Merge pull request #208 from precice/develop

Tutorials v202104.1.0

.github/ISSUE_TEMPLATE/issue-template.md

@@ -0,0 +1,26 @@
+---
+name: Issue template
+about: Check this out before opening an issue
+
+---
+<!-- markdownlint-disable-file MD041 -->
+<!-- 
+       Hey! Thank you for reporting an issue!
+       Just to make sure: is this really an issue or do you need some help
+       with troubleshooting? Please use our community channels if you need help:
+       https://precice.org/community-channels.html
+       Thanks! :-)
+
+       Please wrap any error messages with three backticks before and after:
+       ```
+       This is an error message
+       ```
+
+       If this is a bug, please provide the following information.
+       You can generate log files with `./run.sh > solver.log 2>&1`.
+-->
+
+- Tutorials state (last commit / release):
+- Versions of solvers and adapters used:
+- preCICE version:
+- Log files:

.github/pull_request_template.md

@@ -0,0 +1,3 @@
+<!-- Please submit your Pull Request to the `develop` branch.
+
+It may help to have a look at the file `CONTRIBUTING.md` for a few hints and guidelines. -->

.github/workflows/check-links.yml

@@ -0,0 +1,14 @@
+name: Check links
+on: [push, pull_request]
+jobs:
+  check_links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - name: Check links in markdown files (markdown-link-check)
+        uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+          config-file: '.markdown-link-check-config.json'

.github/workflows/check-markdown.yml

@@ -0,0 +1,14 @@
+name: Lint docs
+on: [push, pull_request]
+jobs:
+  check_md:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - name: Lint markdown files (markdownlint)
+        uses: articulate/actions-markdownlint@v1
+        with:
+          config: .markdownlint.json
+          files: '.'
+          ignore: changelog-entries

.github/workflows/checks.yaml → .github/workflows/check-scripts.yaml

@@ -1,10 +1,14 @@
-name: Checks
+name: Check scripts
 on: [push, pull_request]
 jobs:
-  checks:
+  check_scripts:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
       - run:  bash tools/check.sh
       - run:  bash tools/check-size.sh
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@master
+        env:
+          SHELLCHECK_OPTS: -e SC1091

.markdown-link-check-config.json

@@ -0,0 +1,3 @@
+{
+  "aliveStatusCodes": [429, 403, 200]
+}

.markdownlint.json

@@ -0,0 +1,4 @@
+{
+    "MD013": false,
+    "MD033": false
+}

CODE_OF_CONDUCT.md

@@ -0,0 +1,130 @@
+# Contributor Covenant Code of Conduct
+
+<!-- markdownlint-configure-file {"MD034": false } -->
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+info at precice.org.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -1,3 +1,5 @@
+# Contribute to the preCICE tutorials
+
 It is amazing that you want to contribute a tutorial case for preCICE!
 
-We welcome contributions and we have a few guidelines and tips that you can follow in the [preCICE website](https://precice.org/community-contribute-to-precice.html).
+We welcome contributions and we have a few guidelines and tips that you can follow in the [preCICE website](https://precice.org/community-contribute-to-precice.html).

elastic-tube-1d/README.md

@@ -5,16 +5,18 @@ keywords: OpenFOAM, python
 summary: The 1D Elastic Tube is a FSI case, that consists of an internal flow in a flexible tube. The flow is unsteady and incompressible. This tutorial contains C++ and Python variants of the fluid and solid solvers. Running the simulation takes just 1-2 minutes.  
 ---
 
+{% include note.html content="Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/elastic-tube-1d). Read how in the [tutorials introduction](https://www.precice.org/tutorials.html)." %}
 
 ## Setup
 
 We want to simulate the internal flow in a flexible tube as shown in the figure below (image from [1]).
 
 ![FSI3 setup](images/tutorials-elastic-tube-1d-setup.png)
 
-The flow is assumed to be incompressible flow and gravity is neglected. Due to the axisymmetry, the flow can be described using a quasi-two-dimensional continuity and momentum equations. The motivation and exact formulation of the equations that we consider can be found in [2]. 
+The flow is assumed to be incompressible flow and gravity is neglected. Due to the axisymmetry, the flow can be described using a quasi-two-dimensional continuity and momentum equations. The motivation and exact formulation of the equations that we consider can be found in [2].
 
 The following parameters have been chosen:
+
 - Length of the tube: L = 10
 - Inlet velocity: $$ v_{inlet} = 10 + 3 sin (10 \pi t) $$
 - Initial cross sectional area = 1
@@ -23,27 +25,25 @@ The following parameters have been chosen:
 - Fluid density: $$ \rho = 1 $$
 - Young modulus: E = 10000
 
-
 ## Available solvers
 
 Both fluid and solid participant are supported in:
 
-* *C++*: An example solver using the intrinsic [C++ API of preCICE](couple-your-code-api.html). This solver also depends on LAPACK (e.g. on Ubuntu `sudo apt-get install liblapack-dev`)
-* *Python*: An example solver using the preCICE [Python bindings](installation-bindings-python.html). This solver also depends on the Python libraries `numpy scipy matplotlib vtk mpi4py`, which you can get from your system package manager or with `pip3 install --user <package>`.
-
+- *C++*: An example solver using the intrinsic [C++ API of preCICE](https://www.precice.org/couple-your-code-api.html). This solver also depends on LAPACK (e.g. on Ubuntu `sudo apt-get install liblapack-dev`)
+- *Python*: An example solver using the preCICE [Python bindings](https://www.precice.org/installation-bindings-python.html). This solver also depends on the Python libraries `numpy scipy matplotlib vtk mpi4py`, which you can get from your system package manager or with `pip3 install --user <package>`.
 
 ### Building the C++ Solver
 
 In order to use the C++ solver, you first need to build the scripts `FluidSolver` and `SolidSolver`. Each script needs to be built separately.
 
-```
+```bash
 cd fluid-cpp
 mkdir build && cd build
 cmake ..
 make all
 ```
 
-```
+```bash
 cd solid-cpp
 mkdir build && cd build
 cmake .. 
@@ -52,38 +52,43 @@ make all
 
 Building can be skipped if you do not plan to use the C++ version.  
 
-## Running the Simulation 
+## Running the Simulation
 
 ### C++
 
-Open two separate terminals and start each participant by calling the respective run script. 
+Open two separate terminals and start each participant by calling the respective run script.
 
-```
+```bash
 cd fluid-cpp
 ./run.sh
 ```
+
 and
-```
+
+```bash
 cd solid-cpp
 ./run.sh
 ```
 
-The solvers use the parameters `N = 100`, `tau = 0.01`, `kappa = 100` by default and can be modified in the solver. 
+The solvers use the parameters `N = 100`, `tau = 0.01`, `kappa = 100` by default and can be modified in the solver.
 
 ### Python
 
 Open two separate terminals and start each participant by calling the respective run script. Only serial run is possible:
 
-```
+```bash
 cd fluid-python
 ./run.sh
 ```
+
 and
-```
+
+```bash
 cd solid-python
 ./run.sh
 ```
-Parameters such as `N` can be modified directly at the `FluidSolver.py` and at the `SolidSolver.py`. The parameters must be consistent between the different solvers and participants. 
+
+Parameters such as `N` can be modified directly at the `FluidSolver.py` and at the `SolidSolver.py`. The parameters must be consistent between the different solvers and participants.
 
 **Optional:** Visualization and video output of the fluid participant can be triggered via the options `--enable-plot` and `--write-video` of `FluidSolver.py`. To generate .vtk files during execution, you need to add the flag `--write-vtk`.
 
@@ -94,21 +99,27 @@ Parameters such as `N` can be modified directly at the `FluidSolver.py` and at t
 ## Post-processing
 
 The results from each simulation are stored in each `fluid-<participant>/output/` folder. You can visualize these VTK files using the provided `plot-diameter.sh` script
+
 ```bash
 ./plot-diameter.sh
 ```
+
 which will try to visualize the results from both fluid cases, if available.
 
 This script calls the more flexible `plot-vtk.py` Python script, which you can use as
+
 ```bash
 python3 plot-vtk.py <quantity> <case>/output/<prefix>
 ```
+
 Note the required arguments specifying which quantity to plot (`pressure`, `velocity` or `diameter`) and the name prefix of the target vtk files.
 
-For example, to plot the diameter of the fluid-python case using the default prefix for VTK files, `plot-diamter.sh` executes:
+For example, to plot the diameter of the fluid-python case using the default prefix for VTK files, `plot-diameter.sh` executes:
+
 ```bash
 python3 plot-vtk.py diameter fluid-python/output/out_fluid_
 ```
+
 ![FSI3 setup](images/tutorials-elastic-tube-1d-diameter.png)
 
 ## References
@@ -119,8 +130,3 @@ python3 plot-vtk.py diameter fluid-python/output/out_fluid_
 
 [3] M. Mehl, B. Uekermann, H. Bijl, D. Blom, B. Gatzhammer, and A. van Zuijlen.
 Parallel coupling numerics for partitioned fluid-structure interaction simulations. CAMWA, 2016.  
-
-
-
-
-

elastic-tube-3d/README.md

@@ -5,21 +5,23 @@ keywords: FSI, OpenFOAM, CalculiX, nearest-projection, IMVJ
 summary: Tutorial for an FSI simulation of a three-dimensional expanding tube scenario
 ---
 
+{% include note.html content="Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/elastic-tube-3d). Read how in the [tutorials introduction](https://www.precice.org/tutorials.html)." %}
+
 ## Setup
 
 The expanding tube test case involves a cylindrical fluid domain surrounded by a solid domain. A pressure inlet boundary condition is applied at the inlet for 3 milliseconds, and then 0 set to zero for a further 7 millisecond. The pressure of the fluid expands the tube which then relaxes once the pressure decreases.
 
-The expanding tube test case comes with the interface surface mesh connectivity of the solid domain. This allows the use of nearest-projection mapping of the displacements of the solid domain. In order to run the example with nearest projection mapping, the "node-mesh-with-connectivity" has been specified in the `solid-calculix/config.yml` file. More details can be found in the [CalculiX configuration description](adapter-calculix-config.html#nearest-projection-mapping).
+The expanding tube test case comes with the interface surface mesh connectivity of the solid domain. This allows the use of nearest-projection mapping of the displacements of the solid domain. In order to run the example with nearest projection mapping, the "node-mesh-with-connectivity" has been specified in the `solid-calculix/config.yml` file. More details can be found in the [CalculiX configuration description](https://www.precice.org/adapter-calculix-config.html#nearest-projection-mapping).
 
 ## Available solvers
 
 Fluid participant:
 
-* OpenFOAM. This tutorial is known to work with OpenFOAM 4.1, 5.0, but it should also work with newer versions. The case files are prepared for the latest versions of OpenFOAM and use the solver `pimpleFoam`. In case you are using a previous OpenFOAM version you need to adjust the solver to `pimpleDyMFoam` in the `Fluid/system/controlDict` file. For more information, have a look at the [OpenFOAM adapter documentation](adapter-openfoam-overview.html).
+* OpenFOAM. This tutorial is known to work with OpenFOAM 4.1, 5.0, but it should also work with newer versions. The case files are prepared for the latest versions of OpenFOAM and use the solver `pimpleFoam`. In case you are using a previous OpenFOAM version you need to adjust the solver to `pimpleDyMFoam` in the `Fluid/system/controlDict` file. For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
 Solid participant:
 
-* CalculiX. This tutorial is known to work with CalculiX 2.15, but it should also work with newer versions. For more information, have a look at the [CalculiX adapter documentation](adapter-calculix-overview.html).
+* CalculiX. This tutorial is known to work with CalculiX 2.15, but it should also work with newer versions. For more information, have a look at the [CalculiX adapter documentation](https://www.precice.org/adapter-calculix-overview.html).
 
 ## Running the simulation