Merge branch 'master' into precice-v3

Author: fsimonis

.gitmodules

@@ -10,3 +10,11 @@
 	path = imported/aste
 	url = https://github.com/precice/aste.git
 	branch = develop
+[submodule "imported/micro-manager"]
+	path = imported/micro-manager
+	url = https://github.com/precice/micro-manager.git
+	branch = develop
+[submodule "imported/fmi-runner"]
+	path = imported/fmi-runner
+	url = https://github.com/precice/fmi-runner
+	branch = develop

.markdownlint.json

@@ -1,4 +1,5 @@
 {
     "MD013": false,
-    "MD033": false
-}
+    "MD033": false,
+    "MD034": false
+}

_config.yml

@@ -149,6 +149,30 @@ defaults:
       topnav: topnav
       toc: true
       github_editme_path: https://github.com/precice/aste/edit/develop/ # ends in /
+  -
+    scope:
+      path: "imported/micro-manager/"
+      type: "pages"
+    values:
+      layout: "page"
+      comments: false
+      search: true
+      sidebar: docs_sidebar
+      topnav: topnav
+      toc: true
+      github_editme_path: https://github.com/precice/micro-manager/edit/develop/ # ends in /
+  -
+    scope:
+      path: "imported/fmi-runner/"
+      type: "pages"
+    values:
+      layout: "page"
+      comments: false
+      search: true
+      sidebar: docs_sidebar
+      topnav: topnav
+      toc: true
+      github_editme_path: https://github.com/precice/fmi-runner/edit/develop/ # ends in /
   -
     scope:
       path: "pages/community"
@@ -209,11 +233,15 @@ subprojects:
   - imported/tutorials/perpendicular-flap
   - imported/tutorials/turek-hron-fsi3
   - imported/tutorials/partitioned-pipe
+  - imported/tutorials/partitioned-backwards-facing-step
+  - imported/tutorials/flow-over-heated-plate-partitioned-flow
   - imported/tutorials/volume-coupled-diffusion
   - imported/tutorials/channel-transport
   - imported/tutorials/channel-transport-reaction
   - imported/tutorials/aste-turbine
   - imported/openfoam-adapter/docs
+  - imported/micro-manager/docs
+  - imported/fmi-runner/docs
   - imported/aste/docs
 
 # We use these versions to centrally update links

_data/sidebars/docs_sidebar.yml

@@ -232,7 +232,36 @@ entries:
     - title: Config visualization
       url: /tooling-config-visualization.html
       output: web, pdf
+      
+    - title: FMI runner
+      url: /tooling-fmi-runner.html
+      output: web, pdf
+
+      subfolders:
+      - title: Micro Manager
+        output: web, pdf
+        subfolderitems:
+
+        - title: Overview
+          url: /tooling-micro-manager-overview.html
+          output: web, pdf
+
+        - title: Get the Micro Manager
+          url: /tooling-micro-manager-installation.html
+          output: web, pdf
+        
+        - title: Preparing micro simulation
+          url: /tooling-micro-manager-prepare-micro-simulation.html
+          output: web, pdf
+
+        - title: Configuration
+          url: /tooling-micro-manager-configuration.html
+          output: web, pdf
 
+        - title: Running
+          url: /tooling-micro-manager-running.html
+          output: web, pdf
+    
     - title: Performance analysis
       url: /tooling-performance-analysis.html
       output: web, pdf
@@ -453,6 +482,10 @@ entries:
           url: /couple-your-code-waveform.html
           output: web, pdf
 
+        - title: Global data
+          url: /couple-your-code-global-data.html
+          output: web, pdf
+
       - title: Porting guides for major versions
         output: web, pdf
         subfolderitems:

_data/sidebars/tutorial_sidebar.yml

@@ -77,6 +77,14 @@ entries:
     - title: Partitioned pipe
       url: /tutorials-partitioned-pipe.html
       output: web
+
+    - title: Partitioned flow over a step
+      url: /tutorials-partitioned-backwards-facing-step.html
+      output: web
+
+    - title: Partitioned flow over heated plate
+      url: /tutorials-flow-over-heated-plate-partitioned-flow.html
+      output: web
 
     - title: Oscillator
       url: /tutorials-oscillator.html

_includes/head.html

@@ -1,7 +1,9 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1">
-<meta name="description" content="{% if page.summary %}{{ page.summary | strip_html | strip_newlines | truncate: 160 }}{% endif %}">
+{% if page.summary %}
+  <meta name="description" content="{{ page.summary | strip_html | strip_newlines }}">
+{% endif %}
 <meta name="keywords" content="{{page.tags}}{% if page.tags %}, {% endif %} {{page.keywords}}">
 <meta name="theme-color" content="#0A76BB">
 <meta name="msapplication-square310x310logo" content="images/icon-310x310.png">

_includes/news_banner.html

@@ -8,14 +8,14 @@
 
 {% endraw %}{% endcomment %}
 
-{% if include.onlanding %}
+{% if false %}
 
 <div class="background-light banner-container">
   <div class="container">
     <div class="row no-margin">
       <div class="col-lg-12 banner">
         <p class="no-margin">
-          New paper: <a href="https://doi.org/10.51560/ofj.v3.88">OpenFOAM-preCICE: Coupling OpenFOAM with external solvers for multi-physics simulations</a>, OpenFOAM® Journal
+          Find preCICE at the <a href="https://precice.org/eccomas-coupled-2023.html">ECCOMAS COUPLED 2023</a> this June
         </p>
       </div>
     </div>

_plugins/googlescholar.rb

@@ -17,7 +17,7 @@ def generate(site)
         citations = doc.css('#gs_ab_md .gs_ab_mdw').text.split[1]
         data = { 'id' => CITATION_ID,
                  'citations' => citations }
-      rescue OpenURI::HTTPError => e
+      rescue OpenURI::HTTPError, SocketError => e
         Jekyll.logger.warn "Fetching citation data failed with: #{e.message}"
         data = {}
       end

images/docs/install-wsl.png

@@ -154,6 +154,19 @@ There are a few technical things to take care of before we can merge your contri
 We automate many of these checks with [GitHub actions](https://github.com/features/actions), which you will see running at the bottom of each pull request. To avoid pushing and waiting for the actions to run while you develop, you can alternatively install [act](https://github.com/nektos/act) to execute all or specific workflows locally, running `act` or `act -j <job_name>`. It requires [Docker](https://www.docker.com/) and you can get the latest binary from the [act releases](https://github.com/nektos/act/releases/latest).
 </details>
 
+### Adding a new tutorial to the website
+
+The content of the tutorials is sourced from the develop branch of the tutorials repository, which is specified in the `.gitmodules` file of the website repository. Hence, in general, anything merged to develop in the tutorials appears on the website. Consider putting some `note` [alert box](docs-meta-cheatsheet.html#alerts) on top of your new tutorial page to describe any unreleased requirements.
+
+*New* tutorials will not directly appear on the website, but they need some additional steps. After merging to the tutorials develop, open a pull request with the following changes in the [website repository](https://github.com/precice/precice.github.io) ([example](https://github.com/precice/precice.github.io/pull/275)):
+
+1. Trigger the [update submodules workflow](https://github.com/precice/precice.github.io/actions/workflows/update-submodules.yml) and, after it completes, create a new branch and pull request (this may also happen automatically, or someone from the preCICE team may have to do it for you).
+2. Edit the [`_config.yml` file](https://github.com/precice/precice.github.io/blob/master/_config.yml) to append the directory name of your tutorial under `subprojects:`.
+3. Edit the [tutorials sidebar](https://github.com/precice/precice.github.io/blob/master/_data/sidebars/tutorial_sidebar.yml) to add your tutorial permalink (defined in the heading of the `README.md` you created) to a fitting place, next to a similar tutorial.
+4. Edit the [tutorials landing page](https://github.com/precice/precice.github.io/blob/sidebar-ff-tuts/pages/tutorials/tutorials.md) to add your tutorial to the overview.
+
+After your PR gets reviewed, approved, and merged, the website will be built automatically, and your tutorial will appear online in a couple of minutes.
+
 ## Sharing a simulation case
 
 Did you create a nice simulation case that could be useful for more people, but is not simple enough to serve as a tutorial? You can alternatively share it in the [community projects](https://precice.discourse.group/c/community-projects/11) category of our forum.

imported/fmi-runner

@@ -12,7 +12,15 @@ editme: true
 
 ## preCICE workshops
 
-Do you want to meet the community and learn what is new in preCICE? There is no better way than to join one of our workshops! We already had preCICE workshops in [February 2020](precice-workshop-2020.html) (Munich), [February 2021](precice-workshop-2021.html) (online/Stuttgart), and [February 2022](precice-workshop-2022.html) (online/Stuttgart). We are currently organizing our next workshop again in presence, in Munich, in [February 2023](precice-workshop-2023.html). We are excited to continue to interact with all users/developers/interested-persons and enthusiasts of preCICE.
+Do you want to meet the community and learn what is new in preCICE? There is no better way than to join one of our workshops! We already had preCICE workshops in [February 2020](precice-workshop-2020.html) (Munich), [February 2021](precice-workshop-2021.html) (online/Stuttgart), and [February 2022](precice-workshop-2022.html) (online/Stuttgart). We recently organized our workshop again in presence, in Munich, in [February 2023](precice-workshop-2023.html). We are excited to continue to interact with all users/developers/interested-persons and enthusiasts of preCICE.
+
+Note: The next workshop will probably not be in February 2024, but some other time in 2024. Watch out for announcements.
+
+## The preCICE forum
+
+Meet the community online, ask questions, and help others at the [preCICE forum on Discourse](https://precice.discourse.group/). Structured conversations, which help the future reader. We also post [announcements](https://precice.discourse.group/c/news/5) from time to time, so make sure to register to be the first one to learn about new workshops and releases.
+
+Are you looking for something else? Maybe one of the other [community channels](community-channels.html) is for you.
 
 ## Support preCICE
 

imported/micro-manager

@@ -8,14 +8,44 @@ toc: false
 
 The [ECCOMAS Coupled Problems 2023](https://coupled2023.cimne.com/) will take place on Crete from June 5 to June 7.
 
-We are again organizing a preCICE minisymposium: [Multi-Physics and Multi-Scale Simulations with the Coupling Library preCICE](https://coupled2023.cimne.com/area/d41c23af-2df5-11ed-8e5b-000c29ddfc0c)
+We are again organizing a preCICE minisymposium: [Multi-Physics and Multi-Scale Simulations with the Coupling Library preCICE](https://coupled2023.cimne.com/area/d41c23af-2df5-11ed-8e5b-000c29ddfc0c) (IS14).
 
-Please submit contributions to the minisymposium through the [conference website](https://coupled2023.cimne.com/) after logging in. Please choose our minisymposium code `IS14` as "area" when uploading your abstract.
+Feel free to ask questions in the [corresponding thread of the forum](https://precice.discourse.group/t/call-for-contributions-eccomas-coupled-problems-2023/1278).
 
-We are open for any research developing or using preCICE, particularly research that is of interest to more people in the preCICE community. We are also open for work-in-progress talks.
+## Schedule of the Minisymposium
 
-Current **deadline for one-page abstracts is February 3, 2023**. Submission of conference papers is optional and due till March 20.
+### Tuesday, June 6, 8:30 - 10:30
 
-Feel free to ask questions in the [corresponding thread of the forum](https://precice.discourse.group/t/call-for-contributions-eccomas-coupled-problems-2023/1278).
+Room: Impreial - Hall II,
+Session: [IS14 - I](https://coupled2023.cimne.com/event/session/80059f84-e478-11ed-9a1c-000c29ddfc0c)
+
+* **Frédéric Simonis et al.:** [An introduction to the preCICE coupling library](https://coupled2023.cimne.com/event/contribution/f525c38f-a2f6-11ed-b019-000c29ddfc0c)
+* **Prasad Adhav et al.:** [Investigation of CFD-DEM momentum coupling results for AWJC Nozzle using preCICE](https://coupled2023.cimne.com/event/contribution/088c6322-b693-11ed-9760-000c29ddfc0c)
+* **Bhargav Krishna  Chitneedi et al.:** [Hemodynamic evaluation of aortic aneurysms using FSI simulations](https://coupled2023.cimne.com/event/contribution/228163a7-a3c8-11ed-b019-000c29ddfc0c)
+* **Matthias Freimuth et al.:** [Towards Computational Efficient Fully Coupled Aeroelastic Simulations of Turbomachinery Blades with TRACE and CalculiX](https://coupled2023.cimne.com/event/contribution/01f72245-a305-11ed-b019-000c29ddfc0c)
+* **Ettore Fadiga et al.:** [An HPC Multi-Physics Framework for Next-Generation Industrial Aircraft Simulations](https://coupled2023.cimne.com/event/contribution/2b77d5d8-a3df-11ed-b019-000c29ddfc0c)
+
+### Tuesday, June 6, 16:30 - 18:30
+
+Room: Imperial - Hall II,
+Session: [IS14 - II](https://coupled2023.cimne.com/event/session/5ef3d5c8-e503-11ed-9a1c-000c29ddfc0c)
+
+* **David Schneider et al:** [Efficient Application of Accelerator Cards for Simulation of Coupled Problems](https://coupled2023.cimne.com/event/contribution/665d7477-a3a9-11ed-b019-000c29ddfc0c)
+* **Chaitanya Kandekar et al.:** [An advanced Coupling Approach for Solving Corrosion and Fracture Mechanics using preCICE](https://coupled2023.cimne.com/event/contribution/3cc282be-a3ab-11ed-b019-000c29ddfc0c)
+* **Jean-Marc Gratien et al.:** [Implementing a Comprehensive Hydromechanical Model for Sedimentary Basins by Coupling a 3D Mechanical Code to a Classic Basin Fluid Flow Code with the PreCICE Library](https://coupled2023.cimne.com/event/contribution/11266a17-a20f-11ed-b019-000c29ddfc0c)
+* **Willem Roos et al.:** [Coupled Multiphysics Models in the Field of Pyrometallurgy](https://coupled2023.cimne.com/event/contribution/90b353e2-a388-11ed-b019-000c29ddfc0c)
+* **Alfred Bogaers et al.:** [Implementation and Formulation of a Multi-Region, Electromagnetic Solver for Discontinuous Media](https://coupled2023.cimne.com/event/contribution/f3ab72ed-a38f-11ed-b019-000c29ddfc0c)
+
+### Wednesday, June 7, 09:00 - 10:00
+
+Room: Imprerial - Hall II,
+Session: [IS14 - III](https://coupled2023.cimne.com/event/session/a022f5b7-e50c-11ed-9a1c-000c29ddfc0c)
+
+* **Markus Mühlhäußer et al.:** [Partitioned Flow Simulations with preCICE and OpenFOAM](https://coupled2023.cimne.com/event/contribution/a6344f6f-a346-11ed-b019-000c29ddfc0c)
+* **Gerasimos Chourdakis et al.:** [Flexible and sustainable software for coupling mixed-dimension simulations](https://coupled2023.cimne.com/event/contribution/d6ebfb35-a3f7-11ed-b019-000c29ddfc0c)
+* **Carme Homs-Pons et al.:** [A Biophysically-Based Model of an Agonist-Antagonist Muscle Pair Using the Coupling Library preCICE](https://coupled2023.cimne.com/event/contribution/39fa5b5d-a3ea-11ed-b019-000c29ddfc0c)
+
+## Related talks in other sessions
 
-We will add more details here once we have a preliminary schedule.
+* **Benjamin Uekermann et al.:** [The Community-Driven preCICE Ecosystem](https://coupled2023.cimne.com/event/contribution/e4fce83e-a3d7-11ed-b019-000c29ddfc0c), in [IS33 - I - Progress in Computational Multiphysics Using Open-source Software](https://coupled2023.cimne.com/event/session/802c20f1-e478-11ed-9a1c-000c29ddfc0c) (Monday, June 5, 11:10 - 13:10)
+* **Benjamin Rodenberg et al.:** [A black-box coupling scheme for higher-order multirate time stepping with preCICE](https://coupled2023.cimne.com/event/contribution/8be04eb8-a3ef-11ed-b019-000c29ddfc0c), in [IS03 - I - Advances in analysis, algorithms, and software for the coupling of conventional and data-driven models for heterogeneous multi-scale, multi-physics simulations](https://coupled2023.cimne.com/event/session/7f633f85-e478-11ed-9a1c-000c29ddfc0c) (Wednesday, June 7, 09:00 - 11:00)

imported/openfoam-adapter

@@ -12,10 +12,8 @@ There are various codes - free and proprietary ones - currently coupled with pre
 We host adapters for the following codes in the [preCICE GitHub organization](https://github.com/precice/) and we maintain them to work with the latest release of preCICE (unless stated otherwise).
 
 | Adapter for | Contact | Resources | Typical applications | Comments |
-| [Ansys Fluent](https://www.ansys.com/products/fluids/ansys-fluent) | preCICE Developers | [code](https://github.com/precice/fluent-adapter), [docs](https://github.com/precice/fluent-adapter/wiki) | Fluid part in FSI | Experimental |
 | [CalculiX](http://www.calculix.de/) | preCICE Developers | [code](https://github.com/precice/calculix-adapter), [docs](adapter-calculix-overview.html) | Structure part in CHT, FSI | |
 | [code_aster](https://code-aster.org/) | preCICE Developers | [code](https://github.com/precice/code_aster-adapter), [docs](adapter-code_aster.html) | Structure part in CHT | |
-| [COMSOL Multiphysics](https://www.comsol.com/comsol-multiphysics) | preCICE Developers | [code](https://github.com/precice/comsol-adapter) | Structure part in FSI | Currently not maintained |
 | [deal.II](https://www.dealii.org/) | preCICE Developers | [code](https://github.com/precice/dealii-adapter), [docs](adapter-dealii-overview.html) | Structure part in FSI, any FEM | |
 | [FEniCS](https://fenicsproject.org/) | preCICE Developers | [code](https://github.com/precice/fenics-adapter), [docs](adapter-fenics.html) | Structure part in CHT, FSI, any FEM | See also [FEniCS-X](https://github.com/precice/fenicsx-adapter) below (WIP) |
 | [Nutils](http://www.nutils.org/) | preCICE Developers | [docs](adapter-nutils.html) | Structure part in CHT, any FEM | |
@@ -29,7 +27,9 @@ Wherever meaningful (license, maturity of the project, no other home), we host t
 
 | Adapter for   | Contact | Resources | Typical applications | Comments |
 | [Alya](https://www.bsc.es/research-development/research-areas/engineering-simulations/alya-high-performance-computational) | [TUM SCCS](https://www.in.tum.de/en/i05/) | | Fluid and structure part in FSI | Not actively maintained (but not abandoned) |
+| [Ansys Fluent](https://www.ansys.com/products/fluids/ansys-fluent) | preCICE Developers | [code](https://github.com/precice/fluent-adapter), [docs](https://github.com/precice/fluent-adapter/wiki) | Fluid part in FSI | Experimental |
 | [Ateles (APES)](https://apes.osdn.io/pages/ateles) | [Univ. Siegen STS](https://www.mb.uni-siegen.de/sts/index.html) | [code](https://osdn.net/projects/apes/scm/hg/ateles) | Fluid-Acousting, Fluid-Fluid coupling | |
+| [COMSOL Multiphysics](https://www.comsol.com/comsol-multiphysics) | preCICE Developers | [code](https://github.com/precice/comsol-adapter) | Structure part in FSI | Currently not maintained |
 | [DuMuX](https://dumux.org/) | [Alexander Jaust, University of Stuttgart](https://www.ipvs.uni-stuttgart.de/institute/team/Jaust-00001/) | [code](https://github.com/precice/dumux-adapter) | Free flow and porous-medium flow | Currently only coupled DuMuX to DuMuX. Feedback appreciated. |
 | [DUNE](https://dune-project.org/) | [Max Firmbach, UniBW M](https://www.unibw.de/imcs/team/firmbach) | [Thesis](https://mediatum.ub.tum.de/node?id=1609293), [code](https://github.com/precice/dune-adapter) | Structure part in FSI | |
 | [DUNE-Fem](https://www.dune-project.org/sphinx/content/sphinx/dune-fem/) | [Niklas Kotarsky, Lund University](https://www.lunduniversity.lu.se/lucat/user/9a5a021777b3e7cb0b8aea7ee9094808) | [coupled example code](https://github.com/precice/tutorials/tree/develop/flow-over-heated-plate/solid-dunefem) | Structure part in CHT, any FEM | |