[subgrid] Restructure. Add option for reading from binary file

Based on initial work by Kilian Weishaupt.

dumux/io/grid/subgridmanager.hh

@@ -28,66 +28,101 @@
 
 #include <memory>
 
+#include <dune/common/deprecated.hh>
+#include <dune/common/shared_ptr.hh>
+#include <dune/common/concept.hh>
 #include <dune/subgrid/subgrid.hh>
 
 #include <dumux/common/parameters.hh>
 #include <dumux/common/boundaryflag.hh>
+#include <dumux/io/grid/gridmanager_base.hh>
+#include <dumux/io/grid/gridmanager_yasp.hh>
 
-// TODO: remove this after 3.1 is released
+#include <dumux/io/rasterimagereader.hh>
+
+// TODO: deprecated: remove this after 3.1 is released
 #include <dune/grid/io/file/vtk.hh>
-// TODO: remove this after 3.1 is released
+// TODO: deprecated: remove this after 3.1 is released
 #include <dune/grid/io/file/dgfparser/dgfwriter.hh>
 
 namespace Dumux {
+namespace Concept {
+
+/*!
+ * \ingroup InputOutput
+ * \brief The element selector concept
+ */
+template<class Element>
+struct ElementSelector
+{
+    template<class F>
+    auto require(F&& f) -> decltype(
+        bool(f(std::declval<const Element&>()))
+    );
+};
+} // end namespace Concept
 
 /*!
  * \ingroup InputOutput
- * \brief A grid manager for dune-subgrid.
+ * \brief The base class for grid managers for dune-subgrid.
  */
-template <class HostGrid>
-class SubgridManager
+template <class HostGrid, class HostGridManager>
+class SubGridManagerBase
 {
-    static constexpr auto dim = HostGrid::dimension;
+    static constexpr int dim = HostGrid::dimension;
+    using HostElement = typename HostGrid::template Codim<0>::Entity;
 
 public:
     using Grid = Dune::SubGrid<dim, HostGrid>;
 
+    /*!
+     * \brief Make the grid using an externally created host grid.
+     */
+    template<class ES,
+             typename std::enable_if_t<Dune::models<Concept::ElementSelector<HostElement>, ES>(), int> = 0>
+    void init(HostGrid& hostGrid,
+              const ES& selector,
+              const std::string& paramGroup = "")
+    {
+        subGrid_ = createGrid_(hostGrid, selector, paramGroup);
+        loadBalance();
+    }
+
+    /*!
+     * \brief Make the grid and create the host grid internally.
+     */
+    template<class ES,
+             typename std::enable_if_t<Dune::models<Concept::ElementSelector<HostElement>, ES>(), int> = 0>
+    void init(const ES& selector,
+              const std::string& paramGroup = "")
+    {
+        initHostGrid_(paramGroup);
+        subGrid_ = createGrid_(hostGridManager_->grid(), selector, paramGroup);
+        loadBalance();
+    }
+
     /*!
      * \brief Make the subgrid.
      */
     template<class ElementSelector>
-    static std::unique_ptr<Grid> makeGrid(HostGrid& hostgrid,
+    DUNE_DEPRECATED_MSG("Create an instance of this class and use subgridManager.init(hostGrid, selector, paramGroup)")
+    static std::unique_ptr<Grid> makeGrid(HostGrid& hostGrid,
                                           const ElementSelector& selector,
-                                          const std::string& modelParamGroup = "")
+                                          const std::string& paramGroup = "")
     {
-        // A unique pointer to the subgrid.
-        auto subgridPtr = std::make_unique<Grid>(hostgrid);
+        std::cerr << "Deprecation warning: SubGridManager::makeGrid is deprecated."
+                  << "Create an instance of this class and use subgridManager.init(hostGrid, selector, paramGroup)." << std::endl;
 
-        // A container to store the host grid elements' ids.
-        std::set<typename HostGrid::Traits::GlobalIdSet::IdType> elementsForSubgrid;
-        const auto& globalIDset = subgridPtr->getHostGrid().globalIdSet();
-
-        // Construct the subgrid.
-        subgridPtr->createBegin();
-
-        // Loop over all elements of the host grid and use the selector to
-        // choose which elements to add to the subgrid.
-        auto hostGridView = subgridPtr->getHostGrid().leafGridView();
-        for (const auto& e : elements(hostGridView))
-            if (selector(e))
-                elementsForSubgrid.insert(globalIDset.template id<0>(e));
-
-        subgridPtr->insertSetPartial(elementsForSubgrid);
-        subgridPtr->createEnd();
+        auto subgridPtr = createGrid_(hostGrid, selector, paramGroup);
 
         // TODO: remove this after 3.1 is released
         // If desired, write out the final subgrid as a dgf file.
-        if (getParamFromGroup<bool>(modelParamGroup, "Grid.WriteSubGridToDGF", false))
+        if (getParamFromGroup<bool>(paramGroup, "Grid.WriteSubGridToDGF", false))
         {
             std::cerr << "Deprecation warning: SubGridManager: Grid.WriteSubGridToDGF is deprecated."
                       << "Use Dune::VTKWriter to write out your grid manually." << std::endl;
 
-            const auto postfix = getParamFromGroup<std::string>(modelParamGroup, "Problem.Name", "");
+            const auto postfix = getParamFromGroup<std::string>(paramGroup, "Problem.Name", "");
             const std::string name = postfix == "" ? "subgrid" : "subgrid_" + postfix;
             Dune::DGFWriter<typename Grid::LeafGridView> writer(subgridPtr->leafGridView());
             writer.write(name + ".dgf");
@@ -95,12 +130,12 @@ public:
 
         // TODO: remove this after 3.1 is released
         // If desired, write out the hostgrid as vtk file.
-        if (getParamFromGroup<bool>(modelParamGroup, "Grid.WriteSubGridToVtk", false))
+        if (getParamFromGroup<bool>(paramGroup, "Grid.WriteSubGridToVtk", false))
         {
             std::cerr << "Deprecation warning: SubGridManager: Grid.WriteSubGridToVtk is deprecated."
                       << "Use Dune::VTKWriter to write out your grid manually." << std::endl;
 
-            const auto postfix = getParamFromGroup<std::string>(modelParamGroup, "Problem.Name", "");
+            const auto postfix = getParamFromGroup<std::string>(paramGroup, "Problem.Name", "");
             const std::string name = postfix == "" ? "subgrid" : "subgrid_" + postfix;
             Dune::VTKWriter<typename Grid::LeafGridView> vtkWriter(subgridPtr->leafGridView());
             vtkWriter.write(name);
@@ -109,6 +144,177 @@ public:
         // Return a unique pointer to the subgrid.
         return subgridPtr;
     }
+
+    /*!
+     * \brief Returns a reference to the grid.
+     */
+    Grid& grid()
+    {
+        return *subGrid_;
+    }
+
+    /*!
+     * \brief Distributes the grid on all processes of a parallel
+     *        computation.
+     */
+    void loadBalance()
+    {
+        subGrid_->loadBalance();
+    }
+
+protected:
+
+    /*!
+     * \brief Make the subgrid.
+     */
+    template<class ES,
+             typename std::enable_if_t<Dune::models<Concept::ElementSelector<HostElement>, ES>(), int> = 0>
+    static std::unique_ptr<Grid> createGrid_(HostGrid& hostGrid,
+                                             const ES& selector,
+                                             const std::string& paramGroup = "")
+    {
+        // A unique pointer to the subgrid.
+        auto subgridPtr = std::make_unique<Grid>(hostGrid);
+
+        // A container to store the host grid elements' ids.
+        std::set<typename HostGrid::Traits::GlobalIdSet::IdType> elementsForSubgrid;
+        const auto& globalIDset = subgridPtr->getHostGrid().globalIdSet();
+
+        // Construct the subgrid.
+        subgridPtr->createBegin();
+
+        // Loop over all elements of the host grid and use the selector to
+        // choose which elements to add to the subgrid.
+        auto hostGridView = subgridPtr->getHostGrid().leafGridView();
+        for (const auto& e : elements(hostGridView))
+            if (selector(e))
+                elementsForSubgrid.insert(globalIDset.template id<0>(e));
+
+        if (elementsForSubgrid.empty())
+            DUNE_THROW(Dune::GridError, "No elements in subgrid");
+
+        subgridPtr->insertSetPartial(elementsForSubgrid);
+        subgridPtr->createEnd();
+
+        // Return a unique pointer to the subgrid.
+        return subgridPtr;
+    }
+
+    void initHostGrid_(const std::string& paramGroup)
+    {
+        hostGridManager_ = std::make_unique<HostGridManager>();
+        hostGridManager_->init(paramGroup);
+    }
+
+    /*!
+     * \brief Returns a reference to the host grid.
+     */
+    HostGrid& hostGrid_()
+    {
+        return hostGridManager_->grid();
+    }
+
+    std::shared_ptr<Grid> subGrid_;
+    std::unique_ptr<HostGridManager> hostGridManager_;
+};
+
+/*!
+ * \ingroup InputOutput
+ * \brief A grid manager for dune-subgrid
+ */
+template<class HostGrid, class HostGridManager = GridManager<HostGrid>>
+class SubgridManager : public SubGridManagerBase<HostGrid, HostGridManager>
+{};
+
+/*!
+ * \ingroup InputOutput
+ * \brief A grid manager for dune-subgrid using YaspGrid as the host grid
+ * With YaspGrid as host grid we also support creating grids from raster images
+ */
+template<int dim, class Coordinates>
+class SubgridManager<Dune::YaspGrid<dim, Coordinates>>
+: public SubGridManagerBase<Dune::YaspGrid<dim, Coordinates>, GridManager<Dune::YaspGrid<dim, Coordinates>>>
+{
+    using ParentType = SubGridManagerBase<Dune::YaspGrid<dim, Coordinates>, GridManager<Dune::YaspGrid<dim, Coordinates>>>;
+public:
+    using ParentType::Grid;
+    using ParentType::init;
+
+    /*!
+     * \brief Make the subgrid without host grid and element selector
+     * This means we try to construct the element selector from the input file
+     * \param paramGroup the parameter file group to check
+     */
+    void init(const std::string& paramGroup = "")
+    {
+        // check if there is an image file we can construct the element selector from
+        if (hasParamInGroup(paramGroup, "Grid.Image"))
+        {
+            const auto imgFileName = getParamFromGroup<std::string>(paramGroup, "Grid.Image");
+            const auto ext = getFileExtension_(imgFileName);
+            if (ext == "pbm")
+            {
+                if (dim != 2)
+                    DUNE_THROW(Dune::GridError, "Portable Bitmap Format only supports dim == 2");
+
+                // read image
+                const auto img = NetPBMReader::readPBM(imgFileName);
+                createGridFromImage_(img, paramGroup);
+            }
+            else
+                DUNE_THROW(Dune::IOError, "The SubGridManager doesn't support image files with extension: *." << ext);
+
+        }
+        else
+            DUNE_THROW(Dune::IOError, "SubGridManager couldn't construct element selector. Specify Grid.Image in the input file!");
+    }
+
+private:
+    template<class Img>
+    void createGridFromImage_(const Img& img, const std::string& paramGroup)
+    {
+        // check if the number of cells matches
+        std::array<int, dim> cells; cells.fill(1);
+        cells = getParamFromGroup<std::array<int, dim>>(paramGroup, "Grid.Cells", cells);
+
+        if (img.header().nCols != cells[0])
+            DUNE_THROW(Dune::GridError, "Host grid has wrong number of cells in x-direction. Expected "
+                         << img.header().nCols << ", got " << cells[0]);
+        if (img.header().nRows != cells[1])
+            DUNE_THROW(Dune::GridError, "Host grid has wrong number of cells in y-direction. Expected "
+                         << img.header().nRows << ", got " << cells[1]);
+
+
+        // construct the host grid
+        this->initHostGrid_(paramGroup);
+
+        // check if the marker is customized, per default
+        // we mark all cells that are encoded as 0
+        const bool marked = getParamFromGroup<bool>(paramGroup, "Grid.Marker", 0);
+
+        // Create the selector
+        auto elementSelector = [this, &img, &marked](const auto& element)
+        {
+            const auto eIdx = this->hostGrid_().leafGridView().indexSet().index(element);
+            return img[eIdx] == marked;
+        };
+
+        // create the grid
+        this->subGrid_ = this->createGrid_(this->hostGrid_(), elementSelector, paramGroup);
+        this->loadBalance();
+    }
+
+    /*!
+     * \brief Returns the filename extension of a given filename
+     */
+    std::string getFileExtension_(const std::string& fileName) const
+    {
+        std::size_t i = fileName.rfind('.', fileName.length());
+        if (i != std::string::npos)
+            return(fileName.substr(i+1, fileName.length() - i));
+        else
+            DUNE_THROW(Dune::IOError, "Please provide and extension for your grid file ('"<< fileName << "')!");
+    }
 };
 
 //! dune-subgrid doesn't have this implemented