PPSTM (Probe Particle STM)

Code simulating various various STM techniques, especially for tilting tips (depending on ProkopHapala/ProbeParticleModel ) This is implementation of efficient and simple model for simulation of High-resolution scanning tunneling microscopy (STM). Normall STM simulations using Chen's approximattion is part of the code as well

• BEWARE - latest numpy is probably causing problems within the code, the we have noticed problem with trying to run examples with periodic boundary conditions recently.
• BEWARE - after repairing misteake in d-orbitals the results for FePc are different. We are investigating it.

• currently developed Python3/C++ version of the PPSTM code:
  • works in python3(.7 and higher), matplotlib, cpp>=4.4.8 (look at wiki instruction for problems with MAC compilation), PyQt5 (for GUI ),for some parts ASE and GPAW are imporatant;
  • Part of the code regarding simulations with tilting tips is depending on the ProbeParticleModel developed by Prokop Hapala and co. (https://github.com/Probe-Particle/ppafm), you can easilly install it with pip install ppafm>=0.2.0a3.

For easy introduction to this code and its functionalities, try Graphic User Interface (GUI) or PPSTM_simple.py script.

Documentation is here at Wiki.

It can also simulate IETS images of molecules, if the imaging mechanism is driven by the amplitude of the IETS peak.

References (should be always cited)

• Ondrej Krejčí, Prokop Hapala, Martin Ondráček, and Pavel Jelínek, Principles and simulations of high-resolution STM imaging with a flexible tip apex, Phys. Rev. B 95, 045407 – Published 6 January 2017

References (should be cited for the relaxed scans)

• Niko Oinonen, Aliaksandr V. Yakutovich, Aurelio Gallardo, Martin Ondracek, Prokop Hapala, Ondrej Krejci, Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models, Comput. Phys. Commun. 305, 109341 - Available online 10 August 2024

References (should be cited if IETS or STM-d orbitals were included)

• Bruno de la Torre, Martin Švec, Giuseppe Foti, Ondřej Krejčí, Prokop Hapala, Aran Garcia-Lekue, Thomas Frederiksen, Radek Zbořil, Andres Arnau, Héctor Vázquez, and Pavel Jelínek, Submolecular Resolution by Variation of the Inelastic Electron Tunneling Spectroscopy Amplitude and its Relation to the AFM/STM Signal, Phys. Rev. Lett. 119, 166001 – Published 16 October 2017