VacHopPy: A Python package for vacancy hopping analysis based on molecular dynamics simulations

Abstract

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

References in corpus (6)

• Analysis of diffusion in solid state electrolytes through MD-simulations, improvement of the Li-ion conductivity in β-Li3PS4 as an example
• Scalable Parallel Algorithm for Graph Neural Network Interatomic Potentials in Molecular Dynamics Simulations
• Diffusion of Lithium Ions in Lithium-Argyrodite Solid-State Electrolytes from Equilibrium and Nonequilibrium Molecular Dynamics Simulations
• Accurate Estimation of Diffusion Coefficients and their Uncertainties from Computer Simulation
• Kinetic Monte Carlo Simulations of Sodium Ion Transport in NaSICON Electrodes
• Multiscale Modeling of Metal/Oxide/Metal Conductive Bridging Random Access Memory Cells: from Ab Initio to Finite Element Calculations