Formatting for PDF rendering

fsi-workflow/00_geometry/tasks.md

@@ -1,13 +1,14 @@
 # Community course on preCICE: FSI Workflow
 
-A training module showcasing how to setup an FSI simulation from scratch.
+Introductory course at the preCICE Workshop 2024, Stuttgart, September 24-27, 2024
 
 \vspace{2em}
 
 Claudio Caccia, Politecnico di Milano\newline `<claudiogiovanni.caccia@polimi.it>`
-Gerasimos Chourdakis, University of Stuttgart `<gerasimos.chourdakis@ipvs.uni-stuttgart.de>`
 
-This is a community-contributed part of the course. Contribute on GitHub: https://github.com/precice/community-training
+Gerasimos Chourdakis, University of Stuttgart\newline `<gerasimos.chourdakis@ipvs.uni-stuttgart.de>`
+
+This is a community-contributed part of the course: [Contribute on GitHub](https://github.com/precice/community-training).
 
 ## Dependencies
 
@@ -21,7 +22,11 @@ We will use the following software:
 ## Task 0: Prepare the geometry
 
 We will simulate fluid-structure interaction of a very simple airfoil, in 3D. [NACA airfoils](https://en.wikipedia.org/wiki/NACA_airfoil) are standardized designs that are popular in designing aircraft wings.
-Our case is slightly derived from the paper by *S. Heathcote, Z. Wang, I. Gursul, **Effect of spanwise flexibility on flapping wing propulsion**, Journal of Fluids and Structures, Volume 24, Issue 2, 2008*. In the paper, they considered a *NACA0012* profile, while our training involves a **NACA2312** profile wing (to have some lift at 0° angle of attack) with:
+Our case is slightly derived from the following paper:
+
+*S. Heathcote, Z. Wang, I. Gursul, **Effect of spanwise flexibility on flapping wing propulsion**, Journal of Fluids and Structures, Volume 24, Issue 2, 2008*.
+
+In the paper, they considered a *NACA0012* profile, while our training involves a **NACA2312** profile wing (to have some lift at 0° angle of attack) with:
 
 - *chord* $c=100mm$
 - *span* $b=300mm$
@@ -34,6 +39,8 @@ You'll notice that two different file formats are provided: a `.stl` file and a
 
 When meshing a flow domain, we need to consider whether we are simulating external or internal flow. In this case, we are considering an external flow: we will use the solid geometry to generate the **solid mesh**, and we will subtract it from a sufficiently large box to generate the **fluid mesh**.
 
+\newpage
+
 ### Notes on file formats
 
 You might wonder: "Why two formats?".

fsi-workflow/01_solidMesh/tasks.md

@@ -14,6 +14,8 @@ Select the `FEM Workbench`:
 
 ![FreeCAD: FEM Workbench](./images/FEM_WB.png)
 
+\newpage
+
 Go to:
 
 - Click `Edit` -> `Preferences...`.
@@ -22,7 +24,7 @@ Go to:
 
 Configure as follows:
 
-- Which elements to export `All`.
+- Which elements to export: `All`.
 - Export group data: (check).
 
 Then, click `Apply` and `OK`.
@@ -34,7 +36,7 @@ The first task consists in importing the wing:
 - Create a new project: Click `File` -> `New`.
 - Give the model a name: In the `Combo View/Model` tab on the left, select the unnamed model and change the `Label`: click on the `Unnamed` and rename it to `Wing`.
 
-![FreeCAD: Rename model label](./images/PD_rename.png)
+![FreeCAD: Rename model label to `Wing`](./images/PD_rename.png)
 
 - Select the `Part design` workbench from the drop-down menu and click `create body`:
 
@@ -61,12 +63,12 @@ Now we can generate a mesh for the `Wing`.
 - Switch again to the FEM Workbench from the drop-down menu.
 - From the menu bar, click `Model` -> `Analysis container` (or select the `A` symbol from the toolbar):
 
-![FreeCAD: Analysis container](./images/FEM_Analysis.png)
+![FreeCAD: Add an Analysis container](./images/FEM_Analysis.png)
 
 - We want to mesh the `BaseFeature`: Select it from the sidebar.
 - From the menu bar, click `Mesh` -> `FEM Mesh from shape by GMSH`. The FEM Workbench can generate meshes using different backends; we use [GMSH](https://gmsh.info/) here.
 
-![FreeCAD: Add Analysis container](./images/FEM_Mesh01.png)
+![FreeCAD: Add a mesh](./images/FEM_Mesh01.png)
 
 - In the `Tasks` tab, use the following parameters:
   - Element dimension: `3D`
@@ -115,7 +117,7 @@ Now that we have a mesh, we also need to create the boundaries. We will need to
 
 - In the `Model` tab, select the `MeshGroup` and rename its `Label` to `Nroot`. This will help us define the boundary condition in the Solid domain.
 
-**NOTE**: Node group names need to start with `N`.
+  **NOTE**: Node group names need to start with `N`.
 
 ![FreeCAD: Rename mesh group](./images/Groups05.png)
 

fsi-workflow/02_solidSimulation/tasks.md

@@ -106,5 +106,4 @@ Note that we are a bit lazy here, as the $x, y$ axes are not *principal axes*. N
 
 ## References
 
-- CalculiX user manual: https://www.dhondt.de/ccx_2.20.pdf
-- Web version (possibly outdated): https://web.mit.edu/calculix_v2.7/CalculiX/ccx_2.7/doc/ccx/ccx.html
+- CalculiX 2.20 user manual: [https://www.dhondt.de/ccx_2.20.pdf](https://www.dhondt.de/ccx_2.20.pdf)

fsi-workflow/03_fluidMesh/tasks.md

@@ -140,24 +140,13 @@ In case you get an error that there are not enough slots in your system to run e
 
 Once `snappyHexMesh` has finished, you can reconstruct your domain from the decomposed ones by running `reconstructParMesh`.
 
-When finished, you will see three time folders (0.001, 0.002, 0.003) in the root directory of the case. Each one corresponds to a stage of `snappyHexMesh`:
+When finished, you will see three time folders (0.001, 0.002, 0.003) in the root directory of the case. Each one corresponds to a stage of `snappyHexMesh`. The time step size depends on the `deltaT` parameter in the `controlDict` file, but it is not relevant. You can obtain the final mesh in the `constant` directory, without the intermediate steps, by adding the `-overwrite` option to `snappyHexMesh`. In the next step (fluid simulation), we will use and rename the `0.003` directory.
 
-- 0.001: castellatedMesh
+![snappyHexMesh output: Castellation stage (`0.001` directory)](./images/01_cast.png)
 
-![castellation](./images/01_cast.png)
+![snappyHexMesh output: Snap stage (`0.002` directory)](./images/02_snap.png)
 
-- 0.002: snap
-
-![snap](./images/02_snap.png)
-
-- 0.003: addLayers
-
-![BL](./images/03_BL.png)
-
-Notes:
-
-- The time step size depends on the `deltaT` parameter in the `controlDict` file, but it is not relevant.
-- You can obtain the final mesh in the `constant` directory, without the intermediate steps, by adding the `-overwrite` option to `snappyHexMesh`. In the next step (fluid simulation), we will use and rename the `0.003` directory.
+![snappyHexMesh output: Boundary layer stage (`0.003` directory)](./images/03_BL.png)
 
 ## Checking the mesh
 

fsi-workflow/04_fluidSimulation/tasks.md

@@ -80,7 +80,7 @@ To check the simulation progress and plot the residuals over time, you can use [
 pyFoamPlotWatcher log.solver
 ```
 
-Two pop-up windows with residual graphs should appear:
+A pop-up window with residual graphs should appear:
 
 ![residuals](./images/pyFoam.png)
 

fsi-workflow/05_FSI/tasks.md

@@ -131,9 +131,9 @@ You can monitor the ongoing simulation by running the following scripts from the
 
 Two windows with the following graphs should appear:
 
-![tip displacement](./images/Tip_disp_damp.png)
+![Montoring: Tip displacement (`plotDisplacement.sh`)](./images/Tip_disp_damp.png)
 
-![convergence](./images/convergence.png)
+![Montoring: Convergence (`plotConvergence.py`)](./images/convergence.png)
 
 ### Cleaning
 
@@ -159,17 +159,17 @@ Open a terminal in the `Fluid` folder and type `paraFoam`
 2. In `Case type` select `Decomposed Case`
 3. Then press `Apply`
 
-![open](./images/open_fluid.png)
+![ParaView: Open `Fluid.foam`](./images/open_fluid.png)
 
 You will then have access to the `OpenFOAM` fluid simulation results.
 
-![fluid](./images/parafoam.png)
+![ParaView: Surface plot of flow velocity](./images/parafoam.png)
 
 ### Solid results
 
 In the same ParaView window, select `File->Open...` and point to the `Solid/convert/solidModel.pvd` file.
 
-![FSI](./images/result_FSI.png)
+![ParaView: Combined FSI results](./images/result_FSI.png)
 
 To see the displacement more easily, you can apply a `WarpByVector` filter, using the displacement (`U`) as vector, and a scale factor of your choice.