exercises/exercise-biomineralization/params.input

@@ -10,6 +10,8 @@ Name = biomin
 UpperRight = 20 15 # x-/y-coordinates of the upper-right corner of the grid [m]
 Cells = 20 15 # x-/y-resolution of the grid
 
+# TODO: dumux-course-task 4:
+# vary parameters InjBioTime, InitBiofilm, InjVolumeflux, ConcUrea and ConcCa
 [Initial]
 InitDensityW = 997 # [kg/m³] initial wetting density
 InitPressure = 1e5 # [Pa] initial pressure
@@ -47,5 +49,5 @@ KUrea = 0.355 # [mol/kgH2O] Lauchnor et al. 2014
 [Brine]
 Salinity = 0.1
 
-#TODO: dumux-course-task
+# TODO: dumux-course-task 6:
 # add the power law's exponent parameter PowerLaw.Exponent = 5.0

exercises/exercise-biomineralization/properties.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -19,7 +19,7 @@
 #include <dumux/porousmediumflow/2pncmin/model.hh>
 #include <dumux/porousmediumflow/problem.hh>
 #include <dumux/material/components/simpleco2.hh> //!< Simplified CO2 component based on ideal gas law
-// TODO: dumux-course-task
+// TODO: dumux-course-task 7:
 // include the CO2 component and tabulated values from DuMux
 #include "solidsystems/biominsolidphase.hh" // The biomineralization solid system
 
@@ -52,7 +52,7 @@ struct FluidSystem<TypeTag, TTag::ExerciseBioMin>
 {
 private:
     using Scalar = GetPropType<TypeTag, Properties::Scalar>;
-    // TODO: dumux-course-task
+    // TODO: dumux-course-task 7:
     // use the CO2 component with tabulated values
     using CO2Impl = Components::SimpleCO2<Scalar>;
     using H2OType = Components::TabulatedComponent<Components::H2O<Scalar>>;

exercises/exercise-biomineralization/solidsystems/biominsolidphase.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!

exercises/exercise-coupling-ff-pm/1pspatialparams.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!

exercises/exercise-coupling-ff-pm/2pspatialparams.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!

exercises/exercise-coupling-ff-pm/CMakeLists.txt

-# SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+# SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 add_subdirectory(interface)

exercises/exercise-coupling-ff-pm/interface/CMakeLists.txt

-# SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+# SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 # executables for ex_interface_coupling_ff-pm

exercises/exercise-coupling-ff-pm/interface/freeflowsubproblem.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -71,7 +71,7 @@ public:
 
         const auto& globalPos = scvf.dofPosition();
 
-        // TODO: dumux-course-task 1.A
+        // TODO: dumux-course-task 1.A:
         // Change the boundary conditions here as described in the exercise
         if(onUpperBoundary_(globalPos))
         {
@@ -89,16 +89,15 @@ public:
         // coupling interface
         if(couplingManager().isCoupledEntity(CouplingManager::stokesIdx, scvf))
         {
+            // TODO: dumux-course-task 1.C:
+            // set the Beaver-Joseph-Saffman slip condition for the tangential momentum balance equation,
+            // consider orientation of face automatically
             values.setCouplingNeumann(Indices::conti0EqIdx);
             values.setCouplingNeumann(Indices::momentumYBalanceIdx);
-            // TODO: dumux-course-task 1.B
+            // TODO: dumux-course-task 1.B:
             // Replace Dirichlet BC with Beavers-Joseph-Saffman slip condition for the tangential momentum balance
             values.setDirichlet(Indices::velocityXIdx); // assume no slip on interface
 
-            // TODO: dumux-course-task 1.C
-            // set the Beaver-Joseph-Saffman slip condition for the tangential momentum balance equation,
-            // consider orientation of face automatically
-
         }
 
         return values;
@@ -112,8 +111,10 @@ public:
     PrimaryVariables dirichletAtPos(const GlobalPosition& globalPos) const
     {
         PrimaryVariables values(0.0);
+        // TODO: dumux-course-task 1.A:
+        // set a no-slip, no-flow condition at the top
         values[Indices::velocityYIdx] = -1e-6 * globalPos[0] * (this->gridGeometry().bBoxMax()[0] - globalPos[0]);
-        // TODO: dumux-course-task 1.A
+        // TODO: dumux-course-task 1.A:
         // set fixed pressures on the left and right boundary
 
         return values;

exercises/exercise-coupling-ff-pm/interface/main.cc

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -52,7 +52,7 @@ int main(int argc, char** argv)
     using FreeflowTypeTag = Properties::TTag::FreeflowOneP;
     using PorousMediumTypeTag = Properties::TTag::PorousMediumFlowOneP;
 
-    //TODO: dumux-course-task 1.C
+    //TODO: dumux-course-task 1.C:
     // ******************** comment-out this section for the last exercise **************** //
 
     // create two individual grids (from the given grid file or the input file)
@@ -168,7 +168,7 @@ int main(int argc, char** argv)
     StaggeredVtkOutputModule<FreeflowGridVariables, decltype(freeflowSol)> freeflowVtkWriter(*freeflowGridVariables, freeflowSol, freeflowName);
     GetPropType<FreeflowTypeTag, Properties::IOFields>::initOutputModule(freeflowVtkWriter);
 
-    //TODO: dumux-course-task 1.B
+    //TODO: dumux-course-task 1.B:
     //****** uncomment the add analytical solution of v_x *****//
     // freeflowVtkWriter.addField(freeflowProblem->getAnalyticalVelocityX(), "analyticalV_x");
 

exercises/exercise-coupling-ff-pm/interface/params.input

-# # TODO: dumux-course-task 1.C: uncomment the following group [Grid]
-# # for dune-subgrid
+# TODO: dumux-course-task 1.C: uncomment the following group [Grid]
+# for dune-subgrid
 #[Grid]
 #Positions0 = 0 1
 #Positions1 = 0 0.2 0.3 0.65
@@ -10,6 +10,7 @@
 #Offset = 0.5 # [m]
 #Scaling = 0.2 #[m]
 
+# TODO: dumux-course-task 1.B: change the grid resolution and examine the effects on the velocity profile
 # TODO: dumux-course-task 1.C: comment or delete the group [Freeflow.Grid]
 [Freeflow.Grid]
 Verbosity = true
@@ -19,6 +20,7 @@ Cells0 = 20
 Cells1 = 100
 Grading1 = 1
 
+# TODO: dumux-course-task 1.B: change the grid resolution and examine the effects on the velocity profile
 # TODO: dumux-course-task 1.C: comment or delete the group [PorousMedium.Grid]
 [PorousMedium.Grid]
 Verbosity = true

exercises/exercise-coupling-ff-pm/interface/porousmediumsubproblem.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -65,6 +65,8 @@ public:
     {
         BoundaryTypes values;
 
+        // TODO: dumux-course-task 1.A:
+        // Set for all boundaries Neumann no-flow and keep the coupling conditions
         // set Neumann BCs to all boundaries first
         values.setAllNeumann();
 

exercises/exercise-coupling-ff-pm/interface/properties.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -16,7 +16,7 @@
 #include <dumux/multidomain/staggeredtraits.hh>
 #include <dumux/multidomain/boundary/stokesdarcy/couplingmanager.hh>
 
-// TODO: dumux-course-task 1.C
+// TODO: dumux-course-task 1.C:
 //****** uncomment for the last exercise *****//
 // #include <dumux/io/grid/gridmanager_sub.hh>
 
@@ -86,7 +86,7 @@ struct Grid<TypeTag, TTag::PorousMediumFlowOneP>
     using Scalar = GetPropType<TypeTag, Properties::Scalar>;
     using TensorGrid = Dune::YaspGrid<2, Dune::TensorProductCoordinates<Scalar, dim> >;
 
-// TODO: dumux-course-task 1.C
+// TODO: dumux-course-task 1.C:
 //****** comment out for the last exercise *****//
     // use "normal" grid
     using type = TensorGrid;
@@ -103,7 +103,7 @@ struct Grid<TypeTag, TTag::FreeflowOneP>
     using Scalar = GetPropType<TypeTag, Properties::Scalar>;
     using TensorGrid = Dune::YaspGrid<2, Dune::TensorProductCoordinates<Scalar, dim> >;
 
-// TODO: dumux-course-task 1.C
+// TODO: dumux-course-task 1.C:
 //****** comment out for the last exercise *****//
     // use "normal" grid
     using type = TensorGrid;

exercises/exercise-coupling-ff-pm/models/CMakeLists.txt

-# SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+# SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 # executables for exercise_models_coupling_ff-pm

exercises/exercise-coupling-ff-pm/models/freeflowsubproblem.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!

exercises/exercise-coupling-ff-pm/models/main.cc

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!

exercises/exercise-coupling-ff-pm/models/params.input

@@ -42,6 +42,8 @@ Temperature = 293.15
 
 [Problem]
 Name = models_coupling
+# TODO: dumux-course-task 2.B: enable ExportStorage for .csv output file, 
+# enable plotting for gnuplot, enable ExportFluxes to export to .json file
 ExportStorage = false
 PlotStorage = false
 ExportFluxes = false

exercises/exercise-coupling-ff-pm/models/plotFluxes.py

-# SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+# SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 import json

exercises/exercise-coupling-ff-pm/models/porousmediumsubproblem.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -335,9 +335,9 @@ public:
         PrimaryVariables values(0.0);
         values[pressureIdx] = freeflowPressure;
 
-        // TODO: dumux-course-task 2.A
+        // TODO: dumux-course-task 2.A:
         // Declare here which phases are present.
-        // TODO: dumux-course-task 2.C
+        // TODO: dumux-course-task 2.C:
         // Change initial condition to 2p system with liquid saturation of 0.1
         values[transportCompIdx] = moleFraction_;
 

exercises/exercise-coupling-ff-pm/models/properties.hh

 // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
 // vi: set et ts=4 sw=4 sts=4:
 //
-// SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+// SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 // SPDX-License-Identifier: GPL-3.0-or-later
 //
 /*!
@@ -25,10 +25,10 @@
 #include <dumux/discretization/cctpfa.hh>
 #include <dumux/material/fluidmatrixinteractions/diffusivityconstanttortuosity.hh>
 
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Include 2pnc model here
 #include <dumux/porousmediumflow/1pnc/model.hh>
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Include spatial params for a 2-phase system
 #include "../1pspatialparams.hh"
 #include "porousmediumsubproblem.hh"
@@ -44,7 +44,7 @@ namespace Dumux::Properties {
 // Create new type tags
 namespace TTag {
 struct FreeflowNC { using InheritsFrom = std::tuple<NavierStokesNC, StaggeredFreeFlowModel>; };
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Change the inheritance such that the correct model is used.
 struct PorousMediumOnePNC { using InheritsFrom = std::tuple<OnePNC, CCTpfaModel>; };
 } // end namespace TTag
@@ -70,7 +70,7 @@ template<class TypeTag>
 struct Problem<TypeTag, TTag::FreeflowNC> { using type = Dumux::FreeFlowSubProblem<TypeTag> ; };
 
 // The fluid system
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Change to property of the `FluidSystem` such that `H2OAir` is used directly.
 template<class TypeTag>
 struct FluidSystem<TypeTag, TTag::PorousMediumOnePNC>
@@ -108,11 +108,11 @@ template<class TypeTag>
 struct EffectiveDiffusivityModel<TypeTag, TTag::PorousMediumOnePNC>
 { using type = DiffusivityConstantTortuosity<GetPropType<TypeTag, Properties::Scalar>>; };
 
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Define new formulation for primary variables here.
 
 // Set the spatial parameters type
-// TODO: dumux-course-task 2.A
+// TODO: dumux-course-task 2.A:
 // Adapt the spatial params here.
 template<class TypeTag>
 struct SpatialParams<TypeTag, TTag::PorousMediumOnePNC> {

exercises/exercise-coupling-ff-pm/turbulence/CMakeLists.txt

-# SPDX-FileCopyrightInfo: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
+# SPDX-FileCopyrightText: Copyright © DuMux-Course contributors, see AUTHORS.md in root folder
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 # executables for ex_interface_coupling_ff-pm