Merge pull request precice#208 from precice/develop

Tutorials v202104.1.0

Author: MakisH

.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 renamed to .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.  
-
-
-
-
-