#1405 Review the Coords::GetIndex() use and replace some by more appropriate...

#1405 Review the Coords::GetIndex() use and replace some by more appropriate GetPositionInCoordsListInMesh(). Comments on those two methods have been overhauled to make the distinction clearer.

Sources/Geometry/Coords/Coords.hpp

@@ -228,9 +228,42 @@ namespace MoReFEM
 
     public:
 
-        //! Get the index. This index depends on the format used and might not be contiguous (contrary to position_in_mesh).
+        /*!
+         * \brief Index of the \a Coords as defined in the input mesh.
+         *
+         * This index:
+         * - Stems directly from the input mesh. For instance, Medit ones begins at 1 and are then incremented.
+         * - Is defined at the program-wise level.
+         * - Provides no guarantee about contigousness.
+         *
+         * It is fine to identify a \a Coords uniquely but should not be used for direct access to a \a Coords
+         * in a \a Coords list.
+         *
+         * Remember anyway than MoReFEM strongly suggest to use objects (or pointers to objects) rather than such
+         * indexes; this functionality is there for internal use and for interface with output formats.
+         *
+         * \return The index as it was defined in the original mesh file.
+         */
         unsigned int GetIndex() const noexcept;
 
+        /*!
+         * \brief Get the position in the enclosing mesh list (should be in [0; Ncoords - 1] by design.
+         *
+         * \tparam MpiScaleT If processor-wise, the position after mpi reduction is given. If program-wise, the one
+         * before is yielded. By convention ghosted only Coords are numbered as if the first one was put immediately
+         * after the last processor-wise one.
+         *
+         * This method is what should be used to find a \a Coords in a \a Mesh container (or in the mesh methods
+         * Mesh::GetCoord()).
+         * Remember anyway than MoReFEM strongly suggest to use objects (or pointers to objects) rather than such
+         * indexes; this functionality is mostly there for internal use.
+         *
+         *
+         * \return Position of the \a Coords in the mesh list.
+         */
+        template<MpiScale MpiScaleT>
+        unsigned int GetPositionInCoordsListInMesh() const noexcept;
+
         //! Set the index.
         //! \param[in] index New value of the index.
         void SetIndex(unsigned int index) noexcept;
@@ -260,18 +293,6 @@ namespace MoReFEM
         //! Get the type of the Coords.
         InterfaceNS::Nature GetInterfaceNature() const;
 
-        /*!
-         * \brief Get the position in the enclosing mesh list (should be in [0; Ncoords - 1] by design, contrary to index_).
-         *
-         * \tparam MpiScaleT If processor-wise, the position after mpi reduction is given. If program-wise, the one
-         * before is yielded. By convention ghosted only Coords are numbered as if the first one was put immediately
-         * after the last processor-wise one.
-         *
-         * \return Position of the \a Coords in the mesh list.
-         */
-        template<MpiScale MpiScaleT>
-        unsigned int GetPositionInCoordsListInMesh() const noexcept;
-
 
         /*!
          * \brief Add a new \a Domain that contains the \a Coords.
@@ -468,20 +489,6 @@ namespace MoReFEM
     void WriteVTK_PolygonalDataFormat(const Coords& point, std::ostream& stream);
 
 
-    namespace Internal
-    {
-
-
-        namespace CoordsNS
-        {
-
-
-        } // namespace CoordsNS
-
-
-    } // namespace Internal
-
-
 } // namespace MoReFEM
 
 

Sources/Geometry/Interfaces/Interface.cpp

@@ -120,6 +120,7 @@ namespace MoReFEM
     const std::vector<unsigned int>& Interface
     ::GetVertexCoordsIndexList() const
     {
+        std::cout << "HERE?" << std::endl;
         if (vertex_coords_index_list_.empty()) // means it is not yet initialized.
             vertex_coords_index_list_ = ComputeVertexCoordsIndexList(GetVertexCoordsList());
         
@@ -195,7 +196,7 @@ namespace MoReFEM
             for (const auto& coords_ptr : vertex_coords_list)
             {
                 assert(!(!coords_ptr));
-                ret.push_back(coords_ptr->GetIndex());
+                ret.push_back(coords_ptr->GetPositionInCoordsListInMesh<MpiScale::processor_wise>());
             }
             
             return ret;

Sources/Geometry/Interfaces/Interface.hpp

@@ -135,7 +135,6 @@ namespace MoReFEM
          * \brief Get the list of \a Coords indexes that belongs to the interface.
          *
          * \return List of \a Coords indexes that belongs to the interface.
-         *
          */
         const std::vector<unsigned int>& GetVertexCoordsIndexList() const;
 

Sources/Geometry/Mesh/Internal/ComputeInterfaceListInMesh.cpp

@@ -110,7 +110,8 @@ namespace MoReFEM
                         assert(vertex_coords_list.size() == 1ul);
                         assert(!(!vertex_coords_list.back()));
                         
-                        std::vector<unsigned int> index { vertex_coords_list.back()->GetIndex() };
+                        std::vector<unsigned int> index
+                        { vertex_coords_list.back()->GetPositionInCoordsListInMesh<MpiScale::processor_wise>() };
                         Utilities::PrintContainer(index, out);
                     }
                 }

Sources/Geometry/Mesh/Internal/Format/Medit.cpp

@@ -686,7 +686,8 @@ namespace MoReFEM
                                 }
                                 
                                 for (std::size_t i = 0; i < Ncoord; ++i)
-                                    processor_wise_reindexing.insert(std::make_pair(coords_list[i]->GetIndex(), static_cast<int>(i) + 1));
+                                    processor_wise_reindexing.insert(std::make_pair(coords_list[i]->GetIndex(),
+                                                                                    static_cast<int>(i) + 1));
                                 
                                 // Now we can write into the file with all informations from the map
                                 for (const auto& block : geometric_elt_by_type)

Sources/Geometry/Mesh/Internal/Format/VTK_PolygonalData.cpp

@@ -140,7 +140,9 @@ namespace MoReFEM
                             
                             assert(coords_list.size() == 3);
                             
-                            file_out << "3" << '\t' << geom_elt_coords_list[0]->GetIndex() << '\t' <<  geom_elt_coords_list[1]->GetIndex() << '\t' <<  geom_elt_coords_list[2]->GetIndex() << '\n';
+                            file_out << "3" << '\t' << geom_elt_coords_list[0]->GetIndex()
+                            << '\t' <<  geom_elt_coords_list[1]->GetIndex()
+                            << '\t' <<  geom_elt_coords_list[2]->GetIndex() << '\n';
                         }
                     }
 

Sources/Geometry/Mesh/Mesh.cpp

@@ -282,7 +282,9 @@ namespace MoReFEM
         
         
         
-        auto processor_wise_coords_unique_ptr_list = GenerateReducedList(processor_wise_coords_id_list, program_wise_coords_list);
+        auto processor_wise_coords_unique_ptr_list =
+            GenerateReducedList(processor_wise_coords_id_list, program_wise_coords_list);
+
         SetGhostedCoordsList(GenerateReducedList(ghosted_coords_id_list, program_wise_coords_list));
         
         const auto Nprocessor_wise_coords = processor_wise_coords_unique_ptr_list.size();

Sources/Geometry/Mesh/Mesh.hpp

@@ -500,7 +500,8 @@ namespace MoReFEM
         unsigned int NgeometricElt(unsigned int dimension) const;
 
         //! Get the \a index -th coord on the processor.
-        //! \param[in] index Position of the index in the processor-wise \a Coords list.
+        //! \param[in] index Position of the sought \a Coords in the processor-wise \a Coords list. This index is
+        //! the output of Coords::GetPositionInCoordsListInMesh(), NOT Coords::GetIndex() which might not be contiguous.
         const Coords& GetCoord(unsigned int index) const;
 
         /*!

Sources/Geometry/Mesh/Mesh.hxx

@@ -96,7 +96,9 @@ namespace MoReFEM
 
     inline const Coords& Mesh::GetCoord(unsigned int index) const
     {
-        assert(index < processor_wise_coords_list_.size());
+        assert(index < processor_wise_coords_list_.size()
+               && "Make sure the index is a result of Coords::GetPositionInCoordsListInMesh() and not "
+               "Coords::GetIndex().");
         assert(!(!processor_wise_coords_list_[index]));
         return *processor_wise_coords_list_[index];
     }
@@ -135,13 +137,13 @@ namespace MoReFEM
         return Nvolume_;
     }
 
+
     inline double Mesh::GetSpaceUnit() const noexcept
     {
         return space_unit_;
     }
 
 
-
     template<>
     inline void Mesh::SetNinterface<Vertex>(unsigned int N)
     {

Sources/ParameterInstances/Fiber/Internal/FillGlobalVector.hxx

@@ -67,7 +67,8 @@ namespace MoReFEM
                         const auto& vertex_coords_ptr = vertex_coords_list.back();
                         assert(!(!vertex_coords_ptr));
 
-                        const auto geometric_vertex_index = vertex_coords_ptr->GetIndex();
+                        const auto geometric_vertex_index =
+                            vertex_coords_ptr->GetPositionInCoordsListInMesh<MpiScale::processor_wise>();
 
                         auto it = value_list_per_coord_index.find(geometric_vertex_index);
 

Sources/PostProcessing/Data/Interface.hpp

@@ -98,7 +98,7 @@ namespace MoReFEM
                 unsigned int GetIndex() const noexcept;
 
                 //! Indexes of the Coords that describe the interface.
-                // Only P1 Geometry at this point, so assumption Coords are vertices...
+                // #248 Only P1 Geometry at this point, so assumption Coords are vertices...
                 const std::vector<unsigned int>& GetVertexCoordsIndexList() const noexcept;
 
             private:

Sources/PostProcessing/File/InterfaceFile.cpp

@@ -222,7 +222,7 @@ namespace MoReFEM
                            [](const auto& coords_ptr)
                            {
                                assert(!(!coords_ptr));
-                               return coords_ptr->GetIndex();
+                               return coords_ptr->template GetPositionInCoordsListInMesh<MpiScale::processor_wise>();
                            });
             
             std::sort(coords_index_list.begin(), coords_index_list.end());

Sources/PostProcessing/OutputFormat/Ensight6.cpp

@@ -43,7 +43,6 @@ namespace MoReFEM::PostProcessingNS::OutputFormat
                                RefinedMesh is_mesh_refined);
 
 
-
     } // namespace anonymous
             
                    
@@ -275,7 +274,7 @@ namespace MoReFEM::PostProcessingNS::OutputFormat
 
             using DofWithValuesType = std::pair<Data::DofInformation::const_shared_ptr, double>;
 
-            std::vector<DofWithValuesType> dof_with_values_type;
+            std::vector<DofWithValuesType> dof_with_values;
 
             #ifndef NDEBUG
             if (is_mesh_refined == RefinedMesh::yes)
@@ -331,7 +330,7 @@ namespace MoReFEM::PostProcessingNS::OutputFormat
 
                     assert(processor_wise_index < solution.size());
 
-                    dof_with_values_type.push_back({dof_ptr, solution[processor_wise_index]});
+                    dof_with_values.push_back({dof_ptr, solution[processor_wise_index]});
                 }
             }
 
@@ -341,7 +340,9 @@ namespace MoReFEM::PostProcessingNS::OutputFormat
             // That's the reason refined mesh does not work with model run in parallel.
             if (is_mesh_refined == RefinedMesh::no)
             {
-                std::sort(dof_with_values_type.begin(), dof_with_values_type.end(),
+
+
+                std::sort(dof_with_values.begin(), dof_with_values.end(),
                           [](const DofWithValuesType& lhs, const DofWithValuesType& rhs)
                           {
                               if (lhs == rhs)
@@ -375,18 +376,11 @@ namespace MoReFEM::PostProcessingNS::OutputFormat
                               return lhs_dof->GetUnknownComponent() < rhs_dof->GetUnknownComponent();
                           });
             }
-            std::cout << "CHECK = ";
-            for (const auto& item : dof_with_values_type)
-            {
-                std::cout << item.first->GetInterface().GetVertexCoordsIndexList().back() << "\t";
-
-            }
 
-            std::cout << std::endl;
 
             unsigned int counter = 0u;
 
-            for (const auto& pair : dof_with_values_type)
+            for (const auto& pair : dof_with_values)
             {
                 ensight_output_stream << std::setw(12) << std::scientific << std::setprecision(5)
                 << pair.second;