https://github.com/zyumse/m2dtools
tools for MD-based research projects
https://github.com/zyumse/m2dtools
lammps molecular-dynamics
Last synced: 3 months ago
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tools for MD-based research projects
- Host: GitHub
- URL: https://github.com/zyumse/m2dtools
- Owner: zyumse
- License: mit
- Created: 2025-09-16T15:23:45.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2026-02-10T16:12:00.000Z (4 months ago)
- Last Synced: 2026-02-10T20:47:48.568Z (4 months ago)
- Topics: lammps, molecular-dynamics
- Language: Python
- Homepage: https://zyumse.github.io/m2dtools/
- Size: 858 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# m2dtools
*m2dtools* is a lightweight Python toolkit for molecular simulation workflows, including analysis helpers, coarse-graining pipelines, and LAMMPS structure preparation scripts.
📘 **Full Documentation:**
https://zyumse.github.io/m2dtools/
## Installation
```
pip install m2dtools
```
1. Clone this repository and move into it.
2. (Optional) Create and activate a Python 3.8+ environment.
3. Install the package in editable mode:
```bash
pip install -e .
```
This pulls in the core dependencies (`numpy`, `matplotlib`, `scipy`, `pandas`). Editable mode lets you modify the source and use the changes immediately without reinstalling.
## Features
- `m2dtools.basic` – vectorised analysis functions for bonds, angles, PDFs/SQs, coordination numbers, autocorrelation, MSD, and compressibility.
- `m2dtools.lmp` – utilities to read, modify, and write LAMMPS full-data and dump files for simulation setup.
- `m2dtools.cg` – coarse-graining tools, including iterative Boltzmann inversion (IBI) scripts and polymer-specific helpers.
- `m2dtools.network` – routines for stochastic network generation and conversion to LAMMPS structures.
- `m2dtools.other` – format converters and domain-specific helpers (e.g. GROMACS parsing, local stress extraction, silica and water coarse-graining utilities).
## Contributing
Contributions are welcome.
Please open an issue or submit a pull request on GitHub.
## License
Released under the MIT License.