Papers › VacHopPy: A Python package for vacancy hopping analysis based on ab initio molecular...
VacHopPy: A Python package for vacancy hopping analysis based on ab initio molecular dynamics simulations
Taeyoung Jeong, Kun Hee Ye, Seungjae Yoon, Dohyun Kim, Yunjae Kim, Jung-Hae Choi
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Multiscale modeling, which integrates material properties from ab initio calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while ab initio methods provide diffusion parameters specific to individual migration paths, continuum equations require a single effective set of parameters that captures the overall diffusion behavior. To address this issue, we present VacHopPy, an open-source Python package for vacancy hopping analysis based on molecular dynamics (MD). VacHopPy extracts an effective set of hopping parameters, including hopping distance, hopping barrier, number of effective paths, correlation factor, and attempt frequency, by statistically integrating energetic, kinetic, and geometric contributions across all paths. It also includes tools for tracking vacancy trajectories and for detecting phase transitions during MD simulations. The applicability of VacHopPy is demonstrated in three representative materials: face-centered cubic Al, rutile TiO2, and monoclinic HfO2. The extracted effective parameters reproduce temperature-dependent diffusion behavior and are in good agreement with previous experimental data. Provided in a simplified form, these parameters are well suited for continuum-scale models and remain valid over a wide temperature range spanning several hundred kelvins. Furthermore, VacHopPy inherently accounts for anisotropy in thermal vibrations, a factor often overlooked, making it suitable for simulating diffusion in complex crystals. Overall, VacHopPy establishes a robust bridge between atomic- and continuum-scale models, enabling more reliable multiscale simulation
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