atomea

Extensible schema for atomistic data and calculations.

Documentation

Overview

Atomea is a Python package designed to simplify and standardize the setup and data management for atomistic data and calculations. It leverages the power of Pydantic for schema definition and Jinja2 templates for input file generation, making it easy to automate, document, and prepare input files for various computational chemistry and biology tools.

Key features

• Extensible Schema Definition: Easily define schemas for various computational packages using Pydantic.
• Automated Input File Preparation: Generate input files with Jinja2 templates to ensure consistency and reproducibility.
• Data Digestion: Convert raw output files into optimized storage formats (e.g., Zarr) with a consistent interface.
• YAML Integration: Save and load configurations and data in YAML format for easy sharing and reproducibility.

Installation

atomea requires Python 3.10 or later. You can install it using pip, the Python package installer,

pip install atomea

or directly from the GitHub main branch.

pip install git+https://github.com/oasci/atomea.git

Development

We use pixi to manage Python environments and simplify the developer workflow. Once you have pixi installed, move into atomea directory (e.g., cd atomea) and install the environment using the command

pixi install

Now you can activate the new virtual environment using

pixi shell

License

This project is released under the Apache-2.0 License as specified in LICENSE.md.