Adding the FePc_Au-IETS example

[ondrejkrejci]

Fixes #259

Just to have the IETS image in Fig 5 (b) in the examples easily achievable.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (6f26011) 46.44% compared to head (14cd5cd) 46.44%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #262   +/-   ##
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  Coverage   46.44%   46.44%           
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  Files          35       35           
  Lines        5180     5180           
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  Hits         2406     2406           
  Misses       2774     2774           

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python-3.10	46.45% <ø> (ø)
python-3.11	46.42% <ø> (ø)
python-3.12	46.42% <ø> (ø)
python-3.7	46.25% <ø> (ø)
python-3.9	46.34% <ø> (ø)

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[mondracek]

@ondrejkrejci, the Evib*png and Kvib*png images (examples/FePc_Au-IETS/Evib_atoms_000.png and examples/FePc_Au-IETS/Kvib_atoms_000.png) look virtually identical. Is that to be expected?

[ondrejkrejci]

@ondrejkrejci, the Evib*png and Kvib*png images (examples/FePc_Au-IETS/Evib_atoms_000.png and examples/FePc_Au-IETS/Kvib_atoms_000.png) look virtually identical. Is that to be expected?

Wow, you have tried those. Good job 👍 . At one point, I thought, that the images were uploaded there (which I did not want). Yes, the contrast expected to be the same, but the scale and units are different. Please see:

ppafm/ppafm/cli/plot_results.py

Line 158 in 6f26011

e_vib = common.HBAR * np.sqrt((common.eVA_Nm * eigenvalue_k) / (iets_m * common.AUMASS))

My guess, that to plot both of those, it is comming to historical reasons (Kvib is the first thing that you want to check) and potentially due to the advanced version of IETS that is comming to https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.166001 where we needed the frequency. But to be honnest I do not remember exactly. As the connection to both IETS (in ppafm and ppstm) is pretty complex, I would not change it unless somebody is willing to spend some large time on it. I personally feel that this is not worth of it.

[mondracek]

Wow, you have tried those.

Well @ondrejkrejci , I've got e-mail from GitHub that you explicitly asked me for review, so... You're welcome.

[ProkopHapala]

I personally feel that this is not worth of it.

As the connection to both IETS (in ppafm and ppstm) is pretty complex, I would not change it unless somebody is willing to spend some large time on it. I personally feel that this is not worth of it.

Commentig out saving xsf file is not "pretty complex", if we have clear idea what is better to plot?

• K_vib is nice for rationalization of the results because you can compare it directly to the simulation parameters (K_lat, K_rad of the tip)
• e_vib is more relevant to the experiment