[vale] More fixes.

.vale.ini

@@ -24,7 +24,7 @@ TokenIgnores = \
 (\$[^\n$]+\$), \
 (\\\S*|\{\S*\}), \
 (\w*\set\sal), \
-({{< (rel)?ref (.*)>}})
+({{<\s?(rel)?ref (.*)>}})
 
 # https://regex101.com/r/QWLhgT/1 helped me generating this one:
 BlockIgnores = (?s) *(\$\$.*?\$\$)

web/content/docs/benchmarks/heatconduction/heatconduction-soil-freezing/index.md

@@ -26,14 +26,20 @@ The detailed IBVP problem description for the T+freezing equation, geometric set
 
 Note that $(r,z)\in S$ are denoted as $(x,y)$ which are assumed to be unrelated to the coordinate notations in the original 3d formulation.
 2. The initial condition for $T$ in $S$ is assumed to be a positive function which decays linearly from surface to bottom. For modeling the (time-dependent) boundary conditions on $\Gamma_D$ of $S$, it is assumed that within the first $\widehat{t}$ hours, the temperature on $\Gamma_D$ drops continuously from the initial state to the values prescribed by some continuous piecewise linear function of $y$ and such that at the last depth segment it becomes negative. (The latter mimics the impact of the BHE refrigerant with sub-zero temperature.) The figure sketches the situation:
+
 {{< img src="T1_soil_block.png" >}}
+
 Temperature is given in degrees Celsius. For $t>\widehat{t}$, the prescribed temperature on $\Gamma_D$ and, thus, the heat conduction in the modelled case is triggered by a significant difference between the temperature on $\Gamma_D$ and the initial one within $S$.
 3. The results of modelling are depicted in the following two figures, where we plot the temperature distribution in the soil block after 720 hours (30 days) of cooling, and also compare the outcomes of the two corresponding packages:
+
 {{< img src="T-distribution_(OGS_vs_FF++*2d).png" >}}
 {{< img src="T-distribution*(OGS_vs_FF++*3d).png" >}}
+
 Temperature is given in kelvins. The color legend of $T$ in the corresponding ParaView plots is tuned such that the amount of ice formed around BHEs can be identified. As expected, ice formation occurs in the vicinity of $\Gamma_D$, more specifically, near the segment of $\Gamma_D$ in which the negative temperature has been prescribed. In the rest of the domain, temperature distribution remains almost identical to the initial state, as could also be expected.
 4. Finally, the corresponding results from the previous figure are plotted over the three different directed lines within the domain $S$:
+
 {{< img src="T-over_lines*(OGS_vs_FF++).png" >}}
+
 Here, origin of the horizontal axis on the right plot corresponds to line's origin. For the selected lines, the compared data seems identical point-wise, thus supporting the quantitative similarity of the OGS and FF++ results observed earlier.
 
 ### *Remark*

web/content/docs/devguide/documentation/jupyter-docs/index.md

@@ -140,7 +140,7 @@ On the web site or MR web previews on pages generated by a notebook there is a n
 ![Notebook web banner with BinderHub launch button](binderhub-button.png)
 
 - Click the button to launch the notebook in BinderHub.
-- The environment running in BinderHub is defined in [bilke/binder-ogs-requirements at GitHub](https://github.com/bilke/binder-ogs-requirements)
+- The environment running in BinderHub is defined in [`bilke/binder-ogs-requirements` at GitHub](https://github.com/bilke/binder-ogs-requirements)
 - When clicking the link it launches a Jupyter Lab instance pre-configured with ogs [via wheel](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/requirements-ogs.txt#L2), clones the current ogs repo in it and opens the respective notebook ready to run. Please note that startup times may be several minutes and the computing resources are limited (1 core, 2GB RAM). For improved performance we would need to setup own infrastructure. Also currently only works for serial ogs configurations.
 
 ### PyVista notebooks on headless Linux systems

web/content/docs/devguide/documentation/todo/index.md

@@ -8,11 +8,11 @@ weight = 1027
 
 This list was obtained using grep and added here to provide an  overview of what sections are missing the documentation. In the future it should be generated automatically.
 
-It can be obtained by running script ```todo-check.sh``` from ```/web/content/docs/userguide``` folder.
+It can be obtained by running script `todo-check.sh` from `web/content/docs/userguide` folder.
 
-## TODOs in userguide/basics
+## TODOs in `userguide/basics`
 
-## TODOs in userguide/blocks
+## TODOs in `userguide/blocks`
 
 ```bash
 blocks/curves.md-19-</div>
@@ -96,7 +96,7 @@ blocks/processes.md-158-
 blocks/processes.md:159:The global non-linear equation system can be solved either with Picard fix-point iterations or a Newton scheme. (TODO: Reference NLS scheme)
 ```
 
-## TODOs in userguide/features
+## TODOs in `userguide/features`
 
 ```bash
 features/python_bc.md-31-## Using python boundary condition in project file
@@ -124,4 +124,4 @@ features/mfront.md-109-
 features/mfront.md:110:TODO: add content
 ```
 
-## TODOs in userguide/troubleshooting
+## TODOs in `userguide/troubleshooting`

web/content/docs/devguide/documentation/web-docs/index.md

@@ -88,15 +88,15 @@ We use [Markdown](https://commonmark.org/help/) for the actual content. Hugo use
 
 Use regular Markdown syntax:
 
-```md
+```markdown
 ![Alt text](square_1e2_neumann_gradients.png "Caption text")
 ```
 
 The path to the image is the relative path to the current [page bundle](https://gohugo.io/content-management/page-bundles/).
 
 You can add size attributes to the filename with a `#`-character:
 
-```md
+```markdown
 ![Alt text](square_1e2_neumann_gradients.png#two-third "Caption text")
 ```
 

web/content/docs/devguide/getting-started/build-configuration_for_MPI_PETSc/configure_for_mpi_and_petsc.md

@@ -21,7 +21,7 @@ has many derivatives, e.g intelMPI) has to be installed as prerequisite.
 PETSc is not supported on Windows system.
 As an alternative you can follow the instructions in Section [Install PETSc manually](#install-petsc-manually) and run PETSc using Cygwin or use Windows Subsystem For Linux (WSL).
 The latter option is recommended - using WSL.
-The manual of setting up OpenGeoSys in WSL can be found in our [Windows Subsystem For Linux]({{<ref "wsl">}}) guide.
+The manual of setting up OpenGeoSys in WSL can be found in our [Windows Subsystem For Linux]({{< ref "wsl" >}}) guide.
 After setting up WSL, please follow the Linux tab in this guide.
 
 </div>
@@ -30,7 +30,7 @@ After setting up WSL, please follow the Linux tab in this guide.
 
 ## Set up prerequisites
 
-Before continuing with this guide, please follow all steps from the "Developer guide" articles: [Set Up Prerequisites]({{<ref "prerequisites">}}) and [Get the source code]({{<ref "get-the-source-code">}}).
+Before continuing with this guide, please follow all steps from the "Developer guide" articles: [Set Up Prerequisites]({{< ref "prerequisites" >}}) and [Get the source code]({{< ref "get-the-source-code" >}}).
 
 ### Install MPI
 

web/content/docs/devguide/getting-started/build/index.md

@@ -38,7 +38,7 @@ cd build-directory
 cmake --build . --config Release
 ```
 
-Please that with Visual Studio you have to provide the `--config`-paramter as Visual Studio is a [multi-configuration generator](https://cmake.org/cmake/help/latest/prop_gbl/GENERATOR_IS_MULTI_CONFIG.html) in CMake.
+Please that with Visual Studio you have to provide the `--config`-parameter as Visual Studio is a [multi-configuration generator](https://cmake.org/cmake/help/latest/prop_gbl/GENERATOR_IS_MULTI_CONFIG.html) in CMake.
 
 If you build with the help of a [CMake preset]({{< ref "build-configuration#available-cmake-presets" >}}) then you can omit the `--config`-parameter, e.g.:
 

web/content/docs/tools/geometries/generateGeometry/index.md

@@ -6,28 +6,31 @@ weight = 1
 +++
 
 ## Description
-This tool is used to generate either a quad/rectangle or a line. 
+
+This tool is used to generate either a quad/rectangle or a line.
 For this purpose, two points are used to define the geometry.
-To create a quad, the defining points need to be in a plane parallel to the xy-, xz- or yz-plane. 
-To create a line, they must define a line parallel to the standard basis vectors of 3D space. 
+To create a quad, the defining points need to be in a plane parallel to the XY-, YZ- or YZ-plane.
+To create a line, they must define a line parallel to the standard basis vectors of 3D space.
 Quads and lines then can be combined to create more complex geometries.
-This tool is mainly used to create simple geometries for benchmarking or testing purposes. 
+This tool is mainly used to create simple geometries for benchmarking or testing purposes.
+
 ## Usage
+
 ```bash
-USAGE: 
-   generateGeometry  -o <output file> 
+USAGE:
+   generateGeometry  -o <output file>
           [--polyline_name <name of the generated polyline>]
-          [--geometry_name <name of the geometry>] 
-          [--nz1 <number of subdivisions in z direction>] 
-          [--nz <number of subdivisions in z direction>] 
-          [--ny1 <number of subdivisions in y direction>] 
-          [--ny <number of subdivisions in y direction>] 
-          [--nx1 <number of subdivisions in x direction>] 
-          [--nx <number of subdivisions in x direction>] 
-          --x1 <x1> --y1 <y1> --z1 <z1> --x0 <x0> --y0 <y0> --z0 <z0> 
+          [--geometry_name <name of the geometry>]
+          [--nz1 <number of subdivisions in z direction>]
+          [--nz <number of subdivisions in z direction>]
+          [--ny1 <number of subdivisions in y direction>]
+          [--ny <number of subdivisions in y direction>]
+          [--nx1 <number of subdivisions in x direction>]
+          [--nx <number of subdivisions in x direction>]
+          --x1 <x1> --y1 <y1> --z1 <z1> --x0 <x0> --y0 <y0> --z0 <z0>
           [--] [--version] [-h]
 
-Where: 
+Where:
 
    -o <output file>,  --output <output file>
      (required)  output geometry file (*.gml)
@@ -83,21 +86,26 @@ Where:
    -h,  --help
      Displays usage information and exits.
 ```
-Subdivisions can be made along all 4 edges of a quad. 
-The input is a number that defines the amount of equidistant points that are created on the corresponding edge/line. 
+
+Subdivisions can be made along all 4 edges of a quad.
+The input is a number that defines the amount of equidistant points that are created on the corresponding edge/line.
 When a mesh is generated using this geometry, these points are also integrated into the mesh.
-Generating subdivisions along a line is done by --nx,--ny,--nz, depending on the axis the line is parallel to. 
+Generating subdivisions along a line is done by `--nx`, `--ny` or `--nz` depending on the axis the line is parallel to.
+
+## Example
+
+In this example we generate a line by defining two points p0 = (-4,-2,3) and p1= (15,-2,3).
+Here, a line is generated because y0 = y1 = -2 and z0 = z1 = 3 for the two points.
+This means the defined points are in a line parallel to the x-axis.
 
-## Example:
-In this example we generate a line by defining two points p0 = (-4,-2,3) and p1= (15,-2,3). 
-Here, a line is generated because y0 = y1 = -2 and z0 = z1 = 3 for the two points. 
-This means the defined points are in a line parallel to the x-axis. 
  ```bash
  generateGeometry -o line.gml --x0 -4 --x1 15 --y0 -2 --y1 -2 --z0 3 --z1 3
  ```
+
 In this example we generate a quad by defining two points p0 = (1,2,3) and p1= (10,20,3).
 Here, a plane is generated because z0 = z1 = 3 for the two points.
 This means the defined points are in a plane parallel to x-y-plane.
+
  ```bash
  generateGeometry -o quad.gml --x0 1 --x1 10 --y0 2 --y1 20 --z0 3 --z1 3
  ```
@@ -108,4 +116,3 @@ This means the defined points are in a plane parallel to x-y-plane.
 <p align = "center">
 Fig.1 Visualization of the generated quad and the line viewed along the z-axis.
  </p>
-

web/content/docs/tools/preprocessing/createLayeredMeshFromRasters/index.md

@@ -5,21 +5,24 @@ author = "Julian Heinze"
 +++
 
 ## Description
-createLayeredMeshFromRasters is a tool for creating a 3D mesh from a 2D mesh by adding layers to the 2D mesh. 
-The layers are created from the x-y coordinates of the mesh combined with the z-coordinates from raster files (*.asc, *.grd, *.xyz). 
-The tool builds the 3D mesh starting with the bottom layer. 
+
+createLayeredMeshFromRasters is a tool for creating a 3D mesh from a 2D mesh by adding layers to the 2D mesh.
+The layers are created from the x-y coordinates of the mesh combined with the z-coordinates from raster files (`*.asc`, `*.grd`, `*.xyz`).
+The tool builds the 3D mesh starting with the bottom layer.
 The bottom layer must cover the complete domain, i.e. it needs to have as many nodes as the 2D input mesh.
 If not an error will occur as there is no information on the lower boundary of the mesh.
 Currently, only inputs from line and triangle elements are supported, since mapping quads can result in invalid mesh elements.
-The different layers have to be listed in an extra .txt-file, where the top to bottom arrangement is given by the order of the raster files in the .txt-file.
+The different layers have to be listed in an extra `.txt`-file, where the top to bottom arrangement is given by the order of the raster files in the `.txt`-file.
+
 ## Usage
+
 ```bash
-   createLayeredMeshFromRasters  -i <file name> -o <file name> -r <file name> 
-                                [-t <floating point number>] [--ascii_output] 
+   createLayeredMeshFromRasters  -i <file name> -o <file name> -r <file name>
+                                [-t <floating point number>] [--ascii_output]
                                 [--] [--version] [-h]
 
 
-Where: 
+Where:
 
    -i <file name>,  --input-mesh-file <file name>
      (required)  The file name of the 2D input mesh.
@@ -48,7 +51,7 @@ Where:
      Displays usage information and exits.
 ```
 
-## Example:
+## Example
 
 <p align='center'>
  <img src = 2D.png width = "35%" height = "35%">
@@ -62,7 +65,7 @@ Create layers below a given 2D mesh according to a list of raster files.
 createLayeredMeshFromRasters -i mesh_mapped.vtu -o mesh_layered.vtu -r list_raster_mesh.txt
 ```
 
-The .txt file that contains the list of raster files, in this example it is called "list_raster_mesh.txt", is specified as follows:
+The `.txt`-file that contains the list of raster files, in this example it is called `list_raster_mesh.txt`, is specified as follows:
 
 ```bash
 path/to/raster-file/DEM.asc
@@ -79,5 +82,5 @@ path/to/raster-file/m6.asc
  <img src = 3D.png width = "35%" height = "35%">
 </p>
 <p align = "center">
-Fig.2 The layered 3D output mesh created from raster files. The different colors depict different material IDs. The z-values of the mesh are scaled by a factor of 10. 
- </p>
+Fig.2 The layered 3D output mesh created from raster files. The different colors depict different material IDs. The z-values of the mesh are scaled by a factor of 10.
+ </p>