From 31142087e9f70a087fdcebd5c90d8639bc32d056 Mon Sep 17 00:00:00 2001
From: Tufan Ghosh <tufan.ghosh@iws.uni-stuttgart.de>
Date: Wed, 30 Oct 2024 10:00:38 +0100
Subject: [PATCH 01/12] adding relevant header files for the presentation
 slides

---
 slides/materialsystem.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/slides/materialsystem.md b/slides/materialsystem.md
index c7dea42b..8eadd6d6 100644
--- a/slides/materialsystem.md
+++ b/slides/materialsystem.md
@@ -50,6 +50,8 @@ More resources can be found [in the code documentation](https://dumux.org/docs/d
 
 ## Example interfaces
 
+* See _dumux/dumux/material/components/air.hh_
+
 ```cpp
 static Scalar gasDensity(Scalar temperature, Scalar pressure)
 {
-- 
GitLab


From c716c201f548653ea9590755e5687e9972883b97 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 14:51:12 +0100
Subject: [PATCH 02/12] [slides][materialsystem] Add file paths for code
 blocks.

---
 slides/materialsystem.md | 31 +++++++++++++------------------
 1 file changed, 13 insertions(+), 18 deletions(-)

diff --git a/slides/materialsystem.md b/slides/materialsystem.md
index 8eadd6d6..7e95f813 100644
--- a/slides/materialsystem.md
+++ b/slides/materialsystem.md
@@ -50,8 +50,6 @@ More resources can be found [in the code documentation](https://dumux.org/docs/d
 
 ## Example interfaces
 
-* See _dumux/dumux/material/components/air.hh_
-
 ```cpp
 static Scalar gasDensity(Scalar temperature, Scalar pressure)
 {
@@ -59,24 +57,19 @@ static Scalar gasDensity(Scalar temperature, Scalar pressure)
     return IdealGas::density(molarMass(), temperature, pressure);
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/components/air.hh`</span>
 
 ## Example interfaces
 
 ```cpp
-static Scalar gasHeatCapacity(Scalar temperature, Scalar pressure)
-{
-    constexpr Scalar cpVapA = 19.25;
-    constexpr Scalar cpVapB = 0.05213;
-    constexpr Scalar cpVapC = 1.197e-5;
-    constexpr Scalar cpVapD = -1.132e-8;
-
-    return 1/molarMass()*(
-        cpVapA + temperature*(
-            cpVapB/2 + temperature*(cpVapC/3 + temperature*(cpVapD/4))
-        )
-    );
-}
+static Scalar gasHeatCapacity(Scalar T, Scalar pressure)
+    {
+        const auto cp = shomateMethod.heatCapacity(T); // J/(mol K)
+        return cp / molarMass(); // J/(kg K)
+    }
+
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/components/ch4.hh`</span>
 
 # Fluid systems
 
@@ -111,6 +104,7 @@ static Scalar heatCapacity(const FluidState& fluidState, int phaseIdx)
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/fluidsystems/brine.hh`</span>
 
 # Binary coefficients
 
@@ -141,7 +135,7 @@ static Scalar gasDiffCoeff(Scalar temperature, Scalar pressure)
     return Daw*(pg0/pressure)*pow((temperature/T0), theta);
 }
 ```
-
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/binarycoefficients/h2o_air.hh`</span>
 
 # Solid systems
 
@@ -269,7 +263,7 @@ _CompositionFromFugacities_ : takes all component fugacities, the temperature an
 
 ```cpp
 template<class TypeTag>
-struct FluidSystem<TypeTag, TTag::H2OAir>
+struct FluidSystem<TypeTag, TTag::DrainageProblem>
 {
 private:
     using Scalar = GetPropType<TypeTag, Properties::Scalar>;
@@ -283,6 +277,7 @@ public:
     >;
 };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porenetwork/2pnc/properties.hh`</span>
 
 
 # Example: From components to solid system
@@ -307,7 +302,7 @@ struct SolidSystem<TypeTag, TTag::ThermoChem>
     >;
 };
 ```
-
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/1pncmin/nonisothermal/properties.hh`</span>
 
 # Exercise
 
-- 
GitLab


From 77992217b3e562505e6d1c5ada6b28de2d5ac382 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 14:58:09 +0100
Subject: [PATCH 03/12] [slides][dunemodule] Add file paths for code blocks.

---
 slides/dunemodule.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/slides/dunemodule.md b/slides/dunemodule.md
index dfb87153..bd476e39 100644
--- a/slides/dunemodule.md
+++ b/slides/dunemodule.md
@@ -31,6 +31,7 @@ Depends: dumux dune-alugrid dune-foamgrid dune-uggrid
 # Optional build dependencies
 #Suggests:
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dune.module`</span>
 
 ## Creating a new dune module
 Start the script `duneproject` to initiate creating a new module:
-- 
GitLab


From 3aa2dff5698e7fd68fb9fc64385b1aa647f0415a Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 15:13:35 +0100
Subject: [PATCH 04/12] [slides][grid] Add file paths for code blocks.

---
 slides/grid.md | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/slides/grid.md b/slides/grid.md
index 4477b845..f7788368 100644
--- a/slides/grid.md
+++ b/slides/grid.md
@@ -32,10 +32,11 @@ Implementations of the Dune grid interface
   #include <dune/grid/yaspgrid.hh>
   ...
   template<class TypeTag>
-  struct Grid<TypeTag, TTag::Injection2p>{
+  struct Grid<TypeTag, TTag::TwoPIncompressible>{
       using type = Dune::YaspGrid<2>;
   };
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/properties.hh`</span>
 
 * Include the matching grid manager header files in main file and create the grid via a grid manager instance
   ```cpp
@@ -45,6 +46,7 @@ Implementations of the Dune grid interface
       GridManager<Grid> gridManager;
       gridManager.init();
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/main.cc`</span>
 
 ## Create grid
 
@@ -59,6 +61,7 @@ The grid manager looks for grid information in the runtime parameter tree
   UpperRight = 1 1
   Cells = 10 5
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/params.input`</span>
 
 <img src=img/params_grid.png width="200">
 
@@ -69,6 +72,7 @@ The grid manager looks for grid information in the runtime parameter tree
   [Grid]
   File = ./grids/heterogeneousSmall.dgf
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/io/gridmanager/test_gridmanager_dgf.input`</span>
 
 * Supported grid file formats
   * DGF (Dune Grid Format)
@@ -82,11 +86,13 @@ constructing a `Dune::YaspGrid`:
 
 ```cpp
 constexpr int dim = 2;
+using Yasp = Dune::YaspGrid<dim, Dune::EquidistantOffsetCoordinates<
+  double, dim>>;
 std::array<int, dim> cells; cells.fill(30);
-Dune::FieldVector<double, dim> lowerLeft(1.0), upperRight(2.0);
-using Yasp = Dune::YaspGrid<dim, Dune::EquidistantOffsetCoordinates<double, dim>>;
+Dune::FieldVector<double, dim> lowerLeft(1.1), upperRight(2.2);
 Yasp yasp(lowerLeft, upperRight, cells);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/geometry/test_intersectingentity_cartesiangrid.cc`</span>
 
 # Exercise
 ## Exercise
-- 
GitLab


From 3f8819385322b0435ca2580cbca3d0e2ad5d661e Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 15:23:56 +0100
Subject: [PATCH 05/12] [slides][multidomain] Add file paths for code blocks.

---
 slides/multidomain.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/slides/multidomain.md b/slides/multidomain.md
index 1c58e304..70a9c621 100644
--- a/slides/multidomain.md
+++ b/slides/multidomain.md
@@ -64,6 +64,8 @@ void pointSource(PointSource& source...) const
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/multidomain/embedded/2d3d/1p_1p/problem_matrix.hh`</span>
+
 ## Coupling Residual / Data Transfer (2/3)
 
 ```c++
@@ -80,6 +82,7 @@ void pointSource(PointSource& source...) const
 ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/multidomain/embedded/2d3d/1p_1p/problem_matrix.hh`</span>
 
 ## Coupling Residual / Data Transfer (3/3)
 
@@ -95,6 +98,8 @@ void pointSource(PointSource& source...) const
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/multidomain/embedded/2d3d/1p_1p/problem_matrix.hh`</span>
+
 
 ## Coupling Residual (1/2)
 
@@ -112,6 +117,7 @@ decltype(auto) evalCouplingResidual(Dune::index_constant<i> domainI,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/embedded/couplingmanagerbase.hh`</span>
 
 ## Coupling Residual (2/2)
 
@@ -131,6 +137,8 @@ decltype(auto) evalCouplingResidual(...)
     return residual;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/embedded/couplingmanagerbase.hh`</span>
+
 ## Coupling Stencil
 
 ![](./img/disc.png)
@@ -151,6 +159,7 @@ const CouplingStencil<j>& couplingStencil(domainI,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/embedded/couplingmanagerbase.hh`</span>
 
 ## Coupling Stencil (2/2)
 
@@ -167,6 +176,7 @@ const CouplingStencil<j>& couplingStencil(domainI,
         return emptyStencil(domainI);
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/embedded/couplingmanagerbase.hh`</span>
 
 # Examples
 ## Embedded Fracture Model
-- 
GitLab


From bc8c5e78051ab204ed0076938c7311d15353a6e5 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 15:56:19 +0100
Subject: [PATCH 06/12] [slides][problem] Add file paths for code blocks.

---
 slides/problem.md | 44 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/slides/problem.md b/slides/problem.md
index 18da55ee..f6320c50 100644
--- a/slides/problem.md
+++ b/slides/problem.md
@@ -102,6 +102,8 @@ struct Injection2pCC { using InheritsFrom = std::tuple<TwoP, CCTpfaModel>; };
 
 } // end namespace Dumux::Properties::TTag
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/properties2p.hh`</span>
+
 
 ##
 
@@ -116,6 +118,7 @@ struct Grid<TypeTag, TTag::Injection2pCC>
 
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/properties2p.hh`</span>
 
 ##
 
@@ -130,6 +133,7 @@ struct Problem<TypeTag, TTag::Injection2pCC>
 
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/properties2p.hh`</span>
 
 The problem class `InjectionProblem2P` is discussed
 in one of the following sections.
@@ -153,6 +157,7 @@ struct SpatialParams<TypeTag, TTag::Injection2pCC>
 
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/properties2p.hh`</span>
 
 ##
 
@@ -172,6 +177,7 @@ struct FluidSystem<TypeTag, TTag::Injection2pCC>
 
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/properties2p.hh`</span>
 
 # Problem definition
 
@@ -191,6 +197,7 @@ class InjectionProblem2P : public PorousMediumFlowProblem<TypeTag>
     // - scenario name (for output)
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 Inherit from base class `PorousMediumFlowProblem`, only override
 scenario-specific functions (static polymorphism).
@@ -212,7 +219,7 @@ BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
     return bcTypes;
 }
 ```
-
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 ##
 
@@ -222,6 +229,7 @@ Dirichlet boundary condition values (only called on Dirichlet boundaries)
 PrimaryVariables dirichletAtPos(const GlobalPosition& globalPos) const
 { return initialAtPos(globalPos); }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 `PrimaryVariables` is an array of primary variables (here, the size of the array is 2).
 
@@ -235,6 +243,7 @@ PrimaryVariables dirichlet(const Element &element,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/common/fvproblem.hh`</span>
 ```cpp
 PrimaryVariables dirichlet(const Element &element, 
                            const SubControlVolume &scv) const
@@ -242,6 +251,7 @@ PrimaryVariables dirichlet(const Element &element,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/common/fvproblem.hh`</span>
 
 ##
 
@@ -260,6 +270,7 @@ NumEqVector neumannAtPos(const GlobalPosition& globalPos) const
     return values;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 `NumEqVector` is an array of equations (here, the size of the array is 2).
 
@@ -278,6 +289,8 @@ NumEqVector neumann(const Element& element,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/common/fvproblem.hh`</span>
+
 ##
 
 Initial conditions:
@@ -296,6 +309,7 @@ PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const
     return values;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 
 ##
@@ -306,6 +320,7 @@ Source/sink terms:
 NumEqVector sourceAtPos(const GlobalPosition &globalPos) const
 { return NumEqVector(0.0); }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pproblem.hh`</span>
 
 ##
 
@@ -321,6 +336,7 @@ NumEqVector source(const Element &element,
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/common/fvproblem.hh`</span>
 
 # Spatial Parameters definition
 
@@ -339,6 +355,7 @@ class InjectionSpatialParams
 // e.g. porosity, permeability
 };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pspatialparams.hh`</span>
 
 Inherit from `FVPorousMediumFlowSpatialParamsMP` where
 `FV`: finite volumes, `MP`: multi-phase flow.
@@ -355,6 +372,7 @@ auto permeabilityAtPos(const GlobalPosition& globalPos) const
     return aquiferK_;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pspatialparams.hh`</span>
 
 ##
 
@@ -369,6 +387,7 @@ Scalar porosityAtPos(const GlobalPosition& globalPos) const
     return aquiferPorosity_;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pspatialparams.hh`</span>
 
 ##
 
@@ -384,6 +403,7 @@ auto fluidMatrixInteractionAtPos(const GlobalPosition& globalPos) const
     return makeFluidMatrixInteraction(aquiferPcKrSwCurve_);
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pspatialparams.hh`</span>
 
 ##
 
@@ -392,9 +412,10 @@ Set the (constant) temperature field in the domain:
 ```cpp
 Scalar temperatureAtPos(const GlobalPosition& globalPos) const
 {
-    return 273.15 + 20.0;  // 20°C
+    return 273.15 + 30.0;  // 30°C
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/injection2pspatialparams.hh`</span>
 
 # Runtime parameters
 
@@ -413,6 +434,7 @@ Cells = 24 16
 [Problem]
 Name = test
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/nonisothermal/params.input`</span>
 
 See [Part I: Runtime parameters](./params.html) for details.
 
@@ -436,6 +458,7 @@ int main(int argc, char** argv)
     // initialize MPI+X backends (mandatory)
     Dumux::initialize(argc, argv);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -445,6 +468,7 @@ Parse runtime parameters:
 // parse command line arguments and input file
 Dumux::Parameters::init(argc, argv);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 See [Part I: Runtime parameters](./params.html) for details.
 
@@ -456,6 +480,7 @@ Define an alias for the test problem type tag
 using namespace Dumux;
 using TypeTag = Properties::TTag::Injection2pCC;
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 The tag (tag alias) is used to extract types and values
 via the property system (details on properties in [Part II: Property system](./properties.html)).
@@ -473,6 +498,7 @@ gridManager.init();
 const auto& grid = gridManager.grid();
 const auto& leafGridView = grid.leafGridView();
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 More details on the grid in [Part I: Grid](./grid.html).
 
@@ -490,6 +516,7 @@ auto gridGeometry = std::make_shared<GridGeometry>(leafGridView);
 using Problem = GetPropType<TypeTag, Properties::Problem>;
 auto problem = std::make_shared<Problem>(gridGeometry);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 
 ##
@@ -508,6 +535,7 @@ auto gridVariables
     = std::make_shared<GridVariables>(problem, gridGeometry);
 gridVariables->init(x);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -528,6 +556,7 @@ vtkWriter.addVelocityOutput(
 using IOFields = GetPropType<TypeTag, Properties::IOFields>;
 IOFields::initOutputModule(vtkWriter);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -555,6 +584,7 @@ auto r = std::make_shared<SolutionVector>();
 assembler->setLinearSystem(A, r);
 assembler->assembleJacobianAndResidual(x);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-mainfile/exercise1pamain.cc`</span>
 
 ##
 
@@ -570,6 +600,7 @@ auto linearSolver = std::make_shared<LinearSolver>(
 (*r) *= -1.0; // solve Ax = -r to save update and copy
 linearSolver->solve(*A, x, *r);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-mainfile/exercise1pamain.cc`</span>
 
 ##
 
@@ -585,6 +616,7 @@ Solver solver(assembler, linearSolver);
 // assemble & solve
 solver.solve(x);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/1p/rootbenchmark/main.cc`</span>
 
 ##
 
@@ -600,6 +632,7 @@ Solver solver(assembler, linearSolver);
 // linearize & solve
 solver.solve(x);
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-mainfile/exercise1pbmain.cc`</span>
 
 ##
 
@@ -622,6 +655,7 @@ auto assembler = std::make_shared<Assembler>(
 // assemble linear/non-linear problem as before
 // ...
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -634,6 +668,7 @@ timeLoop->start(); do {
 
 } while (!timeLoop->finished());
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -649,6 +684,7 @@ timeLoop->start(); do
     xOld = x;
     gridVariables->advanceTimeStep();
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ##
 
@@ -667,6 +703,7 @@ Advancing the time loop to the next step:
 // print final report
 timeLoop->finalize(leafGridView.comm());
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 # Build system (CMake)
 
@@ -753,6 +790,7 @@ by defining a name and source file:
 dumux_add_test(NAME exercise_basic_2p
                SOURCES 2pmain.cc)
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/CMakeLists.txt`</span>
 
 ## Build system
 
@@ -772,6 +810,7 @@ dumux_add_test(
             test_2p.input -Problem.Name 2p_box"
 )
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/CMakeLists.txt`</span>
 
 ## Build system
 
@@ -786,6 +825,7 @@ target_compile_definitions(
     test_2p_incompressible_tpfa PUBLIC TYPETAG=TwoPIncompressibleTpfa
 )
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/CMakeLists.txt`</span>
 
 ## Build system
 
-- 
GitLab


From 499dce89203bc51bbebc9ffa63a83f1893cb82ed Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 16:48:23 +0100
Subject: [PATCH 07/12] [slides][biomin] Fix enumeration.

---
 slides/biomin.md | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/slides/biomin.md b/slides/biomin.md
index 07cd6de0..9d6613c0 100644
--- a/slides/biomin.md
+++ b/slides/biomin.md
@@ -307,15 +307,17 @@ PermeabilityType evaluatePermeability(PermeabilityType refPerm,
 
 ## Exercise tasks
 
+<div style="text-align: left; margin-left: 200px">
 <small>
-1. Get familiar with the code
-2. Implement the simplified chemical reactions
-3. Use source()-function to link chemistry-file to problem
-4. Vary parameters, so that leakage pathway is "sealed" (porosity $<0.07$)
-5. Implement new boundary condition for $\mathrm{CO_2}$-injection in lower aquifer
-6. Exchange the permeability law from Kozeny-Carman to a Power Law
+1. Get familiar with the code  
+2. Implement the simplified chemical reactions  
+3. Use source()-function to link chemistry-file to problem  
+4. Vary parameters, so that leakage pathway is "sealed" (porosity $<$ 0.07)  
+5. Implement new boundary condition for $\mathrm{CO_2}$-injection in lower aquifer  
+6. Exchange the permeability law from Kozeny-Carman to a Power Law  
 7. Use tabulated values for $\mathrm{CO_2}$
 </small>
+</div>
 
 ## Exercise
 
-- 
GitLab


From 5f344621efa871d20f303f1cb29487667c1ca7f9 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Mon, 17 Feb 2025 16:56:38 +0100
Subject: [PATCH 08/12] [slides][model] Add file paths for code blocks.

---
 slides/model.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/slides/model.md b/slides/model.md
index e7f8dfac..6d30e3ba 100644
--- a/slides/model.md
+++ b/slides/model.md
@@ -99,6 +99,8 @@ class DiffusionModelLocalResidual
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
+
 Inherits from the `BaseLocalResidual`, which is chosen depending on the discretization scheme, here *Box scheme*.
 
 ## Storage term
@@ -113,6 +115,7 @@ NumEqVector computeStorage(const Problem& problem,
     return storage;
  }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## Flux term
 
@@ -142,6 +145,7 @@ NumEqVector computeFlux(const Problem& problem,
 }
 ```
 </font>
+<span style="font-size: 0.4em; position: relative; top: -60px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## Flux term
 ```cpp
@@ -161,6 +165,7 @@ NumEqVector computeFlux(...) const
     ...
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## Flux term
 ```cpp
@@ -179,6 +184,7 @@ NumEqVector computeFlux(...) const
     return flux;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## `LocalResidual`
 
@@ -197,6 +203,8 @@ namespace Dumux::Properties {
     //define all properties
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
+
 ## Model type tag
 
 The property type tag is an empty struct with the respective name, e.g. `DiffusionModel`.
@@ -208,6 +216,7 @@ namespace Dumux::Properties::TTag {
 struct DiffusionModel {};
 } // end namespace Dumux::Properties::TTag
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## Defining model properties
 
@@ -218,6 +227,7 @@ template<class TypeTag>
 struct LocalResidual<TypeTag, TTag::DiffusionModel>
 { using type = DiffusionModelLocalResidual<TypeTag>; };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
 
 ## Defining model properties
 
@@ -238,6 +248,8 @@ struct ModelTraits<TypeTag, TTag::DiffusionModel>
     };
 };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/diffusion/model.hh`</span>
+
 ## Defining model properties
 Further model specific properties can be set accordingly by using the model property tag,
 i.e. `TTag::DiffusionModel`
-- 
GitLab


From 6062e21901f27f1acfbcab674073e835e2e5f979 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Tue, 18 Feb 2025 10:51:55 +0100
Subject: [PATCH 09/12] [slides][params] Add file paths for code blocks.

---
 slides/params.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/slides/params.md b/slides/params.md
index 6b63f6eb..a021a97b 100644
--- a/slides/params.md
+++ b/slides/params.md
@@ -28,6 +28,7 @@ int main(int argc, char** argv)
     return 0;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
 
 ## Initialize Parameter Tree
 
@@ -40,6 +41,7 @@ int main(int argc, char** argv)
     return 0;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/common/parameters/test_loggingparametertree.cc`</span>
 
 ## Initialize Parameter Tree
 
@@ -57,6 +59,7 @@ int main(int argc, char** argv)
     return 0;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/linear/test_parallel_amg_smoothers.cc`</span>
 
 ## Initialize Parameter Tree
 
@@ -69,6 +72,7 @@ int main(int argc, char** argv)
     return 0;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/common/parameters.cc`</span>
 
 ## Reading Runtime Parameters
 
@@ -115,10 +119,12 @@ via the single parameter tree
   if (hasParam("GROUPNAME.PARAMNAME"))
       // do something with parameter
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/biomineralization/main.cc`</span>
 * With group prefix lookup
   ```cpp
   if (hasParamInGroup("GROUPNAME","PARAMNAME"))
   ```
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/freeflow/rans/problem.hh`</span>
 
 ## Parameter tree logs usage
 
@@ -132,6 +138,8 @@ int main(int argc, char** argv)
     return 0;
 }
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/2pmain.cc`</span>
+
 Reports unused parameters. Great for detecting typos in
 configuration file.
 
@@ -153,6 +161,7 @@ Name = test
 [FreeFlow.Problem]
 Name = test_ff
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-basic/params.input`</span>
 
 ## Command-line arguments
 
-- 
GitLab


From 3e25672ead62246106f7146ad8f6031dd8c822c8 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Tue, 18 Feb 2025 13:36:22 +0100
Subject: [PATCH 10/12] [slides][properties] Add file paths for code blocks.

---
 slides/properties.md | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/slides/properties.md b/slides/properties.md
index 73f33d01..2ff9276d 100644
--- a/slides/properties.md
+++ b/slides/properties.md
@@ -103,6 +103,7 @@ using GOF0 = Dune::GridOperator<
 >;
 
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dune-pdelab/doc/Recipes/recipe-operator-splitting.cc`</span>
 
 ## Technique 1: Traits classes
 
@@ -122,6 +123,7 @@ struct TwoPVolumeVariablesTraits
     using SaturationReconstruction = SR;
 };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/porousmediumflow/2p/model.hh`</span>
 
 ## Technique 2: Type traits
 
@@ -153,6 +155,7 @@ using FluidSystem = typename Traits::FluidSystem
    ...
 
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/porousmediumflow/2p/volumevariables.hh`</span>
 
 Usage: these VolumeVariables will work for various FluidSystems:
 
@@ -332,6 +335,7 @@ struct MyOtherTypeTag
 
 } // end namespace Dumux::Properties::TTag
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-properties/properties.hh`</span>
 
 ## How to use II
 
@@ -341,6 +345,8 @@ namespace Dumux::Properties {
 DUMUX_DEFINE_PROPERTY(Problem)
 } // end namespace Dumux::Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/common/propertysystem/test_propertysystem_aliases.cc`</span>
+
 Usually not needed in user code because
 all necessary properties are already defined in [dumux/common/properties.hh](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/common/properties.hh).
 
@@ -357,6 +363,7 @@ struct Problem<TypeTag, TTag::MyTypeTag>
 
 } // end namespace Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-properties/properties.hh`</span>
 
 ## How to use III (alternative)
 
@@ -374,6 +381,7 @@ struct MyTypeTag {
 
 } // end namespace Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/geomechanics/hyperelastic/properties.hh`</span>
 
 ## How to use IV
 
@@ -388,6 +396,7 @@ struct EnableBoxInterfaceSolver<TypeTag, TTag::MyTypeTag>
 
 } // end namespace Properties
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/boxdfm/properties.hh`</span>
 
 ## How to use IV (alternative)
 
@@ -425,7 +434,7 @@ class Problem
 
 } // end namespace Dumux
 ```
-
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/examples/1ptracer/problem_tracer.hh`</span>
 
 ## Summary
 
@@ -448,16 +457,18 @@ class Problem
 - Use a simple template argument
 
 ```cpp
-template <bool useNeummanBoundaryConditions>
-class Problem
+template<bool enableRegularization = isRegularized()>
+Scalar pcgw(const Scalar sw, const Scalar /*dummySn*/) const
 {
     ...
-    if constexpr (useNeummanBoundaryConditions)
-        ...
-    else
+    if constexpr (enableRegularization)^
+    {
         ...
-};
+    }
+    ...
+}
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/fluidmatrixinteractions/3p/parkervangenuchten.hh`</span>
 
 ## Alternative 2:
 
@@ -468,6 +479,7 @@ template<class CouplingManager>
 struct SupportsMultithreadedAssembly
 : public std::false_type {}
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/fvassembler.hh`</span>
 
 ## Alternative 2:
 
@@ -496,6 +508,7 @@ class Assembler {
    }
 };
 ```
+<span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/multidomain/fvassembler.hh`</span>
 
 # Exercise
 ## Exercise
-- 
GitLab


From d0648802bf5559a07e960f9a5c220002c360bb6c Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Tue, 18 Feb 2025 14:00:29 +0100
Subject: [PATCH 11/12] [slides][grid] Fix TypeTag.

---
 slides/grid.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/slides/grid.md b/slides/grid.md
index f7788368..d797d01d 100644
--- a/slides/grid.md
+++ b/slides/grid.md
@@ -32,11 +32,11 @@ Implementations of the Dune grid interface
   #include <dune/grid/yaspgrid.hh>
   ...
   template<class TypeTag>
-  struct Grid<TypeTag, TTag::TwoPIncompressible>{
+  struct Grid<TypeTag, TTag::Injection2p>{
       using type = Dune::YaspGrid<2>;
   };
   ```
-  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/test/porousmediumflow/2p/incompressible/properties.hh`</span>
+  <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux-course/exercises/exercise-grids/properties.hh`</span>
 
 * Include the matching grid manager header files in main file and create the grid via a grid manager instance
   ```cpp
-- 
GitLab


From 191e1c8debf32140b60400e1afd2401749b13f96 Mon Sep 17 00:00:00 2001
From: IvBu <ivan.buntic@iws.uni-stuttgart.de>
Date: Wed, 19 Feb 2025 08:46:52 +0100
Subject: [PATCH 12/12] [slides][materialsystem] Fix indentation.

---
 slides/materialsystem.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/slides/materialsystem.md b/slides/materialsystem.md
index 7e95f813..29c0505d 100644
--- a/slides/materialsystem.md
+++ b/slides/materialsystem.md
@@ -63,10 +63,11 @@ static Scalar gasDensity(Scalar temperature, Scalar pressure)
 
 ```cpp
 static Scalar gasHeatCapacity(Scalar T, Scalar pressure)
-    {
-        const auto cp = shomateMethod.heatCapacity(T); // J/(mol K)
-        return cp / molarMass(); // J/(kg K)
-    }
+{
+    // apply Shomate method
+    const auto cp = shomateMethod.heatCapacity(T); // J/(mol K)
+    return cp / molarMass(); // J/(kg K)
+}
 
 ```
 <span style="font-size: 0.4em; position: relative; top: -38px; color: gray;">File: `dumux/dumux/material/components/ch4.hh`</span>
-- 
GitLab