Merge pull request #6094 from gassmoeller/doxygen

Update doxygen theme

doc/modules/groups.h

@@ -38,7 +38,7 @@
  */
 
 /**
- * @defgroup InitialTopographyModels Describing the properties of the initial topography of the domain
+ * @defgroup InitialTopographyModels Describing the initial topography of the domain
  *
  * A module for the definition of properties related to initial topography of
  * the geometry. The goal of this module is to return the elevation at a
@@ -76,6 +76,13 @@
  * and radiogenic sources.
  */
 
+/**
+ * @defgroup MeshDeformation Describing how to deform the mesh
+ *
+ * A module for the definition of algorithms and methods to deform the
+ * mesh during the computation, e.g. due to surface processes.
+ */
+
 /**
  * @defgroup MeshRefinement Describing how to refine the mesh
  *
@@ -119,9 +126,9 @@
 
 
 /**
- * @defgroup AdiabaticConditions Adiabatic conditions
+ * @defgroup AdiabaticConditions Describing Adiabatic conditions
  *
- * A group for all things that have to do with adiabatic conditions.
+ * A group for all things that have to do with adiabatic reference profiles.
  *
  * @ingroup InitialConditions
  */
@@ -155,6 +162,15 @@
  * @ingroup BoundaryConditions
  */
 
+/**
+ * @defgroup BoundaryHeatFlux Describing heat flux boundary conditions
+ *
+ * A module for the definition of functions and classes that have to do with
+ * describing heat flux boundary values for the temperature field.
+ *
+ * @ingroup BoundaryConditions
+ */
+
 /**
  * @defgroup BoundaryCompositions Describing boundary conditions for compositional fields
  *

doc/options.dox

@@ -885,6 +885,8 @@ HTML_FOOTER            = footer.html
 
 HTML_STYLESHEET        =
 
+HTML_EXTRA_STYLESHEET = doxygen-awesome.css
+
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
 # that these files will be copied to the base HTML output directory. Use the

include/aspect/mesh_deformation/ascii_data.h

@@ -37,7 +37,7 @@ namespace aspect
      * A class that implements initial topography determined
      * from an AsciiData input file.
      *
-     * @ingroup InitialTopographyModel
+     * @ingroup MeshDeformation
      */
     template <int dim>
     class AsciiData : public Utilities::AsciiDataBoundary<dim>, public Interface<dim>

include/aspect/mesh_deformation/diffusion.h

@@ -38,6 +38,8 @@ namespace aspect
      * A plugin that computes the deformation of surface
      * vertices according to the solution of a dim-1 diffusion
      * problem.
+     *
+     * @ingroup MeshDeformation
      */
     template <int dim>
     class Diffusion : public Interface<dim>, public SimulatorAccess<dim>

include/aspect/mesh_deformation/fastscape.h

@@ -39,6 +39,7 @@ namespace aspect
      * hillslope diffusion, sediment deposition, marine diffusion,
      * and the stream power law, which describes river incision.
      *
+     * @ingroup MeshDeformation
      */
     template <int dim>
     class FastScape : public Interface<dim>, public SimulatorAccess<dim>

include/aspect/mesh_deformation/free_surface.h

@@ -39,6 +39,8 @@ namespace aspect
      * vertices according to the solution of the flow problem.
      * In particular this means if the surface of the domain is
      * left open to flow, this flow will carry the mesh with it.
+     *
+     * @ingroup MeshDeformation
      */
     template <int dim>
     class FreeSurface : public Interface<dim>, public SimulatorAccess<dim>

include/aspect/mesh_deformation/function.h

@@ -33,6 +33,12 @@ namespace aspect
 
   namespace MeshDeformation
   {
+    /**
+     * A class that represents a mesh deformation function that can be
+     * prescribed on the boundary of the domain.
+     *
+     * @ingroup MeshDeformation
+     */
     template <int dim>
     class BoundaryFunction : public Interface<dim>, public SimulatorAccess<dim>
     {

include/aspect/mesh_deformation/interface.h

@@ -85,6 +85,8 @@ namespace aspect
      * mesh vertices and store them in a AffineConstraints<double> object. The velocities
      * for all non-constrained vertices will be computed by solving a Laplace
      * problem with the given constraints.
+     *
+     * @ingroup MeshDeformation
      */
     template <int dim>
     class Interface : public Plugins::InterfaceBase