PyAtoms

Scanning probe measurements are notoriously time-consuming, with topographic images taking mintes to hours and spectroscopic mapping data taking several days. Often it is crucial to know a priori the correct image resolution in order to satisfy the Nyquist relations to capture relevant scattering patterns in Fourier-transformed STM images in reciprocal space. Additionally, when measuring 2D systems that display a moiré pattern — a super-lattice pattern originating from the combination of two or more lattices — it is helpful to have a tool for simulating SPM images in real-time in order to quickly extract the experimental lattice parameters, such as the local twist and/or lattice constants. To address this, we created PyAtoms, an open-source Python-based graphical user interface (GUI) that simulates atomic, charge density wave, and moiré lattices and super-lattices in real time. 

We purposely made PyAtoms user-friendly but incredibly robust, with the ability to simulate square and triangular lattices, the ability to shift the lattice origin, the ability to stack up to 3 atomic lattices, and to deform independent lattices to mimic strain or image drift. PyAtoms is also a powerful educational tool for understanding atomic lattices and their Fourier transforms in real- and reciprocal-space and has been used in senior-level  Introduction to Solid State Physics courses at UCLA. More information about PyAtoms is available on GitHub. A preprint describing the theoretical underpinnings of PyAtoms can be found here.

Download PyAtoms here.

Left: Experimental STM image of highly-ordered pyrolitic graphite (HOPG) using an asymmetric tip that produces an image displaying both A- and B-sublattices.

Right: PyAtoms simulation of a honeycomb structure with A- and B-sublattice amplitudes tuned to match experiment.