DOC: Fixed some doxygen complaints

doc/Doxygen/Doxyfile

@@ -754,7 +754,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = Doxygen.warnings
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files

doc/Doxygen/Macros/tensorOperator.sty

@@ -54,13 +54,14 @@
 
 \newcommand{\Hodge} {\ensuremath{\operatorname{\stackrel{\displaystyle \ast}{}}}}
 \newcommand{\hyd} {\ensuremath{\operatorname{hyd}}}
-\renewcommand{\max} {\ensuremath{\operatorname{max}}}
+%\renewcommand{\max} {\ensuremath{\operatorname{max}}}
-\renewcommand{\min} {\ensuremath{\operatorname{min}}}
+%\renewcommand{\min} {\ensuremath{\operatorname{min}}}
 \newcommand{\inv} {\ensuremath{\operatorname{inv}}}
 \newcommand{\sym} {\ensuremath{\operatorname{symm}}}    % symm ?
 \newcommand{\skw} {\ensuremath{\operatorname{skew}}}    % skew already defined
 \newcommand{\tr} {\ensuremath{\operatorname{tr}}}
 \newcommand{\trans}[1] {\ensuremath{#1^{\operatorname{T}}}}
+\newcommand{\symm}[1] {\ensuremath{frac{1}{2}\left(#1 + {#1}^T\right)}}
 
 % alternative tensor operators for hypersonics etc.
 % ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

src/fvOptions/sources/interRegion/interRegionHeatTransfer/variableHeatTransfer/variableHeatTransfer.H

@@ -38,13 +38,13 @@ Description
     The Nu number is calculated as:
 
     \f[
-        Nu = a \, \text{Re}^b \, \text{Pr}^c
+        Nu = a \, \textrm{Re}^b \, \textrm{Pr}^c
     \f]
 
     and the heat transfer coefficient as:
 
     \f[
-        htc = \frac{\text{Nu} \, K}{ds}
+        htc = \frac{\textrm{Nu} \, K}{ds}
     \f]
 
     where

src/meshTools/sets/cellSources/boxToCell/boxToCell.H

@@ -97,7 +97,7 @@ Usage
       min      | Minimum point (single box)     | vector     | cond'l | -
       max      | Maximum point (single box)     | vector     | cond'l | -
       span     | Box width (single box)         | vector     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/cellToCell/cellToCell.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                    | Type     | Req'd  | Dflt
       sets     | Names of input cellSets        | wordList | cond'l | -
       set      | Name of input cellSet          | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/faceToCell/faceToCell.H

@@ -98,7 +98,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input faceSets    | wordList | cond'l | -
       set      | Name of input faceSet      | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.H

@@ -95,7 +95,7 @@ Usage
       Entry    | Description                    | Type     | Req'd  | Dflt
       zones    | Names of input faceZones       | wordRes  | cond'l | -
       zone     | Name of input faceZone         | wordRe   | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/patchToCell/patchToCell.H

@@ -84,7 +84,7 @@ Usage
       Entry    | Description                   | Type     | Req'd  | Dflt
       patches  | Names of patches or wildcards | wordList | cond'l | -
       patch    | Name of patch or wildcard     | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/pointToCell/pointToCell.H

@@ -95,7 +95,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input pointSets   | wordList | cond'l | -
       set      | Name of input pointSet     | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/cellSources/zoneToCell/zoneToCell.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       zones    | Names of input cellZones   | wordRes  | cond'l | -
       zone     | Name of input cellZone     | wordRe   | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/boxToFace/boxToFace.H

@@ -97,7 +97,7 @@ Usage
       min      | Minimum point (single box)     | vector     | cond'l | -
       max      | Maximum point (single box)     | vector     | cond'l | -
       span     | Box width (single box)         | vector     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/cellToFace/cellToFace.H

@@ -94,7 +94,7 @@ Usage
       Entry    | Description                    | Type     | Req'd  | Dflt
       sets     | Names of input cellSets        | wordList | cond'l | -
       set      | Name of input cellSet          | word     | cond'l | -
-    \verbatim
+    \endverbatm
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/faceToFace/faceToFace.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input faceSets    | wordList | cond'l | -
       set      | Name of input faceSet      | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/patchToFace/patchToFace.H

@@ -85,7 +85,7 @@ Usage
       Entry    | Description           | Type     | Req'd  | Dflt
       patches  | Names of patches      | wordList | cond'l | -
       patch    | Name of patch         | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/pointToFace/pointToFace.H

@@ -96,7 +96,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input pointSets   | wordList | cond'l | -
       set      | Name of input pointSet     | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/faceSources/zoneToFace/zoneToFace.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       zones    | Names of input faceZones   | wordRes  | cond'l | -
       zone     | Name of input faceZone     | wordRe   | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/pointSources/boxToPoint/boxToPoint.H

@@ -97,7 +97,7 @@ Usage
       min      | Minimum point (single box)     | vector     | cond'l | -
       max      | Maximum point (single box)     | vector     | cond'l | -
       span     | Box width (single box)         | vector     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/pointSources/cellToPoint/cellToPoint.H

@@ -93,7 +93,7 @@ Usage
       Entry    | Description                    | Type     | Req'd  | Dflt
       sets     | Names of input cellSets        | wordList | cond'l | -
       set      | Name of input cellSet          | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/pointSources/faceToPoint/faceToPoint.H

@@ -94,7 +94,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input faceSets    | wordList | cond'l | -
       set      | Name of input faceSet      | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/pointSources/pointToPoint/pointToPoint.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       sets     | Names of input pointSets   | wordList | cond'l | -
       set      | Name of input pointSet     | word     | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/meshTools/sets/pointSources/zoneToPoint/zoneToPoint.H

@@ -86,7 +86,7 @@ Usage
       Entry    | Description                | Type     | Req'd  | Dflt
       zones    | Names of input pointZones  | wordRes  | cond'l | -
       zone     | Name of input pointZone    | wordRe   | cond'l | -
-    \verbatim
+    \endverbatim
 
 Note
     The order of precedence among the conditional mandatory entries from the

src/phaseSystemModels/multiphaseInter/phasesSystem/derivedFvPatchFields/timeVaryingMassSorption/timeVaryingMassSorptionFvPatchScalarField.H

@@ -36,11 +36,11 @@ Description
 
     \f[
         \frac{d c}{d t} =
-            k_{abs} w (c_{int} - c_{p_{w}}) + k_{des} (c_{p_{w} - c_{int}})
+            k_{abs} w (c_{int} - c_{p_{w}}) + k_{des} (c_{p_{w}} - c_{int})
     \f]
 
     \f[
-        w = max(1 - c_{p_{w}/max, 0);
+        w = \max(1 - c_{p_{w}}/max, 0)
     \f]
 
     where

src/phaseSystemModels/reactingEuler/multiphaseSystem/populationBalanceModel/coalescenceModels/CoulaloglouTavlaridesCoalescence/CoulaloglouTavlaridesCoalescence.H

@@ -33,7 +33,7 @@ Description
     \f[
         C_1 (v_i^{2/3} + v_j^{2/3}) (v_i^{2/9} + v_j^{2/9})^{1/2}
         \frac{\epsilon_c^{1/3}}{1 + \alpha_d}
-        \text{exp}
+        \textrm{exp}
         \left[
           - C_2 \frac{\mu_c \rho_c}{\sigma^2}
             \frac{\epsilon_c}{(1 + \alpha_d)^{3}}

src/phaseSystemModels/reactingEuler/multiphaseSystem/populationBalanceModel/coalescenceModels/Luo/Luo.H

@@ -30,7 +30,7 @@ Description
     Model of Luo (1993). The coalescence rate is calculated by
 
     \f[
-       &\frac{\pi}{4} (d_i + d_j)^2 u_{ij}
+        \frac{\pi}{4} (d_i + d_j)^2 u_{ij}
         \mathrm{exp}
         \left[
           - C_1

src/thermophysicalModels/radiation/radiationModels/viewFactor/viewFactor.C

@@ -613,7 +613,7 @@ void Foam::radiation::viewFactor::calculate()
         if (pp.size() > 0)
         {
             scalarField& qrp = qrBf[patchID];
-            const scalarField& sf = mesh_.magSf().boundaryField()[patchID];
+            //const scalarField& sf = mesh_.magSf().boundaryField()[patchID];
             const labelList& agglom = finalAgglom_[patchID];
             label nAgglom = max(agglom)+1;