[doxy][multidomain] first version of some multidomain fixes

Remove double/tripple ingroups and correct some doxygen-links

doc/doxygen/Doxylocal

@@ -14,7 +14,6 @@ INPUT                 += @srcdir@/mainpage.txt \
                          @srcdir@/modules.txt \
                          @top_srcdir@/dumux \
                          @top_srcdir@/test \
-                         @top_srcdir@/tutorial \
                          @srcdir@/extradoc/parameterlist.txt \
                          @srcdir@/extradoc/featurelist.txt
 

doc/doxygen/modules.txt

@@ -242,20 +242,20 @@
       * \defgroup PorousmediumflowTests Porous-Medium Flow Tests
       * \brief Single and multi-phase tests for flow and transport in porous materials
       */
-          /*!
+         /*!
           * \ingroup PorousmediumflowTests
-           * \defgroup OnePTests 1p (one phase) benchmarks and tests
+          * \defgroup OnePTests 1p (one phase) benchmarks and tests
           * \brief Various tests using a OnePModel. The files are listed below.
           */
          /*!
           * \ingroup PorousmediumflowTests
-           * \defgroup OnePNCTests 1pnc (one phase, multi-component) benchmarks and tests
-           * \brief Various tests using a OnePNCModel. The files are listed below.
-           */
+          * \defgroup OnePNCTests 1pnc (one phase, multi-component) benchmarks and tests
+          * \brief Various tests using a OnePNCModel. The files are listed below.
+          */
          /*!
           * \ingroup PorousmediumflowTests
           * \defgroup OnePNCMinTests 1pncmin (one phase, multi-component mineralization) benchmarks and tests
-         * \brief Various tests using the OnePNCMinModel. The files are listed below.
+          * \brief Various tests using the OnePNCMinModel. The files are listed below.
           */
          /*!
           * \ingroup PorousmediumflowTests
@@ -265,7 +265,7 @@
          /*!
           * \ingroup PorousmediumflowTests
           * \defgroup TwoPOneCTests 2p1c (two phase, one component) benchmarks and tests
-           * \brief Various tests using the TwoPOneCModel. The files are listed below.
+          * \brief Various tests using the TwoPOneCModel. The files are listed below.
           */
          /*!
           * \ingroup PorousmediumflowTests
@@ -297,7 +297,7 @@
           * \defgroup ThreePWaterOilTests 3pwateroil (three phase, water oil) benchmarks and tests
           * \brief A SAGD test problem using the ThreePWaterOilModel. The files are listed below.
           */
-        /*!
+         /*!
           * \ingroup PorousmediumflowTests
           * \defgroup CO2Tests CO2 (two phase, two component) benchmarks and tests
           * \brief A CO2 injection test problem using the TwoPTwoCModel and heterogeneous spatial parameters. The files are listed below.
@@ -305,7 +305,7 @@
          /*!
           * \ingroup PorousmediumflowTests
           * \defgroup MPNCTests MPNC (multi-phase, multi-component) benchmarks and tests
-         * \brief Various tests using the MPNCModel. The files are listed below.
+          * \brief Various tests using the MPNCModel. The files are listed below.
           */
          /*!
           * \ingroup PorousmediumflowTests
@@ -327,12 +327,12 @@
       * \defgroup FreeflowTests Free Flow Tests
       * \brief Varios tests for single-phase Navier-Stokes / Stokes tests
       */
-           /*!
+         /*!
           * \ingroup FreeflowTests
           * \defgroup NavierStokesTests Single-phase Navier-Stokes tests
           * \brief Various tests using a Single-phase Navier-Stokes flow. The files are listed below.
           */
-           /*!
+         /*!
           * \ingroup FreeflowTests
           * \defgroup NavierStokesNCTests Single-phase Navier-Stokes nc tests
           * \brief Various tests using a Single-phase Navier-Stokes flow. The files are listed below.
@@ -373,7 +373,11 @@
      * \defgroup StaggeredDiscretization Staggered FV scheme
      * \brief A staggered finite volume scheme with degrees of freedom at cell-centers and facets.
      */
-
+/* ***************** Flux ******************/
+     /*!
+      * \defgroup Flux
+      * \brief All flux related things available in DuMu<sup>x</sup>
+      */
 /* ***************** Material ******************/
 /*!
  * \defgroup Material Material and Fluid Framework
@@ -517,7 +521,7 @@
  * \defgroup Common Common
  * \brief Common classes, functions, properties and concepts
  */
-     /*!
+      /*!
        * \ingroup Common
        * \defgroup Properties Properties
        * \brief Basic properties of all models in DuMu<sup>x</sup>
@@ -570,3 +574,13 @@
       * \defgroup BoundaryCoupling Boundary coupling mode
       * \brief Couples problems of different or equal dimension that touch at the domain boundary. Examples are equal-dimension multi-physics problems like Darcy-Stokes coupling or PNM (pore network model)-Darcy coupling.
       */
+        /*!
+         * \ingroup BoundaryCoupling
+         * \defgroup DarcyDarcyCoupling Darcy-Darcy domain coupling
+         * \brief Couples domains with equal-dimension multi-physics problems in a Darcy-Darcy coupling.
+         */
+        /*!
+         * \ingroup BoundaryCoupling
+         * \defgroup StokesDarcyCoupling Stokes-Darcy domain coupling
+         * \brief Couples domains with equal-dimension multi-physics problems in a Stokes-Darcy coupling.
+         */

dumux/multidomain/boundary/darcydarcy/couplingmanager.hh

@@ -18,8 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup DarcyDarcyCoupling
  * \brief Coupling manager for equal-dimension boundary coupling
  */
@@ -44,8 +42,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup DarcyDarcyCoupling
  * \brief Coupling manager for equal-dimension boundary coupling of darcy models
  */

dumux/multidomain/boundary/darcydarcy/couplingmapper.hh

@@ -18,10 +18,8 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup DarcyDarcyCoupling
- * \copydoc Dumux::BoundaryCouplingMapper
+ * \copydoc Dumux::DarcyDarcyBoundaryCouplingMapper
  */
 
 #ifndef DUMUX_MULTIDOMAIN_DARCYDARCY_BOUNDARY_COUPLINGMAPPER_HH
@@ -42,8 +40,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup DarcyDarcyCoupling
  * \brief the default mapper for conforming equal dimension boundary coupling between two domains (box or cc)
  * \todo how to extend to arbitrary number of domains?

dumux/multidomain/boundary/stokesdarcy/couplingdata.hh

@@ -18,8 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \copydoc Dumux::StokesDarcyCouplingData
  */
@@ -36,8 +34,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief This structs holds a set of options which allow to modify the Stokes-Darcy coupling mechanism during runtime.
  */
@@ -73,8 +69,6 @@ struct StokesDarcyCouplingOptions
 };
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief This structs helps to check if the two sub models use the same fluidsystem.
  *        Specialization for the case of using an adapter only for the free-flow model.
@@ -89,8 +83,6 @@ struct IsSameFluidSystem
 };
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief This structs helps to check if the two sub models use the same fluidsystem.
  * \tparam FS The fluidsystem
@@ -107,8 +99,6 @@ template <class TypeTag, DiscretizationMethod discMethod>
 class FicksLawImplementation;
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief This structs indicates that Fick's law is not used for diffusion.
  * \tparam DiffLaw The diffusion law.
@@ -117,8 +107,6 @@ template<class DiffLaw>
 struct IsFicksLaw : public std::false_type {};
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief This structs indicates that Fick's law is used for diffusion.
  * \tparam DiffLaw The diffusion law.
@@ -127,8 +115,6 @@ template<class T, DiscretizationMethod discMethod>
 struct IsFicksLaw<FicksLawImplementation<T, discMethod>> : public std::true_type {};
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Helper struct to choose the correct index for phases and components. This is need if the porous-medium-flow model
           features more fluid phases than the free-flow model.
@@ -141,8 +127,6 @@ template<std::size_t stokesIdx, std::size_t darcyIdx, class FFFS, bool hasAdapte
 struct IndexHelper;
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Helper struct to choose the correct index for phases and components. This is need if the porous-medium-flow model
           features more fluid phases than the free-flow model. Specialization for the case that no adapter is used.
@@ -169,8 +153,6 @@ struct IndexHelper<stokesIdx, darcyIdx, FFFS, false>
 };
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Helper struct to choose the correct index for phases and components. This is need if the porous-medium-flow model
           features more fluid phases than the free-flow model. Specialization for the case that a adapter is used.
@@ -210,7 +192,6 @@ template<class MDTraits, class CouplingManager, bool enableEnergyBalance, bool i
 class StokesDarcyCouplingDataImplementation;
 
 /*!
-* \ingroup MultiDomain
 * \ingroup BoundaryCoupling
 * \brief Data for the coupling of a Darcy model (cell-centered finite volume)
 *        with a (Navier-)Stokes model (staggerd grid).
@@ -221,8 +202,6 @@ using StokesDarcyCouplingData = StokesDarcyCouplingDataImplementation<MDTraits,
                                                                       (GetPropType<typename MDTraits::template SubDomain<0>::TypeTag, Properties::ModelTraits>::numComponents() > 1)>;
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief A base class which provides some common methods used for Stokes-Darcy coupling.
  */
@@ -458,8 +437,6 @@ private:
 };
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Coupling data specialization for non-compositional models.
  */
@@ -622,8 +599,6 @@ private:
 };
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Coupling data specialization for compositional models.
  */

dumux/multidomain/boundary/stokesdarcy/couplingmanager.hh

@@ -18,8 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \copydoc Dumux::StokesDarcyCouplingManager
  */
@@ -42,8 +40,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Coupling manager for Stokes and Darcy domains with equal dimension.
  */

dumux/multidomain/boundary/stokesdarcy/couplingmapper.hh

@@ -18,8 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \copydoc Dumux::StokesDarcyCouplingMapper
  */
@@ -43,8 +41,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
- * \ingroup BoundaryCoupling
  * \ingroup StokesDarcyCoupling
  * \brief Coupling mapper for Stokes and Darcy domains with equal dimension.
  */

dumux/multidomain/couplingjacobianpattern.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup Assembly
  * \ingroup MultiDomain
  * \brief Helper function to generate Jacobian pattern for multi domain models
  */
@@ -33,7 +32,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup Assembly
  * \ingroup MultiDomain
  * \brief Helper function to generate coupling Jacobian pattern (off-diagonal blocks)
  *        for cell-centered schemes
@@ -72,7 +70,6 @@ Dune::MatrixIndexSet getCouplingJacobianPattern(const CouplingManager& couplingM
 }
 
 /*!
- * \ingroup Assembly
  * \ingroup MultiDomain
  * \brief Helper function to generate coupling Jacobian pattern (off-diagonal blocks)
  *        for the box scheme
@@ -114,7 +111,6 @@ Dune::MatrixIndexSet getCouplingJacobianPattern(const CouplingManager& couplingM
 }
 
 /*!
- * \ingroup Assembly
  * \ingroup MultiDomain
  * \brief Helper function to generate coupling Jacobian pattern (off-diagonal blocks)
  *        for the staggered scheme (degrees of freedom on cell centers)
@@ -141,7 +137,6 @@ Dune::MatrixIndexSet getCouplingJacobianPattern(const CouplingManager& couplingM
 }
 
 /*!
- * \ingroup Assembly
  * \ingroup MultiDomain
  * \brief Helper function to generate coupling Jacobian pattern (off-diagonal blocks)
  *        for the staggered scheme (degrees of freedom on faces)

dumux/multidomain/couplingmanager.hh

@@ -130,6 +130,7 @@ public:
 
 
     /*!
+     * \ingroup MultiDomain
      * \brief updates all data and variables that are necessary to evaluate the residual of the element of domain i
      *        this is called whenever one of the primary variables that the element residual depends on changes in domain j
      *
@@ -188,6 +189,7 @@ public:
     // \}
 
     /*!
+     * \ingroup MultiDomain
      * \brief evaluates the element residual of a coupled element of domain i which depends on the variables
      *        at the degree of freedom with index dofIdxGlobalJ of domain j
      *

dumux/multidomain/embedded/circlepoints.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Helper function to compute points on a circle
  */
@@ -35,7 +34,6 @@ namespace Dumux {
 namespace EmbeddedCoupling {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief returns a vector of points on a circle
  * \param center the circle center

dumux/multidomain/embedded/couplingmanager1d3d.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Coupling manager for low-dimensional domains embedded in the bulk
  *        domain. Point sources on each integration point are computed by an AABB tree.
@@ -42,7 +41,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief The coupling mode
  */
@@ -71,7 +69,6 @@ public:
 };
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        Point sources on each integration point are computed by an AABB tree.
@@ -80,7 +77,6 @@ template<class MDTraits, EmbeddedCouplingMode mode>
 class EmbeddedCouplingManager1d3d;
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        Point sources on each integration point are computed by an AABB tree.
@@ -559,7 +555,6 @@ private:
 
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        Point sources on each integration point are computed by an AABB tree.
@@ -836,7 +831,6 @@ private:
 
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        Point sources on each integration point are computed by an AABB tree.

dumux/multidomain/embedded/couplingmanager2d3d.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Coupling manager for embedded fractures
  */
@@ -31,7 +30,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Coupling manager for embedded fractures
  * \note we just use the default coupling manager

dumux/multidomain/embedded/couplingmanagerbase.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Coupling manager for low-dimensional domains embedded in the bulk
  *        domain. Point sources on each integration point are computed by an AABB tree.
@@ -68,7 +67,6 @@ public:
 };
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        Point sources on each integration point are computed by an AABB tree.

dumux/multidomain/embedded/extendedsourcestencil.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Extended source stencil helper class for coupling managers
  */
@@ -39,7 +38,6 @@ namespace Dumux {
 namespace EmbeddedCoupling {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief A class managing an extended source stencil
  * \tparam CouplingManager the coupling manager type

dumux/multidomain/embedded/integrationpointsource.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief An integration point source class,
  *        i.e. sources located at a single point in space
@@ -36,7 +35,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief An integration point source class with an identifier to attach data
  *        and a quadrature weight and integration element

dumux/multidomain/embedded/mixeddimensionglue.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup MixedDimension
  * \brief A class glueing two grids of different dimension geometrically
  *        Intersections are computed using axis-aligned bounding box trees
@@ -48,7 +47,6 @@ template<class BulkGridView, class LowDimGridView, class BulkMapper, class LowDi
 class MixedDimensionGlue;
 
 /*!
- * \ingroup MultiDomain
  * \ingroup MixedDimension
  * \brief Range generator to iterate with range-based for loops over all intersections
  *        as follows: for (const auto& is : intersections(glue)) { ... }
@@ -61,7 +59,6 @@ intersections(const MixedDimensionGlue<BulkGridView, LowDimGridView, BulkMapper,
 namespace Glue {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup MixedDimension
  * \brief An intersection object representing an intersection
  *        between two grid entites of different grids

dumux/multidomain/embedded/pointsourcedata.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief Data associated with a point source
  */
@@ -35,7 +34,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief A point source data class used for integration in multidimension models
  * \note The point source and related data are connected via an identifier (id)
@@ -138,7 +136,6 @@ private:
 };
 
 /*!
- * \ingroup MultiDomain
  * \ingroup EmbeddedCoupling
  * \brief A point source data class used for integration in multidimension models
  * \note The point source and related data are connected via an identifier (id)

dumux/multidomain/facet/box/couplingmanager.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \copydoc Dumux::FacetCouplingManager
  */
@@ -37,7 +36,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \brief Manages the coupling between bulk elements and lower dimensional elements
  *        where the coupling occurs across the facets of the bulk grid. This implementation

dumux/multidomain/facet/box/couplingmapper.hh

@@ -16,7 +16,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \copydoc Dumux::FacetCouplingMapper
  */
@@ -34,7 +33,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \brief Base class for the coupling mapper that sets up and stores
  *        the coupling maps between two domains of dimension d and (d-1).

dumux/multidomain/facet/box/darcyslaw.hh

@@ -18,7 +18,6 @@
  *****************************************************************************/
 /*!
  * \file
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \copydoc Dumux::BoxFacetCouplingDarcysLaw
  */
@@ -38,7 +37,6 @@
 namespace Dumux {
 
 /*!
- * \ingroup MultiDomain
  * \ingroup FacetCoupling
  * \brief Darcy's law for the box scheme scheme in the context of coupled models
  *        where coupling occurs across the facets of the bulk domain elements