lammps-structgen 0.1.0

Generator for LAMMPS initial atomic structures for glassy systems.

Structgen

LAMMPS structure generator for LAMMPS, developed by Vasilii Maksimov at the Functional Glasses and Materials Modeling Laboratory (FGM²L) at the University of North Texas, under the supervision of Dr. Jincheng Du.

Structgen is a command-line utility for generating initial atomic configurations for use with LAMMPS simulations of disordered systems, especially oxide glasses. It supports CHARGE-style atom definitions and allows flexible control over atomic counts, charges, and overall density.

Features

• Command-line interface with argparse-based subcommands
• Generates LAMMPS .structure files with atomic positions and box boundaries
• Supports charged species via atom_style charge
• Automatically estimates simulation box size based on input density
• Modular design: atom placement strategies are handled via handler classes
• Written for reproducible initial structure generation workflows

Installation

Install from PyPI (coming soon)

This package will be published to PyPI. Once available, you'll be able to install it with:

pip install lammps-structgen

Install directly from GitHub (bleeding-edge)

For the latest development version:

pip install git+https://github.com/superde1fin/structgen.git

Clone & install locally

For local experimentation or contributing:

git clone https://github.com/superde1fin/structgen.git
cd structgen

# Standard install (no dev extras)
pip install .

# OR editable install (auto-reload while editing)
pip install -e .

Tip: add the [dev] extra to pull in testing, linting, and publishing tools:

pip install .[dev]

Requires Python ≥ 3.9 and numpy.

Usage

After installation, invoke the CLI with:

structgen [subcommand] [options]

Available subcommands:

• charge: Generate an initial structure for charge atom_style

Example usage:

structgen charge -a 28.085 -a 16.00 2 -1.2 -d 2.2 -f 100 -o si_o_glass.structure

This generates a structure with 100 Si atoms (mass 28.085) and 200 O atoms (mass 16.00, charge -1.2), with an overall density of 2.2 g/cm³. The structure will be written to si_o_glass.structure.

Documentation

All subcommands support -h or --help flags for detailed usage:

structgen charge --help

Design Overview

The project is modular:

• cli.py: Main entry point, defines CLI and parses arguments
• handlers/: Contains one handler class per placement strategy (CHARGE, etc.)
• constants.py: Shared constants (default count and charge)
• __init__.py: Exposes version metadata
• pyproject.toml: Build and dependency metadata

Each handler:

• Parses user-provided atomic specs
• Calculates simulation box size from density
• Randomly places atoms while avoiding overlap
• Returns header and atom sections for LAMMPS input

Development

Install dev dependencies:

pip install .[dev]

Run tests (if defined):

pytest

License

GNU General Public License v3.0 (GPLv3). See LICENSE for details.

Author

Vasilii Maksimov
University of North Texas
✉️ [e-mail]

Links

• LAMMPS Official Site
• GitHub Repository