CoPc-IETS example broken

[NikoOinonen]

Throws this error currently:

Traceback (most recent call last):
  File "/home/work/git/ppafm/.venv/bin/ppafm-relaxed-scan", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/work/git/ppafm/ppafm/cli/relaxed_scan.py", line 191, in main
    tip_positions_x, tip_positions_y, tip_positions_z, lvec_scan = common.prepareScanGrids()
                                                                   ^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: prepareScanGrids() missing 1 required positional argument: 'parameters'

Seems to be another leftover from refactoring the parameter handling.

[NikoOinonen]

Also affected is the FePc_Au-IETS example.

[NikoOinonen]

And another related problem in the paper-figure example.

[NikoOinonen]

I tried adding the missing parameter argument at

ppafm/ppafm/cli/relaxed_scan.py

Line 191 in 4097baf

tip_positions_x, tip_positions_y, tip_positions_z, lvec_scan = common.prepareScanGrids()

However, the CoPc-IETS example then fails with a segmentation fault:

./run.sh: line 4: 114571 Segmentation fault      (core dumped) ppafm-relaxed-scan --vib 3

[ondrejkrejci]

I guess the reason is caused by wrong initialization of the grids, before calculation goes to C++ but it fails in C++ only. I remember we had the same issue a long time ago. @ProkopHapala - you found a fix to it then (some pointer was wrongly assigned).

In principle, we could also wait, until #347 is implemented and then try to fix it after that.

[ProkopHapala]

Yes I don't really remember. But I guess it could be that the arrays where IETS store outputs (hessian eigen vectors and eigenvalues) is not properly initialized (I mean pointer to it is not valid)
We were solving this for other array.

I don't want to look on it right now but what makes debugging segfaults easier nowadays is ASan (memory sanitizer, it can be turned on with GCC with single flag )

https://www.perplexity.ai/search/how-to-use-asan-memory-sanitiz-lP4lwjEFRcqp9obocj_KHA