Adding atoms to the npy and xsf format for fixed scan to PPSTM_simple.py

[ondrejkrejci]

If you have fixed scan, then the information about atoms is not put into the XSF file or an NPY. We could obtain them from given format (e.g. input_plot.xyz as it is for plotting atoms to png - then I would actually suggest an try/except way) or we could get them from the geometry through ReadSTM.py

here is a function, that we could use: def At2XSF(atoms):