Co-authored-by: Benjamin Uekermann <benjamin.uekermann@ipvs.uni-stuttgart.de>

Found via `codespell -q 3 -L nd,precice,sur`

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>
Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>
Co-authored-by: Gertjan van Zwieten <gertjanvanzwieten@evalf.nl>
Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>

…odes to v7.0 (#273)

* updated heat.py

* updated flow-over-heated-plate

In the quickstart guide change the download link of preCICE from 2.3.0 to 2.4.0

Co-authored-by: Nille <niklas.kotarsky@math.lu.se>
Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>
Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>

Co-authored-by: Philip Cardiff <philip.cardiff@ucd.ie>
Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>

* added calculix modal dynamic case

* update README and number of frequencies

* moved to one folder

* finished script

* Removed old folder

* removed dead code

* refactored run.sh

* updated calculix cleanup script

* schellcheck

* Readme

* Update perpendicular-flap/README.md

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* improved doc

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* Added mesh, case and config

* Updated instructions for CalculiX.

* Moved to new folder

* restored README

* removed case

* removed redundant file

* first README draft

* format

* expanded post processing

* format

* format with correct args

* Update flow-over-heated-plate-calculix/README.md

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* added adapter version

* moved generate mesh script into run

* fixed non matching end times

* refined solid mesh

* fix wrong link in readme

* added explanation for time shift

* added reference to main tutorial

* renamed dir

* Update OpenFOAM write frequency

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* concision

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* Improved post-processing description

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

* renamed folder

* added blank line

* format

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>

This is not supported by Intel oneAPI C++ compiler:
```
rigid_body_solver.cpp(117): error: expression must have a constant value
    constexpr double inertia_moment = (1. / 12) * mass * (4 * std::pow(length, 2) + std::pow(height, 2));
                                      ^
/usr/include/c++/8/cmath(418): note: cannot call non-constexpr function "pow" (declared at line 140 of "/usr/include/bits/mathcalls.h")
        return pow(__type(__x), __type(__y));
               ^
```

* Add turbine blade tutorials for ASTE

Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>
Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>

* first draft

* updated time stepping & output folder name

* plotting script

* renamed tutorial

* added runnable scripts

* clean.sh

* removed export

* first README draft

* linting

* minor text fix

Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>

* description reformulation

Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>

* Update channel-transport-reaction/README.md

Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>

* Update channel-transport-reaction/README.md

Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>

* improved BC doc

* improved integrals doc

* update plot script

* Formatting

* Changing file names to more suitable terminologies

* update postprocessing script

* update import

* one more try

* one more try

* renamed config file

* renamed folder

* cleanup

* renamed participant

* fixed bad names

* added missing import

* added pics

* Minor tweaks to README

* removed extra rm in cleaning tool

Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>
Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

* Fix cleaning tool
* Port docs to new names
* Overhaul script comments
* Extend documentation

Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>
Co-authored-by: Benjamin Uekermann <benjamin.uekermann@ipvs.uni-stuttgart.de>

According to precice/openfoam-adapter#252

Does not need a changelog entry (not previously released).

* forward compatibility

This patch removes the leading dashes for cli arguments in the run script,
which were always optional but have recently been forbidden. The changes are
compatible with all versions of nutils.

* disable rich output

This patch disables rich output by default, in order for standard output
logging to co-exist nicely with precice's log messages.

* remove droptol for projection of initial condition

This patch removes the droptol argument in the projection of the initial
condition, which is a full domain projection that should include all degrees of
freedom.

* simplify definition of sqr0

This patch simplifies the boundary constraints by using uexact.

* switch from asfunction to sample.basis

This patch replaces sample.asfunction by sample.basis combined with an argument
for readdata. While both constructions yield the same object internally
(asfunction uses basis under the hood), the new form makes it possible to
construct functionals ahead of time and benefit from cached data structures,
rather that recreate them at every iteration (see next commit).

* remove redefinition of sqr and res in time loop

This patch defines res and sqr outside the time loop, so that the only things
changing per timestep are the arguments (including readdata). The resulting
code is both cleaner and faster due to reuse of cached structures.

* introduce precice_read, precice_write

This patch simplifies the read and write instructions by sticking the arguments
inside functools.partial, leaving a more readable remainder of the code.

* improve flux evaluation

This patch replaces the projection matrix by a functional based equivalent that
is a bit more ideomatic nutils. It also fixes a consistency issue at the ends
of the boundary and adds an elaborate comment to explain the construction.

* streamline checkpointing

This patch bundles the checkpointed state in a single `checkpoint' tuple and
unifies output if the initial condition and following time steps.

* make parameters into function arguments

This patch makes all parameters into arguments of main so that they can be
configured from the command line (though not via run.sh). This makes it
possible, for example, to experiment with different timesteps on either half of
the simulation.

in partitioned-heat tutorial

* Tutorial illustrates a simple case which can be used for convergence studies and waveforms
* Case is taken from V. Schüller, B. Rodenberg, B. Uekermann and H. Bungartz, A Simple Test Case for Convergence Order in Time and Energy Conservation of Black-Box Coupling Schemes, in: WCCM-APCOM2022. URL https://www.scipedia.com/public/Rodenberg_2022a

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>

* Put images of channel-transport-reaction in images/ folder

* Changing image names to have a prefix tutorials-channel-transport-reaction-

Co-authored-by:  Gertjan van Zwieten  <git@gjvz.nl>
Co-authored-by: Benjamin Uekermann <benjamin.uekermann@ipvs.uni-stuttgart.de>
Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>
Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>
Co-authored-by: Gerasimos Chourdakis <chourdak@in.tum.de>

* Rename multiple-perpendicular-flaps mesh names

* Rename participant and meshes

Solid1 becomes Solid-Left, and Solid2 becomes Solid-Right following the directory names.
We could further rename these, together with the directory names.

For the Fluid meshes, we just use Upstream and Downstream as indicators.

For the Solid meshes, we follow the usual Participant-Mesh name.

The data fields are named based on the Upstream/Downstream.

* Rename OpenFOAM interfaces based on patches

* Rename OpenFOAM interfaces

* Rename Left and Right to Upstream and Downstream

* Rename folder left and right

* Fix more outdated things in README

* Update plotDispls script

* Fix the other script as well

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@ipvs.uni-stuttgart.de>

Closes precice/openfoam-adapter#259

While it fixed the segfault, it actually disabled the Force coupling.

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@ipvs.uni-stuttgart.de>