[asl] 79/177: Fixing Doxygen related issues

[Ghislain Vaillant]

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ghisvail-guest pushed a commit to branch master
in repository asl.

commit 88e9a37c68eefc7abbb1d8ce27adb4bed38a645f
Author: Avtech Scientific <AvtechScientific at users.noreply.github.com>
Date:   Wed Jul 8 14:30:28 2015 +0300

    Fixing Doxygen related issues
---
 doc/Developer-Guide/Doxyfile.in                 |  2 +-
 examples/elastic/cubeIncompressibleGravity.cc   |  2 +-
 src/doxygenDefinitions.h                        | 16 +++++++++++-----
 src/math/aslInterpolation.h                     | 16 ++++++----------
 src/num/aslFDAdvectionDiffusion2.h              | 25 +++++++------------------
 src/num/aslFDAdvectionDiffusionInhomogeneous.h  |  7 ++-----
 src/numExtend/aslFDAdvectionDiffusionExtended.h |  4 ----
 7 files changed, 28 insertions(+), 44 deletions(-)

diff --git a/doc/Developer-Guide/Doxyfile.in b/doc/Developer-Guide/Doxyfile.in
index 5769d05..93f925d 100644
--- a/doc/Developer-Guide/Doxyfile.in
+++ b/doc/Developer-Guide/Doxyfile.in
@@ -2151,7 +2151,7 @@ DOT_NUM_THREADS        = 4
 # The default value is: Helvetica.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_FONTNAME           = FreeSans.ttf
+DOT_FONTNAME           = Helvetica
 
 # The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
 # dot graphs.
diff --git a/examples/elastic/cubeIncompressibleGravity.cc b/examples/elastic/cubeIncompressibleGravity.cc
index 47acbaa..8d2fbb4 100644
--- a/examples/elastic/cubeIncompressibleGravity.cc
+++ b/examples/elastic/cubeIncompressibleGravity.cc
@@ -22,7 +22,7 @@
 
 
 /**
-	\example cubeGravity.cc
+	\example cubeIncompressibleGravity.cc
  */
 
 #include <aslDataInc.h>
diff --git a/src/doxygenDefinitions.h b/src/doxygenDefinitions.h
index 3f4c3ec..999ac3a 100644
--- a/src/doxygenDefinitions.h
+++ b/src/doxygenDefinitions.h
@@ -116,7 +116,7 @@
  */
 
 /**
- \defgroup NumMethods NumericalMethods
+ \defgroup NumMethods Numerical Methods
  \ingroup Numerics
  */
 
@@ -132,7 +132,7 @@
 
 
 /**
- \defgroup TransportProcesses Transport processes
+ \defgroup TransportProcesses Transport Processes
  \ingroup Physics
 */
 
@@ -142,13 +142,13 @@
 */
 
 /**
- \defgroup GenericBC Generic boundary conditions
+ \defgroup GenericBC Generic Boundary Conditions
  \ingroup BoundaryConditions
 */
 
 
 /**
- \defgroup TransportProcessesBC Transport processes boundary conditions
+ \defgroup TransportProcessesBC Transport Processes Boundary Conditions
  \ingroup TransportProcesses
  \ingroup BoundaryConditions
  */
@@ -169,7 +169,7 @@
  */
 
 
-/// \defgroup DataAnalysis Data analysis tools
+/// \defgroup DataAnalysis Data Analysis Tools
 /// \ingroup Numerics
 
 
@@ -196,6 +196,12 @@
 /// \ingroup Utilities
 
 
+/**
+  \defgroup Splines Splines
+*/
+
+
+
 namespace boost
 { 
 	template<class T> class shared_ptr {}; 
diff --git a/src/math/aslInterpolation.h b/src/math/aslInterpolation.h
index e183003..a1a37d0 100644
--- a/src/math/aslInterpolation.h
+++ b/src/math/aslInterpolation.h
@@ -36,22 +36,18 @@ namespace asl
 	class ElementBase;
 	typedef std::shared_ptr<ElementBase> Element;
 
-	/**
-	 \defgroup Splines
-	 */
-	
 	template <class Func> class UniversalFunction
 	{
 		public:
 			inline double operator()(double x);
 			inline double operator()(Element x);
-	};	
-	
+	};
+
 	///Linear spline function
-	/**	
+	/**
 	 \ingroup Splines
 
-	this class defines a spline function \f$ (1-|x/r_0|),~~~ |x|<r_0 \f$	 
+	this class defines a spline function \f$ (1-|x/r_0|),~~~ |x|<r_0 \f$
 	 \image html linearS.png ""
 	*/
 	class LinearSpline
@@ -64,10 +60,10 @@ namespace asl
 	};
 
 	///Quadratic spline function
-	/**	
+	/**
 	 \ingroup Splines
 
-	this class defines a spline function \f$ (1-|x|/r_0)^2,~~~ |x|<r_0 \f$	 
+	this class defines a spline function \f$ (1-|x|/r_0)^2,~~~ |x|<r_0 \f$
 	 \image html quadraticS.png ""
 	*/
 	class QuadraticSpline
diff --git a/src/num/aslFDAdvectionDiffusion2.h b/src/num/aslFDAdvectionDiffusion2.h
index f415711..87b23d7 100644
--- a/src/num/aslFDAdvectionDiffusion2.h
+++ b/src/num/aslFDAdvectionDiffusion2.h
@@ -26,16 +26,6 @@
 
 #include "aslNumMethod.h"
 
-/**
- \defgroup TransportProcesses Transport Processes
- \ingroup Physics
- */
-
-/**
- \defgroup NumMethods NumericalMethods
- \ingroup Numerics
- */
-
 
 namespace acl{
 	class Kernel;
@@ -50,13 +40,13 @@ namespace asl
 	typedef std::shared_ptr<DataWithGhostNodesACLData> SPDataWithGhostNodesACLData;
 	class AbstractDataWithGhostNodes;
 	typedef std::shared_ptr<AbstractDataWithGhostNodes> SPAbstractDataWithGhostNodes;
-	
+
 	/// Numerical method which computes multicomponent transport processes; \f$O^2(dt)\f$
 	/**
 		 \ingroup TransportProcesses
 		 \ingroup NumMethods
-		 
-		 \f[ \partial_t c_i= D_i \Delta c_i 
+
+		 \f[ \partial_t c_i= D_i \Delta c_i
 		    					-\nabla\left(\frac{c_i q}{k} \nabla(\phi+f_2)  \right)\f]
 		 where
 		 \param cData corresponds to \f$c_i\f$
@@ -64,7 +54,7 @@ namespace asl
 		 \param efFactor1 corresponds to \f$k\f$
 		 \param efFactor2 corresponds to \f$f_2\f$
 		 \param efPhi corresponds to \f$\phi\f$
-		 \param efChargeAnd corresponds to \f$q\f$	 
+		 \param efChargeAnd corresponds to \f$q\f$ 
 	*/
 	class FDAdvectionDiffusion2: public NumMethod
 	{
@@ -72,17 +62,16 @@ namespace asl
 			typedef SPDataWithGhostNodesACLData Data;
 			typedef SPAbstractDataWithGhostNodes ScalarField;
 		private:
-			std::unique_ptr<acl::Kernel> kernel; 
-			
+			std::unique_ptr<acl::Kernel> kernel;
 			std::vector<Data> cData;
-			std::vector<Data> cInternalData;			
+			std::vector<Data> cInternalData;
 
 			bool electricField;
 			ScalarField efPhi;
 			ScalarField efFactor1;
 			ScalarField efFactor2;
 			std::vector<ScalarField> efChargeAnd;
-				
+
 			const VectorTemplate* vectorTemplate;
 
 			int t;
diff --git a/src/num/aslFDAdvectionDiffusionInhomogeneous.h b/src/num/aslFDAdvectionDiffusionInhomogeneous.h
index 9be6e37..da35a9b 100644
--- a/src/num/aslFDAdvectionDiffusionInhomogeneous.h
+++ b/src/num/aslFDAdvectionDiffusionInhomogeneous.h
@@ -26,12 +26,9 @@
 
 #include "aslNumMethod.h"
 
-/**
- \defgroup TransportProcesses Transport Processes
- */
-
 
-namespace acl{
+namespace acl
+{
 	class Kernel;
 	class VectorOfElementsData;
 }
diff --git a/src/numExtend/aslFDAdvectionDiffusionExtended.h b/src/numExtend/aslFDAdvectionDiffusionExtended.h
index 900667c..6183fed 100644
--- a/src/numExtend/aslFDAdvectionDiffusionExtended.h
+++ b/src/numExtend/aslFDAdvectionDiffusionExtended.h
@@ -26,10 +26,6 @@
 
 #include "../num/aslNumMethod.h"
 
-/**
- \defgroup TransportProcesses Transport Processes
- */
-
 
 namespace acl{
 	class Kernel;

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