PyAtoms: An interactive tool for simulating atomic scanning tunneling microscopy images of 2D materials, moir\'e systems and superlattices

TL;DR

PyAtoms is an open-source Python tool that enables rapid, customizable simulations of atomic-scale STM images for 2D materials, aiding experimental planning and analysis.

Contribution

It introduces a Fourier-space based method for simulating STM images with a user-friendly GUI, supporting diverse 2D materials and system parameters.

Findings

Successfully simulates images of graphene, twisted tri-layer graphene, and charge-density wave systems.

Allows detailed tuning of lattice and imaging parameters for experimental planning.

Provides time estimates for spectroscopic measurements to optimize experimental workflows.

Abstract

We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems, and superlattices. Rooted in a Fourier-space description of ideal atomic lattice images, PyAtoms is a Python-based graphical user interface (GUI) with robust capabilities for tuning lattice parameters (lattice constants, strain, number of layers, twist angles) and STM imaging parameters (pixels, scan size, scan angle) and provides time estimates for spectroscopic measurements. These capabilities allow users to efficiently plan time-consuming STM experiments. We provide an overview of PyAtoms' current features, describe its underlying mathematical principles, and then demonstrate simulations of several 2D materials including graphene with variable sublattice asymmetry, twisted tri-layer graphene moir\'{e} systems, and several charge- and bond-density wave systems.