hitting a processorPatch
+        //  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&,
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
index 4356a4ee62..a5f82d375c 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
+++ b/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"
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
index 7ab692ef1f..a8ee7b89d1 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
+++ b/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"
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
index 4306dba017..33b3bf99f6 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
+++ b/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"
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
index cbbebc5350..45156e5711 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
+++ b/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"
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
index efe4b52582..2566941f24 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
+++ b/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"
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
index 8382ae4422..998be3d7f2 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
@@ -26,22 +26,24 @@ Class
     Foam::pairPotentials::azizChen
 
 Description
+    Foam::pairPotentials::azizChen
 
     From:
-
-    @article{MA_Aziz_Chen,
-    author = {R. A. Aziz and H. H. Chen},
-    collaboration = {},
-    title = {An accurate intermolecular potential for argon},
-    publisher = {AIP},
-    year = {1977},
-    journal = {The Journal of Chemical Physics},
-    volume = {67},
-    number = {12},
-    pages = {5719-5726},
-    url = {http://link.aip.org/link/?JCP/67/5719/1},
-    doi = {10.1063/1.434827}
-    }
+    @verbatim
+        @article{MA_Aziz_Chen,
+        author = {R. A. Aziz and H. H. Chen},
+        collaboration = {},
+        title = {An accurate intermolecular potential for argon},
+        publisher = {AIP},
+        year = {1977},
+        journal = {The Journal of Chemical Physics},
+        volume = {67},
+        number = {12},
+        pages = {5719-5726},
+        url = {http://link.aip.org/link/?JCP/67/5719/1},
+        doi = {10.1063/1.434827}
+        }
+    @endverbatim
 
 SourceFiles
     azizChen.C
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
index cea92c8c90..a9c7bdfa28 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
@@ -26,28 +26,32 @@ Class
     Foam::pairPotentials::maitlandSmith
 
 Description
+    Foam::pairPotentials::maitlandSmith
 
     From:
-
-    @ARTICLE{MA_Maitland_Smith,
-    author = {{Maitland}, G.~C. and {Smith}, E.~B.},
-    title = {A simplified representation of intermolecular potential energy},
-    journal = {Chemical Physics Letters},
-    year = 1973,
-    month = oct,
-    volume = 22,
-    pages = {443-446},
-    adsurl = {http://adsabs.harvard.edu/abs/1973CPL....22..443M},
-    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-    }
+    @verbatim
+        @ARTICLE{MA_Maitland_Smith,
+        author = {{Maitland}, G.~C. and {Smith}, E.~B.},
+        title = {A simplified representation of intermolecular potential energy},
+        journal = {Chemical Physics Letters},
+        year = 1973,
+        month = oct,
+        volume = 22,
+        pages = {443-446},
+        adsurl = {http://adsabs.harvard.edu/abs/1973CPL....22..443M},
+        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+        }
+    @endverbatim
 
     Parameters for other monoatomics from:
-    @BOOK{MD_Maitland_Rigby_Smith_Wakeham,
-    AUTHOR =       {Geoffrey C. Maitland and Maurice Rigby and E. Brian Smith and William A. Wakeham},
-    TITLE =        {Intermolecular Forces: Their Origin and Determination},
-    PUBLISHER =    {Oxford University Press},
-    YEAR =         {1981}
-    }
+    @verbatim
+        @BOOK{MD_Maitland_Rigby_Smith_Wakeham,
+        AUTHOR =       {Geoffrey C. Maitland and Maurice Rigby and E. Brian Smith and William A. Wakeham},
+        TITLE =        {Intermolecular Forces: Their Origin and Determination},
+        PUBLISHER =    {Oxford University Press},
+        YEAR =         {1981}
+        }
+    @endverbatim
 
 SourceFiles
     maitlandSmith.C
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
index bd51dfd970..b88b28b46c 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
+++ b/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"
diff --git a/src/meshTools/directMapped/directMappedPolyPatch/directMappedPolyPatch.H b/src/meshTools/directMapped/directMappedPolyPatch/directMappedPolyPatch.H
index f77f922d14..6439020f5d 100644
--- a/src/meshTools/directMapped/directMappedPolyPatch/directMappedPolyPatch.H
+++ b/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
-    all processors to keep the addressing calculation simple.
+Note
+    Storage is not optimal. It stores all face centres and cells on all
+    processors to keep the addressing calculation simple.
 
 SourceFiles
     directMappedPolyPatch.C
diff --git a/src/postProcessing/fieldAverage/fieldAverage/fieldAverage.H b/src/postProcessing/fieldAverage/fieldAverage/fieldAverage.H
index 5c080e1873..7d7b22af82 100644
--- a/src/postProcessing/fieldAverage/fieldAverage/fieldAverage.H
+++ b/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
diff --git a/src/postProcessing/forces/forces/forces.H b/src/postProcessing/forces/forces/forces.H
index 7f37217b98..7b03805b9c 100644
--- a/src/postProcessing/forces/forces/forces.H
+++ b/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
diff --git a/src/sampling/outputFilters/OutputFilterFunctionObject/OutputFilterFunctionObject.H b/src/sampling/outputFilters/OutputFilterFunctionObject/OutputFilterFunctionObject.H
index 00a95fc72c..62834c67e2 100644
--- a/src/sampling/outputFilters/OutputFilterFunctionObject/OutputFilterFunctionObject.H
+++ b/src/sampling/outputFilters/OutputFilterFunctionObject/OutputFilterFunctionObject.H
@@ -26,8 +26,14 @@ Class
     Foam::OutputFilterFunctionObject
 
 Description
-    FunctionObject wrapper around OutputFilter to allow them to be created
-    via the functions list within controlDict.
+    A functionObject wrapper around OutputFilter to allow them to be
+    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
diff --git a/src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinLexer.L b/src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinLexer.L
index 18e5366eb5..bfbb4de1e6 100644
--- a/src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinLexer.L
+++ b/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)
 {
diff --git a/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L b/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L
index eaef9e7803..e0652edd8c 100644
--- a/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L
+++ b/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
diff --git a/src/turbulenceModels/LES/incompressible/dynOneEqEddy/dynOneEqEddy.H b/src/turbulenceModels/LES/incompressible/dynOneEqEddy/dynOneEqEddy.H
index b680174e69..3ba67f6b24 100644
--- a/src/turbulenceModels/LES/incompressible/dynOneEqEddy/dynOneEqEddy.H
+++ b/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
diff --git a/src/turbulenceModels/RAS/incompressible/LienCubicKELowRe/LienCubicKELowRe.H b/src/turbulenceModels/RAS/incompressible/LienCubicKELowRe/LienCubicKELowRe.H
index 3fac316cdf..1708dde244 100644
--- a/src/turbulenceModels/RAS/incompressible/LienCubicKELowRe/LienCubicKELowRe.H
+++ b/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