From c4e4920eca5639d449ceeab6fab4f64bcc0601aa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dennis=20Gl=C3=A4ser?= <dennis.glaeser@iws.uni-stuttgart.de>
Date: Fri, 20 Oct 2023 15:18:46 +0200
Subject: [PATCH] [examples][upscaling] regenerate docs

---
 examples/porenetwork_upscaling/README.md             | 12 ++++++------
 examples/porenetwork_upscaling/doc/main.md           |  2 +-
 examples/porenetwork_upscaling/doc/problem.md        | 12 +++++++-----
 .../porenetwork_upscaling/doc/upscalinghelper.md     | 10 ++++++----
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/examples/porenetwork_upscaling/README.md b/examples/porenetwork_upscaling/README.md
index 92b1b7c60a..50076569d5 100644
--- a/examples/porenetwork_upscaling/README.md
+++ b/examples/porenetwork_upscaling/README.md
@@ -46,11 +46,11 @@ Furthermore, the ratio of apparent permeability to Darcy permeability is plotted
     </center>
 </figure>
 
-In addition, in Fig. 3, the inverse of the apparent permeability versus $`\varrho v /\mu`$ is plotted to compare the data from the pore-network model simulation and the data obtained by applying the Forchheimer equation using the Forchheimer permeability and coefficient. As evident in the figure, the Forchheimer equation is not able to accurately predict the flow behavior in the low-velocity regime. 
+In addition, in Fig. 3, the inverse of the apparent permeability versus $`\varrho v /\mu`$ is plotted to compare the data from the pore-network model simulation and the data obtained by applying the Forchheimer equation using the Forchheimer permeability and coefficient. As evident in the figure, the Forchheimer equation is not able to accurately predict the flow behavior in the low-velocity regime.
 <figure>
     <center>
         <img src="img/inverse_apppermeability_versus_rhovmu-1.png" alt="Inverse of apparent permeability vs. rhovmu-1" width="60%"/>
-        <figcaption> <b> Fig.3 </b> - Inverse of apparent permeability versus &#961v / &#956. 
+        <figcaption> <b> Fig.3 </b> - Inverse of apparent permeability versus &#961v / &#956.
         </figcaption>
     </center>
 </figure>
@@ -67,7 +67,7 @@ __Table of contents__. This description is structured as follows:
 We consider a single-phase problem within a randomly generated pore network of 20x20x20 pores cubed from which some of the pore throats were [deleted randomly](https://doi.org/10.1029/2010WR010180).
 The inscribed pore body radii follow a truncated log-normal distribution.
 To calculate the upscaled properties, $`10`$ pressure differences in the range of $`10`$ to $`10^{10}`$ Pa/m are applied sequentially in directions specified by the user by setting the parameter `Problem.Directions` in the `params.input` file, while all lateral sides are closed.
-The resulting mass flow rates are then used to determine upscaled properties as described [later](upscalinghelper.md).
+The resulting mass flow rates are then used to determine upscaled properties as described [later](doc/upscalinghelper.md).
 
 ## Mathematical and numerical model
 
@@ -81,19 +81,19 @@ where $`Q_{ij}`$ is the discrete volume flow rate in a throat connecting pore bo
 ```math
  Q_{ij} = g_{ij} (p_i - p_j),
 ```
-or 
+or
 
 ```math
  (p_i - p_j) = Q_{ij} / g_{ij} .
 ```
 
-In the simulation of non-creeping flow, to capture inertial effects in fluid flow, an extension of the Hagen-Poiseuille-type law which includes the expansion and contraction of the pore space when moving from a throat to a pore and vice versa. 
+In the simulation of non-creeping flow, to capture inertial effects in fluid flow, an extension of the Hagen-Poiseuille-type law which includes the expansion and contraction of the pore space when moving from a throat to a pore and vice versa.
 
 ```math
   (p_i - p_j) = Q_{ij} / g_{ij}  + (C_{exp} + C_{cont})Q^2,
 ```
 
-where $`C_{exp}`$ and $`C_{cont}`$ are the expansion and the contraction coefficient, respectively. 
+where $`C_{exp}`$ and $`C_{cont}`$ are the expansion and the contraction coefficient, respectively.
 
 # Implementation & Post processing
 
diff --git a/examples/porenetwork_upscaling/doc/main.md b/examples/porenetwork_upscaling/doc/main.md
index 644ed99c6d..5d646066be 100644
--- a/examples/porenetwork_upscaling/doc/main.md
+++ b/examples/porenetwork_upscaling/doc/main.md
@@ -187,7 +187,7 @@ Get the maximum and minimum pressure gradient and the population of sample point
     const int numberOfSamples = getParam<int>("Problem.NumberOfPressureGradients", 1);
 ```
 
-Iterate over all directions specified before, apply several pressure gradient, calculated the mass flux
+Iterate over all directions specified before, apply several pressure gradients, calculate the mass flux
 and finally determine the the upscaled properties.
 
 ```cpp
diff --git a/examples/porenetwork_upscaling/doc/problem.md b/examples/porenetwork_upscaling/doc/problem.md
index 778c5e350e..f6d1871a92 100644
--- a/examples/porenetwork_upscaling/doc/problem.md
+++ b/examples/porenetwork_upscaling/doc/problem.md
@@ -78,7 +78,7 @@ The classes that define the problem and parameters used in this simulation
 ### `TypeTag` definition
 Two `TypeTag` for our simulation are defined, one for creeping flow and another for non-creeping flow,
 which inherit properties from the single-phase pore network model. The non-creeping flow inherits
-all properties from the creeping flow simulation but sets an own property for the `AdvectionType`.
+all properties from the creeping flow simulation but overrides the `AdvectionType` property.
 
 ```cpp
 namespace Dumux::Properties {
@@ -337,6 +337,11 @@ Return the label of outlet pores assuming a previously set direction.
         static constexpr std::array<int, 3> label = {2, 4, 6};
         return label[direction_];
     }
+```
+
+</details>
+
+```cpp
 
 private:
 
@@ -355,11 +360,7 @@ private:
         else
             return scv.dofPosition()[direction_] > this->gridGeometry().bBoxMax()[direction_] - eps_;
     }
-```
-
-private data members
 
-```cpp
     Scalar eps_;
     Scalar pressureGradient_;
     int direction_;
@@ -370,6 +371,7 @@ private data members
 } // end namespace Dumux
 ```
 
+</details>
 
 </details>
 
diff --git a/examples/porenetwork_upscaling/doc/upscalinghelper.md b/examples/porenetwork_upscaling/doc/upscalinghelper.md
index 3dc54ece3a..377b649331 100644
--- a/examples/porenetwork_upscaling/doc/upscalinghelper.md
+++ b/examples/porenetwork_upscaling/doc/upscalinghelper.md
@@ -255,11 +255,12 @@ We determine the domain side length by using the bounding box of the network
     {
         directions_ = directions;
     }
-    // [[codeblock]]
+```
+
+### Save the relevant data for plot of permeability ratio vs. Forchheimer number
 
+```cpp
 private:
-    // ### Save the relevant data for plot of permeability ratio vs. Forchheimer number
-    // [[codeblock]]
     void writePermeabilityratioVsForchheimerNumber_(std::size_t dirIdx)
     {
         // open a logfile
@@ -379,6 +380,7 @@ private:
     }
 ```
 
+<details><summary> Click to show private data members</summary>
 
 ```cpp
     std::array<std::vector<Scalar>, 3> samplePointsX_;
@@ -397,7 +399,7 @@ private:
 } // end namespace Dumux
 ```
 
-[[/codeblock]]
+</details>
 
 </details>
 
-- 
GitLab