Merge branch 'master' into develop

Author: MakisH

elastic-tube-1d/README.md

@@ -5,7 +5,9 @@ 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://precice.org/tutorials.html)." %}
+{% note %}
+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).
+{% endnote %}
 
 ## Setup
 
@@ -31,8 +33,8 @@ Additionally the solvers use the parameters `N = 100` (number of cells), `tau =
 
 Both fluid and solid participant are supported in:
 
-- *C++*: An example solver using the intrinsic [C++ API of preCICE](https://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://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>`.
+- *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
 
@@ -90,6 +92,10 @@ cd solid-python
 
 **Optional:** A run-time plot visualization can be trigged by passing `--enable-plot` in `run.sh` of `FluidSolver.py`. Additionally a video of the run-time plot visualization can be generated by additionally passing `--write-video`
 
+{% warning %}
+The C++ and Python solvers lead to different results. Please consider the Python results as the correct ones and refer to this [open issue](https://github.com/precice/tutorials/issues/195) for more insight. Contributions are particularly welcome here.
+{% endwarning %}
+
 ## Post-processing
 
 ![Elastic tube animation](images/tutorials-elastic-tube-1d-animation.gif)

elastic-tube-3d/README.md

@@ -5,27 +5,25 @@ 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://precice.org/tutorials.html)." %}
+{% note %}
+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).
+{% endnote %}
 
 ## 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](https://precice.org/adapter-calculix-config.html#nearest-projection-mapping).
-
-{% tip %}
-Are you new to CalculiX? Watch this [amazing contributed tutorial](https://www.youtube.com/playlist?list=PLWHQIdms-YHT8Ybt9psE8lJpaWRyy3fNf) explaining how to set up a very similar case with preCICE, OpenFOAM, and CalculiX.
-{% endtip  %}
+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](https://precice.org/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](https://precice.org/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
 
@@ -37,4 +35,6 @@ You can visualize the results using paraView or `cgx`(for native CalculiX resul
 
 ![result tube](images/tutorials-elastic-tube-3d-tube-result.png)
 
-{% include disclaimer.html content="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." %}
+{% 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 %}

flow-over-heated-plate-nearest-projection/README.md

@@ -5,23 +5,25 @@ keywords: OpenFOAM, nearest-projection, CHT
 summary: This tutorial introduces an example simulation setup for a nearest-projection mapping, based on the "flow over a heated plate" scenario.
 ---
 
-{% include note.html content="Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate-nearest-projection). Read how in the [tutorials introduction](https://precice.org/tutorials.html)." %}
+{% note %}
+Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate-nearest-projection). Read how in the [tutorials introduction](https://www.precice.org/tutorials.html).
+{% endnote %}
 
 ## Setup
 
-The setup is exactly the same as described in our [flow-over-heated-plate tutorial](https://precice.org/tutorials-flow-over-heated-plate.html).
+The setup is exactly the same as described in our [flow-over-heated-plate tutorial](https://www.precice.org/tutorials-flow-over-heated-plate.html).
 
 ## Available solvers
 
 Fluid participant:
 
-* OpenFOAM (buoyantPimpleFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM (buoyantPimpleFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
 Solid participant:
 
-* OpenFOAM (laplacianFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM (laplacianFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
-The solvers are currently only OpenFOAM related. For information regarding the nearest-projection mapping, have a look in the [OpenFOAM configuration section](https://precice.org/adapter-openfoam-config.html).
+The solvers are currently only OpenFOAM related. For information regarding the nearest-projection mapping, have a look in the [OpenFOAM configuration section](https://www.precice.org/adapter-openfoam-config.html).
 
 ## Running the Simulation
 
@@ -66,12 +68,14 @@ From the preCICE point of view, the simulation here is in 3D, as opposed to the
 
 ## Post-processing
 
-Have a look at the [flow-over heated-plate](https://precice.org/tutorials-flow-over-heated-plate.html) tutorial for the general aspects of post-processing.
+Have a look at the [flow-over heated-plate](https://www.precice.org/tutorials-flow-over-heated-plate.html) tutorial for the general aspects of post-processing.
 Since we now defined mesh connectivity on our interface, we can export the coupling interface with the tag `<export:vtk directory="preCICE-output" />` in our `precice-config.xml`.
 Visualizing these files (e.g. using ParaView) will show a triangular mesh, even though you use hexahedral meshes. This has nothing to do with your mesh and is just caused by the way the connectivity is defined in preCICE. As described above, the function `setMeshTriangles` is used to define the connectivity. Hence, every interface cell/face is represented by two triangles. The following image should give you an impression of a possible triangulated coupling mesh, which consists purely of hexahedral cells:
 
 ![triangulated](https://user-images.githubusercontent.com/33414590/55974257-96b07d80-5c87-11e9-9965-972b922c483d.png)
 
 Connectivity is defined on meshes associated with mesh nodes, which are named respectively e.g. `Fluid-Mesh-Nodes`. In this case, you could directly see the interface without applying filters by loading the `.vtk` files. In order to visualize additionally center based meshes, where no connectivity is provided, select a Glyph filter in ParaView. Furthermore, it makes a difference, on which participant the `<export...` tag is defined in your `precice-config.xml` file. Each participant exports interface meshes, which he provides or receives. The receiving participant filters out mesh parts that it does not need (for the mapping). Hence, a received mesh might look incomplete.
 
-{% include disclaimer.html content="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." %}
+{% 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 %}

flow-over-heated-plate-steady-state/README.md

@@ -5,23 +5,27 @@ keywords: CHT, steady-state, Code_Aster, OpenFOAM
 summary: Using a steady-state OpenFOAM solver for a CHT coupling with code_aster. This tutorial is based on the "flow over a heated plate" scenario.
 ---
 
-{% include note.html content="Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate-steady-state). Read how in the [tutorials introduction](https://precice.org/tutorials.html)." %}
+{% note %}
+Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate-steady-state). Read how in the [tutorials introduction](https://www.precice.org/tutorials.html).
+{% endnote %}
 
 ## Setup
 
-The setup for this tutorial is similar to the [flow over a heated plate](https://precice.org/tutorials-flow-over-heated-plate.html) using OpenFOAM. In this tutorial OpenFOAM is used as the solver for the fluid domain, and code_aster is the solver for the solid domain. A difference here is that we are using a steady-state OpenFOAM solver for demonstration purposes, therefore the results between the two tutorials are not comparable.
+The setup for this tutorial is similar to the [flow over a heated plate](https://www.precice.org/tutorials-flow-over-heated-plate.html) using OpenFOAM. In this tutorial OpenFOAM is used as the solver for the fluid domain, and code_aster is the solver for the solid domain. A difference here is that we are using a steady-state OpenFOAM solver for demonstration purposes, therefore the results between the two tutorials are not comparable.
 
-{% include note.html content="This is a pseudo-2D case, but we still set a 3D `solver-interface` in `precice-config.xml`, because the code_aster case is set up like this at the moment. Contributions here are particularly welcome!" %}
+{% note %}
+This is a pseudo-2D case, but we still set a 3D `solver-interface` in `precice-config.xml`, because the code_aster case is set up like this at the moment. Contributions here are particularly welcome!
+{% endnote %}
 
 ## Available solvers
 
 Fluid participant:
 
-* OpenFOAM. We use buoyantSimpleFoam instead of the transient buoyantPimpleFoam. For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM. We use buoyantSimpleFoam instead of the transient buoyantPimpleFoam. For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
 Solid participant:
 
-* code_aster. The [code_aster adapter documentation](https://precice.org/adapter-code_aster.html) is oriented on this tutorial case. In particular the described configuration settings.
+* code_aster. The [code_aster adapter documentation](https://www.precice.org/adapter-code_aster.html) is oriented on this tutorial case. In particular the described configuration settings.
 
 ## Running the Simulation
 
@@ -41,4 +45,6 @@ The `.rmed` file output from Code_Aster can be viewed using [GMSH](https://gmsh.
 
 ![code-aster-result](images/tutorials-flow-over-heated-plate-steady-state-result.png)
 
-{% include disclaimer.html content="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." %}
+{% 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 %}

flow-over-heated-plate/README.md

@@ -5,7 +5,9 @@ keywords: tutorial, CHT, conjugate-heat transfer, OpenFOAM, FEniCS, Nutils
 summary: This tutorial describes how to run a conjugate heat transfer coupled simulation using preCICE and any fluid-solid solver combination of our <a href="adapters-overview.html">officially provided adapter codes</a>.
 ---
 
-{% include note.html content="Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate). Read how in the [tutorials introduction](https://precice.org/tutorials.html)." %}
+{% note %}
+Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/flow-over-heated-plate). Read how in the [tutorials introduction](https://www.precice.org/tutorials.html).
+{% endnote %}
 
 ## Setup
 
@@ -15,21 +17,21 @@ This scenario consists of one fluid and one solid participant and it is inspired
 
 The test case is two-dimensional and a serial-implicit coupling with Aitken underrelaxation is used for the coupling.
 
-The inlet velocity is $$ u_{\infty} = 0.1 m/s $$, the inlet temperature is $$ T_{\infty} = 300K $$ and ambient pressure is $$ p_0 = 103500 Pa $$ . The fluid and solid have the same thermal conductivities $$ k_S = k_F = 100 W/m/K $$ and densities $$ rho_S = rho_F = 1 kg/m^3 $$. Further material properties of the fluid are its viscosity $$ mu = 0.0002 kg/m/s $$ and specific heat capacity $$ c_p = 5000 J/kg/K $$. The Prandtl number $$ Pr = 0.01 $$ follows from thermal conductivity, viscosity and specific heat capacity. The solid has the thermal diffusivity $$ \alpha = 1 m^2/s $$. The gravitational acceleration is $$ g = 9.81 m/s^2 $$.
+The inlet velocity is $$ u_{\infty} = 0.1 m/s $$, the inlet temperature is $$ T_{\infty} = 300K $$. The fluid and solid have the same thermal conductivities $$ k_S = k_F = 100 W/m/K $$. Further material properties of the fluid are its viscosity $$ mu = 0.0002 kg/m/s $$ and specific heat capacity $$ c_p = 5000 J/kg/K $$. The Prandtl number $$ Pr = 0.01 $$ follows from thermal conductivity, viscosity and specific heat capacity. The solid has the thermal diffusivity $$ \alpha = 1 m^2/s $$. The gravitational acceleration is $$ g = 9.81 m/s^2 $$.
 
 ## Available solvers
 
 By default, the fluid participant reads heat-flux values and the solid participant reads temperature values for the coupled simulation. The following participants are available:
 
 Fluid participant:
 
-* OpenFOAM (buoyantPimpleFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM (buoyantPimpleFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
 Solid participant:
 
-* OpenFOAM (laplacianFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
+* OpenFOAM (laplacianFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://www.precice.org/adapter-openfoam-overview.html).
 
-* FEniCS. For more information, have a look at the [FeniCS adapter documentation](https://precice.org/adapter-fenics.html).
+* FEniCS. For more information, have a look at the [FeniCS adapter documentation](https://www.precice.org/adapter-fenics.html).
 
 * Nutils. For more information, have a look at the [Nutils adapter documentation](https://precice.org/adapter-nutils.html).
 
@@ -87,4 +89,6 @@ After that running a case from this tutorial will export data into `solid-*/preC
 
 [1]  M. Vynnycky, S. Kimura, K. Kanev, and I. Pop. Forced convection heat transfer from a flat plate: the conjugate problem. International Journal of Heat and Mass Transfer, 41(1):45 – 59, 1998.
 
-{% include disclaimer.html content="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." %}
+{% 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 %}