aton 0.0.1b1

Aton is an all-in-one Python package that provides powerful and comprehensive tools for cutting-edge materials research.

Welcome to the Ab-iniTiO and Neutron research toolbox, or Aton. Inspired by its ancient Egyptian deity counterpart, this all-in-one Python package provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.

Aton provides a range of spectral analysis tools, from spectra normalisation to deuteration estimation using the DINS impulse approximation.
A set of physico-chemical constants and definitions is also included.

Aton also allows you to easily create, edit and analyse all kinds of text files, with a special focus on ab-initio calculations. In particular, it contains interfaces for Quantum ESPRESSO, Phonopy and CASTEP.

Check the full documentation online.

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Installation

As always, it is recommended to install your packages in a virtual environment:

python3 -m venv .venv
source .venv/bin/activate

With pip

The fastest way to install Aton is through pip:

pip install aton

From source

Optionally, you can install Aton from the GitHub repository.

First install the dependencies:

pip install pandas numpy scipy

Then clone the repository or download the latest stable release as a ZIP, unzip it, and run inside the Aton/ directory:

pip install .

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Documentation

The full Aton documentation is available online.
An offline version of the documentation is found at docs/aton.html.
Code examples are included in the examples/ folder.

Submodules

Aton contains the following modules:

• text. See General text edition.
• interface. See Interfaces for ab-initio codes.
• spectra. See Spectral analysis tools.
• units. Physical constants and conversion factors.
• atoms. Megadictionary with data for all chemical elements.
• elements. Sort and analyse element data, and manage the atoms dictionary.
• file. Manipulate files.
• call. Run bash scripts and related.
• alias. Useful dictionaries for user input correction.

General text edition

The text module includes the following general text-related submodules:

• text.find. Search for specific content in a text file.
• text.edit. Manipulate text files.
• text.extract. Extract data from raw text strings.

Interfaces for ab-initio codes

The interface module contains interfaces for several ab-initio codes. These are powered by the text module and can be easily extended. The following interfaces are included:

• interface.qe. Interface for Quantum ESPRESSO calculations.
• interface.phonopy. Interface for Phonopy calculations.
• interface.castep Interface for CASTEP calculations.

Spectral analysis tools

The spectra module IS YET TO BE IMPLEMENTED.

• Things...

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Contributing

If you are interested in opening an issue or a pull request, please feel free to do so on GitHub.
For major changes, please get in touch first to discuss the details.

Code style

Please try to follow some general guidelines:

• Use a code style consistent with the rest of the project.
• Include docstrings to document new additions.
• Include tests for new features or modifications.
• Arrange function arguments by order of relevance. Most implemented functions follow something similar to function(file, key/s, value/s, optional).

Testing with PyTest

If you are modifying the source code, you should run the automated tests of the tests/ folder to check that everything works as intended. To do so, first install PyTest in your environment,

pip install pytest

And then run PyTest inside the Aton/ directory,

pytest -vv

Compiling the documentation

The documentation can be compiled automatically to docs/aton.html with pdoc and Aton itself, by running:

python3 makedocs.py

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License

Copyright (C) 2024 Pablo Gila-Herranz
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the attached GNU Affero General Public License for more details.