Nanosurf Lab

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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]].

The creation of input files for the PP-AFM pre-calcultions is described at [[http://nanosurf.fzu.cz/wiki/doku.php?id=dft_inputs]]. From a GPAW DFT code there is now way, how to get a hartree potential at the moment. But the L-J force field can still be created from an *.xyz file with geometry of the sample's system.

The __params.ini__ file is necessary for the creation, but it do not differ from that at [[http://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model]].

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 can be in *.xyz *.xsf or *.cube format.

Or it can be created together 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]].

Unlike in the PP-AFM code, where both - xsf format and npy binaries - can be used for storing of the force-fields and intermediate results, the PP-STM branch is nowadays written purely for npy binaries.

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