reaxkit 1.0.0

A toolkit for parsing, analyzing, and visualizing ReaxFF simulation data.

ReaxKit

ReaxKit is a modular, extensible Python toolkit for pre‑processing, post‑processing, and analysis of ReaxFF molecular dynamics simulations. It provides a clean separation between file parsing, analysis routines, and reproducible workflows, with both Python APIs and a CLI interface.

ReaxKit is designed for researchers who want a transparent, scriptable bridge between raw ReaxFF files and quantitative, publication‑ready results.

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Key Capabilities

File IO (Parsing & Generation)

• Robust handlers for ReaxFF input and output files:
  • xmolout, fort.7, fort.13, molfra, and more
• Input file generators:
  • control, geo, eregime, tregime, and more
• Unified handler interface for consistent data access

Analysis

• Per‑file analyzers (one analyzer per ReaxFF file type)
• Composed analyzers that combine multiple data sources:
  • Coordination numbers
  • Connectivity graphs
  • Electrostatics and dipoles
  • Radial distribution functions (RDF)
• Numerical utilities for smoothing, extrema detection, and signal processing

Workflows

• Reproducible, CLI‑driven workflows for:
  • Single‑file analysis
  • Multi‑file composed analysis
  • Plotting and media generation
• Designed to automate common ReaxFF post‑processing tasks

Visualization & Media

• Publication‑ready plotting utilities (2D, dual‑axis, tornado plots, 3D scatter, heatmaps)
• Trajectory and plot video generation

See the full documentation (API reference, tutorials, examples) on ReaxKit Site.

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Project Layout

src/reaxkit/
├── analysis/        # Analysis routines (per-file and composed)
├── io/              # File handlers and generators
├── utils/           # Shared utilities (aliases, units, constants, numerics)
├── workflows/       # CLI and automation workflows
├── help/            # Introspection and help system
└── cli.py           # Command-line entry point

Additional resources:

• Installation notes — Full installation instructions (requires Python ≥ 3.9).
• Quickstart — Get up and running with core ReaxKit workflows in minutes.
• Tutorials notes and source files — Step-by-step guides for common ReaxKit workflows and use cases.
• Examples and source files — Minimal, runnable Python examples using public APIs.
• ReaxFF Reference — Reference documentation for ReaxFF input and output files.
• Contributing — Guidelines for contributing to ReaxKit.
• File Templates and Docstring Conventions — Development guidelines and code templates.
• AUTHORS.md — Full credits and acknowledgments.
• LICENSE — Full license terms under the MIT License

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Testing

Run unit tests with:

pytest -s tests/

to test the package and get the timing for their execution.

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Citation

If you use ReaxKit in your work, please cite:

Dinani, A. M., van Duin, A., Shin, Y. K., & Sepehrinezhad, A. (2025).
ReaxKit: A modular Python toolkit for ReaxFF simulation analysis.
Zenodo. https://doi.org/10.5281/zenodo.18485384

Source code: https://github.com/ali-m-dinani/reaxkit

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Future Directions

• Add support for other analyzers including autocorrelation functions, thermodynamic properties calculations, etc.
• Develop GUI dashboard for interactive ReaxFF data inspection
• Implement ML-based trend prediction for simulation outputs

If you have any feature request, you can submit it through the ReaxKit's GitHub page, or directly sending an email to [e-mail].