All tests involving relaxed scanning fail

[LauriKurki]

As PPAFM has seen major changes, now some of the features of PPSTM dependent on PPAFM have been broken as mentioned in #12. For example running tests/4N-coronene/run_test.sh fails as the LJ field used to be generated with python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/generateLJFF.py -i YOUR_INPUT_FILE.cube --npy but the --npy option has been replaced with -f npy. Example error attached.

This requires at least changing the way PPAFM is called within PPSTM.

[ondrejkrejci]

Once more, please could you check with the newest npy version? Thank you!

[LauriKurki]

Thanks for the update and sorry for the delay!

A couple of problems remain, and I think I can fix these apart from number 4:

1. In PPAFM, the module pyProbeParticle was renamed to ppafm so all the imports have to be renamed in PPSTM as well
2. Location and usage of e.g. generateLJFF.py has changed in PPAFM so instructions for generating the LJ and electrostatic FFs has to be updated as well.
3. Installing PPAFM should be done with pip install ppafm==0.2.0a1 now instead of the script. With this we could use ppafm-generate-ljff etc. for the force fields. Edit: That version actually doesn't have the updated npz saving function, but version 0.2.0a2 was launched today. Should be available in pip soon?

4. Saving the atoms within PPAFM seems to be not working, I'm commenting more in here Edit: This was not working in the earlier release but should be now.