This is an old revision of the document!
Generating force-fields and running AFM scans in PP-STM do not differ that much from those showed at http://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model. However, all the grids created by the way are not in an xsf format but in npy binaries.
L-J force-field can be created by running:
python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/gen_LJFF.py -i YOUR_INPUT_FILE
where the input file is in *.xyz *.xsf or *.cube.
Or it can be created toge ther with an electrostatic force-field:
python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/gen_bothFF.py -i YOUR_HARTREE_POTENTIAL -g YOUR_FILE_WITH geometry
where the -g part is optional, if it is not there, only electrostatic force field is crated. The grid specification are not taken from params.ini, but from the hartree potential file. The flags for the electrostatic potential creation are the same as those introduced at http://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model. The params.ini do not differ from that at http://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model.
