The abTEM code: transmission electron microscopy from first principles

Area of Science:

• Materials Science
• Computational Physics
• Chemistry

Background:

• Transmission electron microscopy (TEM) simulations are crucial for interpreting experimental data.
• The independent atom model, commonly used, neglects valence bonding, limiting accuracy.
• Advanced instrumentation reveals subtle scattering potential details previously unobservable.

Purpose of the Study:

• To develop an open-source simulation code, abTEM, for advanced TEM image and diffraction pattern analysis.
• To integrate density functional theory (DFT) calculations for accurate scattering potential determination.
• To provide a user-friendly, modular, and extensible Python-based tool for researchers.

Main Methods:

• Developed abTEM, a Python-based simulation code integrating DFT for scattering potential calculations.
• Implemented a modular software design for flexibility and extensibility.
• Leveraged open-source libraries like Atomic Simulation Environment and GPAW for performance and functionality.
• Designed for interactive Python notebooks for a seamless workflow from structure definition to result analysis.

Main Results:

• Demonstrated abTEM's capability to detect valence bonding in hexagonal boron nitride.
• Performed 4D-STEM simulations of molybdenum disulfide with ptychographic phase reconstruction.
• Compared molecular dynamics (MD) and frozen phonon modeling for silicon systems using convergent-beam electron diffraction.
• Evaluated the performance of the PRISM algorithm implementation for gold nanoparticles.

Conclusions:

• abTEM provides a powerful, accessible tool for advanced TEM simulations, incorporating valence bonding effects.
• The code's integration with DFT and modular design facilitates accurate and reproducible materials analysis.
• abTEM supports various imaging modes and algorithmic developments, enhancing its utility for researchers.