Nanosurf Lab

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 flags for the electrostatic potential creation are the same as those introduced at http://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model.