Welcome to VacHopPy’s documentation!

VacHopPy is a Python package for analyzing vacancy-mediated diffusion from molecular dynamics (MD) simulations. The package facilitates a reliable multiscale modeling workflow by calculating key vacancy hopping parameters that can be directly incorporated into continuum-scale models.

Key Features

• Effective Parameter Extraction

  Derives a single set of effective hopping parameters from the MD simulations, providing ready-to-use inputs for continuum-scale models.

• Ensemble Analysis

  Simultaneously processes an ensemble of multiple MD trajectories. This approach efficiently samples rare hopping events in high-barrier systems, avoiding the need for a single, prohibitively long simulation.

• Memory-Efficient Processing

  Reads and interprets large-scale trajectories via a streaming approach, enabling the analysis of massive datasets within just a few gigabytes of RAM.

Note

This package is designed for analyzing MD simulations performed under the NVT (canonical) ensemble with periodic boundary conditions (PBC).

How to Cite

If this package was used in your work, please cite this paper.

• 20. Jeong et al., Comput. Phys. Commun. 320, 110010 (2026)