This is an old revision of the document!
A Python/C based package, available at http://github.com/ProkopHapala/ProbeParticleModel/tree/PPSTM, which primary purpose is to simulate STM or dI/dV signal obtained with tilting tip apex (like CO, or Xe tip). It is based on the original PPAFM Python/C by Prokop Hapala and Co. http://github.com/ProkopHapala/ProbeParticleModel/ for simulation of tilting tip apex' AFM images.
You can get it easily from terminal by running these two commands:
git clone http://github.com/ProkopHapala/ProbeParticleModel/ cd ProbeParticleModel git checkout PPSTM
The PP-STM code calculates an STM or dI/dV signal based on the input from various Linear Combination of Atomic Orbitals (LCAO)-DFT codes. These inputs are eigen-energies of eigen-states (molecular orbitals) and LCAO coefficients (for each state and atomic orbital of sample). Sample can be approximated by freestanding molecule, or by full system - molecule/substrate.
Nowadays these LCAO DFT codes can be used for the creation of necessary STM inputs: Fireball http://sites.google.com/site/fireballofficialsite/, FHI-AIMS http://aimsclub.fhi-berlin.mpg.de and GPAW in the LCAO mode http://wiki.fysik.dtu.dk/gpaw/documentation/lcao/lcao.html
Detailed description of the PP-STM code principle is shown in PRB 95, 045407 (2017) - see the literature.
Necessary:
python-2.7; python-2.7-numpy(-1.8); gcc(-4.8); python-2.7-matplotlib(-1.3) - for plotting of figures;
Optional:
python-ase(-3.8.1) - needed for reading of FHI-AIMS inputs and GPAW input; GPAW - needed for reading of GPAW input;
- input parameters
- reading input files
- running fixed tip STM calculations
- running PP-dI/dV
Theoretical prediction for Coronene molecule modified with with four nitrogen atoms :
LDA predicted HOMO for this molecule:
and LUMO:
Example of scans over this molecule, with different probing orbitals and different scanning modes (AFM, STM, dI/dV … ).
Scans at the energy of HOMO:
Scans at the energy of LUMO:
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 (2017); http://journals.aps.org/prb/abstract/10.1103/PhysRevB.95.045407