Merge pull request #261 from precice/develop

Release v202202.0

Author: MakisH

.github/workflows/check-links.yml

@@ -1,5 +1,5 @@
-name: Check links
-on: [push, pull_request]
+name: Check links (manual)
+on: workflow_dispatch
 jobs:
   check_links:
     runs-on: ubuntu-latest

.markdown-link-check-config.json

@@ -1,3 +1,11 @@
 {
-  "aliveStatusCodes": [429, 403, 200]
-}
+  "aliveStatusCodes": [429, 200],
+  "ignorePatterns": [
+    {
+      "pattern": "^https://openfoamwiki.net/"
+    },
+    {
+      "pattern": "^https://doi.org/"
+    }
+  ]
+}

.markdownlint.json

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

CHANGELOG.md

@@ -0,0 +1,58 @@
+# preCICE tutorials changelog
+
+All notable changes to this repository will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+<!-- markdownlint-configure-file {"MD024": { "siblings_only": true } } -->
+
+## [Unreleased]
+
+## [v202202.0] 2022-02-09
+
+### Added
+
+- Added new volume-coupled-diffusion tutorial with FEniCS [#219](https://github.com/precice/tutorials/pull/219).
+- Added OpenFOAM case to partiitoned-heat [#223](https://github.com/precice/tutorials/pull/223).
+- Added DUNE case to perpendicular-flap [#239](https://github.com/precice/tutorials/pull/239).
+- Added FEniCS case to elastic-tube-3d [#223](https://github.com/precice/tutorials/pull/223).
+- Added this changelog, describing also changes in previous releases [#225](https://github.com/precice/tutorials/pull/225).
+
+### Changed
+
+- Changed C3D8 elements to C3D8I elements in perpendicular-flap solid-calculix to improve the results [#250](https://github.com/precice/tutorials/pull/250).
+- Ported the `visualize.py` script of the partitioned-elastic-beam to Python 3 [#247](https://github.com/precice/tutorials/pull/247).
+- Reduced the writing frequency of the partitioned-pipe OpenFOAM cases [#257](https://github.com/precice/tutorials/pull/257).
+- Renamed the output directories of all FEniCS cases for consistency [#256](https://github.com/precice/tutorials/pull/257).
+- Removed unnecessary (wrong) read statment in `elastic-tube-1d` [#232](https://github.com/precice/tutorials/pull/232).
+- Removed unnecessary (relic) OpenFOAM parameter `nMoles` from flow-over-heated-plate cases with OpenFOAM [#234](https://github.com/precice/tutorials/pull/234).
+- Removed unnecessary (relic) OpenFOAM parameter `RAS` from the `turbulenceProperties` files of all OpenFOAM cases (we model a laminar flow everywhere and this was confusing) [#258](https://github.com/precice/tutorials/pull/258).
+- Removed unnecessary (relic) OpenFOAM files `RASProperties` and `couplingProperties` from elastic-tube-3d [#258](https://github.com/precice/tutorials/pull/258).
+- Removed unnecessary (relic) OpenFOAM file `radiationProperties` from heat-exchanger [#258](https://github.com/precice/tutorials/pull/258).
+- Removed duplicate default settings from the `fvSchemes` OpenFOAM file of the heat-exchanger [#258](https://github.com/precice/tutorials/pull/258).
+- Removed unnecessary (relic) fields and inaccurate copyright notices from the headers of several OpenFOAM files [#258](https://github.com/precice/tutorials/pull/258).
+- Adjusted the formatting in several OpenFOAM files [#258](https://github.com/precice/tutorials/pull/258).
+- Changed the versioning scheme from `<yearmonth>.<minor>.<bugfix>` to `<yearmonth>.<bugfix>`.
+
+## [v202104.1.1] 2021-05-02
+
+### Changed
+
+- Modified the helper tool `openfoam_remove_empty_dirs` such that it also respects results in the compressed OpenFOAM format (76f4482).
+- Synced the post-processing functionality of the elastic-tube-1d and the respective documentation. (#209)
+
+## [v202104.1.0] 2021-04-23
+
+### Added
+
+- Created a first tagged version of this repository along with a [release](https://github.com/precice/tutorials/releases/tag/v202104.1.0).
+- Added a standard run script in each case folder which can be executed as `./run.sh`.
+- Added a standard clean script in each case folder which can be executed as `./clean<what>.sh`.
+- Added an easy-to-run tutorial called [quickstart](https://precice.org/quickstart.html).
+- Added a validated Turek-Hron FSI3 case with OpenFOAM and non-linear deal.II.
+
+### Changed
+
+- Moved all documentation to the [redesigned preCICE website](https://precice.org/tutorials.html).
+- Created a new directory structure for easy access and also for [contributions](https://precice.org/community-contribute-to-precice.html).
+- Modified the 2D cases to use 2D mode in preCICE and also corresponding 2D functionality in the adapters.

README.md

@@ -1,7 +1,7 @@
 # preCICE tutorials
 
-This repository contains ready-to-run tutorial cases for the coupling library [preCICE](http://www.precice.org/).
-The purpose of these cases is not to teach you how to use preCICE from scratch, but to serve as starting points for setting up similar simulation cases, as well as test cases. Read more on our [preCICE tutorials](https://www.precice.org/tutorials.html) documentation section.
+This repository contains ready-to-run tutorial cases for the coupling library [preCICE](https://precice.org/).
+The purpose of these cases is not to teach you how to use preCICE from scratch, but to serve as starting points for setting up similar simulation cases, as well as test cases. Read more on our [preCICE tutorials](https://precice.org/tutorials.html) documentation section.
 
 As a general rule, you can start each participant from inside their `<tutorial>/<participant>-<solver>` using `./run.sh`. Look into these short scripts and copy the parts you need for your new case. Before running again, execute the cleaning scripts you can find at each level, to clean from this point and deeper.
 

elastic-tube-1d/fluid-cpp/src/FluidSolver.cpp

@@ -101,10 +101,6 @@ int main(int argc, char **argv)
       interface.markActionFulfilled(actionWriteIterationCheckpoint());
     }
 
-    if (interface.isReadDataAvailable()) {
-      interface.readBlockScalarData(crossSectionLengthID, chunkLength, vertexIDs.data(), crossSectionLength.data());
-    }
-
     fluidComputeSolutionSerial(
         // values from last time window
         velocity_old.data(), pressure_old.data(), crossSectionLength_old.data(),

elastic-tube-3d/README.md

@@ -1,7 +1,7 @@
 ---
 title: Elastic tube 3D
 permalink: tutorials-elastic-tube-3d.html
-keywords: FSI, OpenFOAM, CalculiX, nearest-projection, IMVJ
+keywords: FSI, OpenFOAM, CalculiX, FEniCS, nearest-projection, IMVJ
 summary: Tutorial for an FSI simulation of a three-dimensional expanding tube scenario
 ---
 
@@ -19,22 +19,28 @@ The expanding tube test case comes with the interface surface mesh connectivity
 
 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](https://www.precice.org/adapter-openfoam-overview.html).
+* OpenFOAM (pimpleFoam). In case you are using a very old OpenFOAM version, you will 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](https://www.precice.org/adapter-calculix-overview.html).
+* CalculiX. For more information, have a look at the [CalculiX adapter documentation](https://www.precice.org/adapter-calculix-overview.html).
+
+* FEniCS. The structural model is currently limited to linear elasticity. Currently 3D functionality is experimental in the FEniCS adapter and more details can be found [here](https://github.com/precice/fenics-adapter/pull/133) For more information, have a look at the [FeniCS adapter documentation](https://www.precice.org/adapter-fenics.html).
 
 ## Running the simulation
 
-You can start the simulation by running the script `./run.sh` located in each participant directory. OpenFOAM can be executed in parallel by using an additional `run.sh -parallel` flag. The default setting uses 4 MPI ranks.
+You can start the simulation by running the script `./run.sh` located in each participant directory. OpenFOAM can be executed in parallel using `run.sh -parallel`. The default setting uses 4 MPI ranks.
 
 ## Post-processing
 
 You can visualize the results using paraView or `cgx`(for native CalculiX resul files), as usual. The total deformation is rather small. Multiplying the deformation by factor of 10 (warp by vector filter in paraView) and visualizing the fluid domain at `t=0.005s` looks as follows:
 
 ![result tube](images/tutorials-elastic-tube-3d-tube-result.png)
 
+You can also plot the displacement of the midpoint of the tube by running `sh plot-displacement.sh <filename>`. The displacement plot for each solver combination looks like:
+
+![plot tube](images/tutorials-elastic-tube-3d-plot.png)
+
 {% disclaimer %}
 This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM®  and OpenCFD®  trade marks.
 {% enddisclaimer %}

elastic-tube-3d/fluid-openfoam/0/U

@@ -3,10 +3,8 @@ FoamFile
     version     2.0;
     format      ascii;
     class       volVectorField;
-    location    "0";
     object      U;
 }
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 dimensions      [0 1 -1 0 0 0 0];
 
@@ -28,6 +26,3 @@ boundaryField
         type            zeroGradient;
     }
 }
-
-
-// ************************************************************************* //

elastic-tube-3d/fluid-openfoam/0/p

@@ -3,10 +3,8 @@ FoamFile
     version     2.0;
     format      ascii;
     class       volScalarField;
-    location    "0";
     object      p;
 }
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 dimensions      [0 2 -2 0 0 0 0];
 
@@ -17,13 +15,13 @@ boundaryField
     auto0
     {
         type            uniformFixedValue;
-	uniformValue	table
-	(
-	(0 1.3332)
-	(3e-3 1.3332)
-	(3.1e-3 0)
-	(1e-2 0)
-	);
+	    uniformValue	table
+                        (
+                            (0 1.3332)
+                            (3e-3 1.3332)
+                            (3.1e-3 0)
+                            (1e-2 0)
+                        );
     }
     interface
     {
@@ -35,6 +33,3 @@ boundaryField
         value           uniform 0;
     }
 }
-
-
-// ************************************************************************* //

elastic-tube-3d/fluid-openfoam/0/pointDisplacement

@@ -5,7 +5,6 @@ FoamFile
     class       pointVectorField;
     object      pointDisplacement;
 }
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 dimensions      [0 1 0 0 0 0 0];
 
@@ -21,7 +20,7 @@ boundaryField
 
     interface
     {
-	type            fixedValue;
+	    type            fixedValue;
         value           $internalField;
     }
 
@@ -32,6 +31,3 @@ boundaryField
     }
 
 }
-
-
-// ************************************************************************* //