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probe_particle_stm

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Introduction

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

Basic Principles

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.

Software requirements

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;

Inputs for DFT Codes

Running PP-STM

PP-AFM pre-calculations
PP-STM calculations

- input parameters

- reading input files

- running fixed tip STM calculations

- running PP-dI/dV

Example

Theoretical prediction for Coronene molecule modified with with four nitrogen atoms :

LDA predicted HOMO for this molecule:

and LUMO:

Example test outputs

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:

Literature

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

probe_particle_stm.1485438648.txt.gz · Last modified: 2017/01/26 14:50 (external edit)