AaltoAtoms Python package

For semi-automated atom manipulation experiments and analysis of Createc STM-AFM dI/dV spectrum and topography files.

Example outputs using functions / notebooks available here:

• Line spectra over Co adatoms in quantum corrals on Ag(111)

• Line spectra over H2Pc molecules in quantum corrals on Ag(111)

Example notebooks for data analysis and for automated experimentation:

Data analysis:

- line_spectrum_plot
    Display spectroscopic data at various spatial positions
    Along with the related topography data

- measure_corral_radius_from_scan
    Load a topography scan from the instrument software
    Analyze the topography to extract the corral radius in nm

- fit_fano_resonance_to_spectrum
    Load a .VERT (spectroscopy) file
    Fit a Fano resonance using the given initial conditions and bounds
    Extract width w, center of lineshape E0, asymmetry parameter q, etc.

Automated experiments:

- freeform_manipulation_GUI
    Detect atom positions from a topography scan
    Click to program manipulation paths in the order labeled in the image
    Shift-enter to run procedure and move atoms in order of programming
    Stop if there is a suspected tip change to prevent destroying structure

- expand_or_contract_corral
    Detect atom positions from topography scan
    Fit atom positions to circle
    Input the size of new corral
    Move wall atoms to new locations for larger/smaller size corral

Miscellaneous scripts:

animate_grid:
- for reading grid spectra and saving movie file
- also takes fit_fano functions from read_vertfile to fit Fano resonance to grid spectra over occupied corrals

find_atom_positions
- contains CircCorralData class, main function that analyzes all .dat files

fit_lattice
- script for testing CircCorralData functions (fitting Gaussians to atom positions, fitting circle to corral walls, fitting lattice to atom positions)

play_latfile
- for converting .LAT files into .wav's for auditory discrimination of successful/unsuccessful lateral manipulations.

scattering_model
- for simulating LDOS rho(r, E) given a set of atom positions and a lattice

Installation

Use pip install . or pip3 install . when inside the main directory.

Reproducibility and data availability

To reproduce manuscript figures from https://arxiv.org/abs/2312.03364, check Jupyter notebook Create Figures.ipynb and Phenomenological model fit.ipynb as well as MATLAB codes under AaltoAtoms/MATLAB/Main figure scripts.

Data for the manuscript can be found at https://zenodo.org/records/10214707. Some manual editing of file paths may be necessary. For analyses done in Python, tabulated data is found in data_array.py which is used for subsequent analysis routines.