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

<p>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".</p> <p>Included files:</p> <ul> <li>CO_tip_densities.tar.gz: the total and delta electron densities for a CO tip.</li> <li>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).</li> <li>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 &Aring;ngstr&ouml;ms under the key 'scan_window'.</li> <li>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.</li> <li>KPFM_Hartree.tar.gz: Hartree potentials of FFPB with a bias voltage for KPFM simulations.</li> </ul> <p>Reproducing the figures in the manuscript:</p> <ul> <li>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.</li> <li>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.</li> <li>Fig. 4 (STM dI/dV map): Download and compile the PPSTM code (<a href="https://github.com/Probe-Particle/PPSTM">https://github.com/Probe-Particle/PPSTM</a>). After that navigate to tests/PTCDA_mol and use the run_all.sh script.</li> <li>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.</li> </ul> <p>The ppafm version 0.3.1, and PPSTM version 1.0.2 (<a href="https://doi.org/10.5281/zenodo.10669867" rel="nofollow">https://doi.org/10.5281/zenodo.10669867</a>) was used when producing the images for the manuscript.</p>