Python API GPU tutorial

[NikoOinonen]

Fixes #268

Added a tutorial to the sphinx docs for how to run GPU-accelerated simulations via the Python API.

I found a way to write the document in Markdown instead of reST, using the myst-parser extension in sphinx, so this should also work as an example of how to add documentation if we decide to migrate the wiki content to the sphinx docs like we were briefly discussing previously.

A preview of the added page can be seen here: https://ppafm.readthedocs.io/en/api-tutorials/tutorials/afmulator-tutorial.html.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 46.44%. Comparing base (063cc9a) to head (90b4550).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #269 +/- ## ======================================= Coverage 46.44% 46.44% ======================================= Files 35 35 Lines 5180 5180 ======================================= Hits 2406 2406 Misses 2774 2774 ``` | [Flag](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | Coverage Δ | | |---|---|---| | [python-3.10](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | `46.45% <ø> (ø)` | | | [python-3.11](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | `46.42% <ø> (ø)` | | | [python-3.12](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | `46.42% <ø> (ø)` | | | [python-3.7](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | `46.25% <ø> (ø)` | | | [python-3.9](https://app.codecov.io/gh/Probe-Particle/ppafm/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle) | `46.34% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Probe-Particle#carryforward-flags-in-the-pull-request-comment) to find out more.

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[NikoOinonen]

@ProkopHapala is someone who used and developed this API before, so could maybe offer an expert opinion.

For others (@ondrejkrejci, @mondracek, @yakutovicha) who probably don't know this part of the code could maybe give more of a newcomer's perspective on whether the tutorial makes sense.

[NikoOinonen]

Thanks @yakutovicha, I applied the suggestions.

[ProkopHapala]

@NikoOinonen - I read it now. I think it is great. Thanks that you did it.

• Maybe it would be nice if @mondracek give you some feedback, I remember he was recently trying to run PPAFM on LUNA cluster using OpenCL. @mondracek can you please tell us what problems you had?

• Later I would maybe edit some formulations, but currently I don't see any problem content-wise to change. So I recommand to merge it now.

  • I'm not sure I understood exactly what you wrote here:
    • I found a way to write the document in Markdown instead of reST, using the myst-parser extension in sphinx, so this should also work as an example of how to add documentation
  • Do I need to instal something or do any other procedures if I want to edit doc/sphinx/source/tutorials/afmulator-tutorial.md ?

[NikoOinonen]

@ProkopHapala

I'm not sure I understood exactly what you wrote here:

• I found a way to write the document in Markdown instead of reST, using the myst-parser extension in sphinx, so this should also work as an example of how to add documentation
  • Do I need to instal something or do any other procedures if I want to edit doc/sphinx/source/tutorials/afmulator-tutorial.md ?

By default the sphinx system uses reStructuredText (reST) instead of Markdown, which is what the Github wiki uses. So with this addition it should be easier to just copy-paste material between the wiki and the sphinx docs, if we want to do that.

I recently put some instructions on how the documentation system works in the wiki here: https://github.com/Probe-Particle/ppafm/wiki/For-Developers#sphinx-documentation. Basically there are a couple of additional dependencies for building the HTML pages locally, but editing the document itself does not require anything extra, the web page will get automatically updated once a commit is made to the main branch.