Flexible Tip Simulations

The simulations with the Flexible Tip are directly depending on the PP-AFM simulation code (to be updated to new repository).

Running PP-AFM:

Generating force-fields and running AFM scans in PP-STM do not differ from those showed at here (to be changed later). The creation of DFT input files for the PP-AFM pre-calcultions is described at here (to be changed later). (From a GPAW DFT code there is now way, how to get a hartree potential at the moment.) But the Lennard-Jones force field can still be created from an *.xyz or *.in file with geometry of the sample's system.

Since the PP-STM calculations takes much longer, than the PPAFM, the proposed strategy for the PP-STM is following:

To tune the parameters for the spring constant K, the charge Q, FWHM of the charge cloud σ and/or multipole a AFM pre-calculations should be done. Once the position of the sharp edges in the AFM figures is in agreement with the position of sharp edges in the STM maps, then the PP-STM simulations should proceed from the positions of the Probe Particle (PP) from these best simulations. Be aware, that when there are sharp edges in the STM, the scan is just between the height, when the 1st unwanted artefacts due to the proximity of tip appears, and 0.2-0.3 Â above it. If the scan was done with oscillating tip, then the figures which should be compared are df images, if the STM scan is done with fixed tip, then the figures of positions should be more important.

For the PP-STM calculations the positions of the PP are necessary. You can get them by running:

python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/relaxed_scan.py --pos

The positions in PPpos_*.xsf or PPpos_*.npy will then be used (and automatically read) by the PPSTM_simple.py script or the Graphic User Interface - GUI.