Datasets for the paper "Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models"

Input data for probe-particle (PP) atomic force microscopy (AFM), scanning tunnelling microscopy (STM), and Kelvin probe microscopy (KPFM) simulations in the paper "Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models".

Included files:

CO_tip_densities.tar.gz: the total and delta electron densities for a CO tip.

hartree-density.tar.gz: the hartree potential (LOCPOT.xsf), electron density (CHGCAR.xsf), and xyz geometry with point charges (mol.xyz) for 6 example molecules: C60 fullerene, formic acid dimer (FAD), 4-(4-(2,3,4,5,6- pentafluorophenylethynyl)-2,3,5,6- tetrafluorophenylethynyl) phenylethynylbenzene (FFPB), pentacene, phtalocyanine, perylene carboxylic anhydride (PTCDA).

dft-afm.tar.gz: DFT-calculated forces for the CO-tip for all of the example molecules. Saved as numpy npz files that containt the force arrays under the key 'force' and the physical extent of the region in Ångströms under the key 'scan_window'.

Fig_4_STM_data.tar.gz: Hartree potential (cube_001_hartree_potential.cube) and eigenvectors (KS_eigenvectors.band_1.kpt_1.out) of PTCDA for PPSTM simulations.

KPFM_Hartree.tar.gz: Hartree potentials of FFPB with a bias voltage for KPFM simulations.

Reproducing the figures in the manuscript:

Fig. 2 (comparison of force-field models): Install ppafm with the [opencl] option, and run the example script in the ppafm repository at examples/paper_figure/run_simulation.py. The image is saved into the same folder with the script.

Fig. 3 (KPFM LCPD map): Install ppafm, navigate to examples/FFPB_KPFM, and run the script ./run.sh. After running the script, the LCPD map of Fig. 3(a) can be found in LCPD_atoms_cbar_018.png and the AFM map of Fig. 3(b) in Q-0.10K0.25V0.00/Amp0.50/df_atoms_cbar_018.png.

Fig. 4 (STM dI/dV map): Download and compile the PPSTM code (https://github.com/Probe-Particle/PPSTM). After that navigate to tests/PTCDA_mol and use the run_all.sh script.

Fig. 5 (IETS): Install ppafm, navigate to examples/FePc_Au-IETS, and run the script run_ppafm-iets.sh. The IETS image can be found in the Q0.00K0.24 folder.

The ppafm version 0.3.1, and PPSTM version 1.0.2 (https://doi.org/10.5281/zenodo.10669867) was used when producing the images for the manuscript.