.. vachoppy documentation master file, created by sphinx-quickstart on Sat Oct 11 14:05:35 2025. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to VacHopPy's documentation! ==================================== .. image:: _static/logo.png :align: center :width: 550px :alt: VacHopPy Logo **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 `_. * T. Jeong *et al*., *Comput. Phys. Commun.* **320**, 110010 (2026) .. toctree:: :hidden: :maxdepth: 2 :caption: Contents: introduction installation cli_usage tutorial api_reference changelog