update transport test to new parametrization files

dune/dorie/interface/transport_simulation.cc

@@ -5,10 +5,13 @@ namespace Dorie{
 
 template<typename Traits>
 TransportSimulation<Traits>::TransportSimulation(
-    Dune::MPIHelper& _helper, 
-    std::shared_ptr<Grid> _grid, 
-    Dune::ParameterTree& _inifile)
-  : helper(_helper), grid(_grid), inifile(_inifile), gv(grid->leafGridView())
+  Dune::ParameterTree& _inifile,
+  std::shared_ptr<GridMapper> _grid_mapper,
+  Dune::MPIHelper& _helper
+) : helper(_helper)
+  , grid(_grid_mapper->get_grid())
+  , inifile(_inifile)
+  , gv(grid->leafGridView())
   , mbe_slop(estimate_mbe_entries<typename MBE::size_type>(Traits::dim,Traits::GridGeometryType))
   , mbe_tlop(1)
   , verbose(inifile.get<int>("output.verbose"))

dune/dorie/interface/transport_simulation.hh

@@ -18,14 +18,12 @@
 #include "util.hh"
 #include "adaptivity.hh"
 #include "simulation_base.hh"
-#include "../solver/util_interpolator.hh"
-#include "../solver/param_base.hh"
-#include "../solver/param_factory.hh"
 #include "../solver/transport_initial.hh"
 #include "../solver/transport_boundary.hh"
 #include "../solver/transport_operator_FV.hh"
 #include "../solver/util_controller.hh"
 #include "../solver/util_writer.hh"
+#include "../solver/util_grid_creator.hh"
 
 namespace Dune{
 namespace Dorie{
@@ -67,7 +65,9 @@ struct TransportSimulationTraits : public BaseTraits
   /// GFS Constraints Container
   using CC = typename GFSHelper::CC;
 
-  // -- D/*ORiE Class Definitions -- //
+  // -- DORiE Class Definitions -- //
+  /// Wrapper for grid and volume & boundary mappings
+  using GridMapper = Dune::Dorie::GridMapper<typename BaseTraits::Grid>;
   /// Class defining boundary conditions
   using SoluteBoundary = Dune::Dorie::SoluteBoundary<BaseTraits>;
   /// Class defining source terms
@@ -152,6 +152,8 @@ protected:
   using CC = typename Traits::CC;
 
   // -- D/*ORiE Class Definitions -- //
+  /// Wrapper for grid and volume & boundary mappings
+  using GridMapper = typename Traits::GridMapper;
   /// Class defining boundary conditions
   using SoluteBoundary = typename Traits::SoluteBoundary;
   /// Class defining source terms
@@ -241,16 +243,17 @@ protected:
   bool operator_setup_flag = true;
 public:
 
-  /// Construct basic simulation. Prepare setup for basic simulation.
-  /**
-   *  \param _helper Dune MPI instance controller
-   *  \param _grid Shared pointer to the grid
-   *  \param _inifile Dune parameter file parser
+  /*------------------------------------------------------------------------*//**
+   * @brief      Construct basic simulation. Prepare setup for basic simulation.
+   *
+   * @param      _grid_mapper Mapper for grid and volume/boundary data
+   * @param      _helper   Dune MPI instance controller
+   * @param      _inifile  Dune parameter file parser
    */
-  TransportSimulation(
-    Dune::MPIHelper& _helper, 
-    std::shared_ptr<Grid> _grid, 
-    Dune::ParameterTree& _inifile
+  TransportSimulation (
+    Dune::ParameterTree& _inifile,
+    std::shared_ptr<GridMapper> _grid_mapper,
+    Dune::MPIHelper& _helper
   );
 
   // TODO: Define data exchange with richards

dune/dorie/test/test-simulation-dummy-transport.cc

@@ -4,9 +4,17 @@
 #include "config.h"
 #endif
 
+#include <string>
+#include <iostream>
+#include <cstdio>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+
 #include "../interface/transport_simulation.hh"
 #include "../interface/transport_simulation.cc"
 #include "../solver/util_grid_creator.hh"
+#include "../solver/util_grid_creator.hh"
 
 #include <dune/common/exceptions.hh>
 #include <dune/common/parametertree.hh>
@@ -92,10 +100,11 @@ int main(int argc, char** argv) {
     {
       if (gtype == "rectangular")
       {
-        auto grid = Dune::Dorie::build_grid_cube<Dune::YaspGrid<2>>(inifile,helper);
+        Dune::Dorie::GridCreator<Dune::YaspGrid<2>> grid_creator(inifile, helper);
+        auto grid_mapper = grid_creator.get_mapper();
 
         using Traits = Cube<2>;
-        Sim<Traits> sim(helper,grid,inifile_transport);
+        Sim<Traits> sim(inifile_transport,grid_mapper,helper);
 
         typename Traits::Vector flux;
         typename Traits::Scalar sat;
@@ -106,6 +115,8 @@ int main(int argc, char** argv) {
         using GFFlux = typename Traits::GFWaterFlux;
         using GFSat = typename Traits::GFSaturation;
 
+        auto grid = grid_mapper->get_grid();
+
         auto gfFlux = std::make_shared<GFFlux>(grid->leafGridView(),flux);
         auto gfSat = std::make_shared<GFSat>(grid->leafGridView(),sat);
 
@@ -123,10 +134,11 @@ int main(int argc, char** argv) {
     {
       if (gtype == "rectangular")
       {
-        auto grid = Dune::Dorie::build_grid_cube<Dune::YaspGrid<3>>(inifile,helper);
+        Dune::Dorie::GridCreator<Dune::YaspGrid<3>> grid_creator(inifile, helper);
+        auto grid_mapper = grid_creator.get_mapper();
 
         using Traits = Cube<3>;
-        Sim<Traits> sim(helper,grid,inifile_transport);
+        Sim<Traits> sim(inifile_transport,grid_mapper,helper);
 
         typename Traits::Vector flux;
         typename Traits::Scalar sat;
@@ -134,6 +146,8 @@ int main(int argc, char** argv) {
         flux[dim-1] = inifile.get<double>("_constantWater.flux",-5.5e-8);
         sat = inifile.get<double>("_constantWater.saturation",1.);
 
+        auto grid = grid_mapper->get_grid();
+        
         using GFFlux = typename Traits::GFWaterFlux;
         using GFSat = typename Traits::GFSaturation;
 

dune/dorie/test/test-simulation-dummy-transport.mini.in

@@ -7,20 +7,29 @@ _asset_path = "${CMAKE_CURRENT_LIST_DIR}/../../../test/"
 
 grid.gridType = rectangular
 grid.initialLevel = 0
-grid.cells = 40 40 
+grid.cells = 40 40
+
+grid.mappingFile = none
+grid.globalIndex = 0
 
 adaptivity.useAdaptivity = false
 
-transport.output.fileName = test-simulation-dummy-transport | unique
-transport.output.outputPath = test-simulation-dummy-transport | unique
-transport.output.verbose = 0
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+
+parameters.file = "{_asset_path}/param/param.yml"
+
+[transport]
+
+output.fileName = test-simulation-dummy-transport | unique
+output.outputPath = test-simulation-dummy-transport | unique
+output.verbose = 0
 
-transport.boundary.file = "{_asset_path}/bcs/solute_2d.dat"
+boundary.file = "{_asset_path}/bcs/solute_2d.dat"
 
-transport.parameters.molecularDifussion = 2E-9, 0 | expand prec
+parameters.molecularDifussion = 2E-9, 0 | expand prec
 
-transport.time.end = 1E8
-transport.time.maxTimestep = 1E7
-transport.time.startTimestep = 1E4
+time.end = 1E8
+time.maxTimestep = 1E7
+time.startTimestep = 1E4
 
-transport.numerics.timestepMethod = alex2
\ No newline at end of file
+numerics.timestepMethod = alex2
\ No newline at end of file