Automatic Rescalling intensities according to elements

[ondrejkrejci]

Problem:

In the current version of the code the intensity of each wavefunction for each element is only given by the setted Workfunction and is the same for everyone. This means that we have the same intensity for C or O, s, p or d orbitals (radial function). The intensity differences to match the experiment could also differ code to code (and used basis within the DFT codes).

Temporal solution:

All the reading procedures in https://github.com/Probe-Particle/PPSTM/blob/master/pyPPSTM/ReadSTM.py as well as in PPSTM_simple.py allows to name the atoms and coefficients to be rescalled.

Problems of Temporal solution:

This does not take into account of different intensity from s and p orbitals of the same elements. Also the d orbitals are lowered by factor of 5 to match s (or p) / d ratio of most of the transition metals.

Possible solution:

If we consider that the intensity is given by the overlap which is somehow proportional to the intensity of the wavefunction for each of the n layer of each element at the distance 3, 4 or 5 Å, I have created a table of these for at least FHI-aims valence basis set. I have somewhere working but not-properly tested version for automatic rescalling of these, and I will try to dig it out and put it here. First test have not shown enough intensity for FePc results, that is why I did not finnished this work, Can be related to #5.
It would be good to have it working in PPSTM_simple.py and GUI.py, later.