The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
Just like its ancient Egyptian deity counterpart, this all-in-one Python package contains a range of tools from INS spectra analysis to ab-initio interfaces for Quantum ESPRESSO, Phonopy and CASTEP. Conversion factors and universal constants from the 2022 CODATA Recommended Values of the Fundamental Physical Constants are also included.
The source code is available on GitHub.
Check the full documentation online.
As always, it is recommended to install your packages in a virtual environment:
python3 -m venv .venv
source .venv/bin/activateInstall ATON with
pip install atonOr upgrade to a new version as
pip install aton -UOptionally, you can install ATON from the GitHub repo.
Clone the repository or download the latest stable release
as a ZIP, unzip it, and run inside the ATON/ directory:
pip install .The full ATON documentation is available online.
An offline version is found at docs/aton.html.
Code examples are included in the examples/ folder.
The interface module contains Python interfaces for several ab-initio codes. These are powered by the aton.txt module and can be easily extended.
| interface.qe | Interface for Quantum ESPRESSO's pw.x module |
| interface.phonopy | Interface for Phonopy calculations |
| interface.castep | Interface for CASTEP calculations |
| interface.slurm | Batch jobs via Slurm |
The phys module contains physico-chemical definitions.
Values are accessed directly as phys.value or phys.function().
| phys.units | Physical constants and conversion factors |
| phys.atoms | Megadictionary with data for all chemical elements |
| phys.functions | Functions to sort and analyse element data |
The QRotor module is used to study quantum rotations, such as those of methyl and amine groups.
| qrotor.rotate | Rotate specific atoms from structural files |
| qrotor.constants | Bond lengths and inertias |
| qrotor.system | Definition of the quantum System object |
| qrotor.systems | Functions to manage several System objects |
| qrotor.potential | Potential definitions and loading functions |
| qrotor.solve | Solve rotation eigenvalues and eigenvectors |
| qrotor.plot | Plotting functions |
The spx module includes tools for spectral analysis from Inelastic Neutron Scattering, Raman, Infrared, etc.
| spx.classes | Class definitions for the spectra module |
| spx.fit | Spectra fitting functions |
| spx.normalize | Spectra normalization |
| spx.plot | Plotting |
| spx.deuterium | Deuteration estimations via INS |
| spx.samples | Sample materials for testing |
The txt module handles text files. It powers more complex subpackages, such as aton.interface.
| txt.find | Search for specific content in text files |
| txt.edit | Manipulate text files |
| txt.extract | Extract data from raw text strings |
The st module contains System Tools for common system tasks across subpackages.
| st.file | File manipulation |
| st.call | Run bash scripts and related |
| st.alias | Useful dictionaries for user input correction |
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.
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 automated tests for new features or modifications, see automated testing.
- Arrange function arguments by order of relevance. Most implemented functions follow something similar to
function(file, key/s, value/s, optional).
If you are modifying the source code, you should run the automated tests of the ATON/tests/ folder to check that everything works as intended.
To do so, first install PyTest in your environment,
pip install pytestAnd then run PyTest inside the ATON/ directory,
pytest -vvThe documentation can be compiled automatically to docs/aton.html with Pdoc and ATON itself, by running:
python3 makedocs.pyThis runs Pdoc, updating links and pictures, and using the custom theme CSS template from the css/ folder.
ATON development started for the following paper, please cite if you use ATON in your work:
Cryst. Growth Des. 2024, 24, 391−404
Copyright (C) 2025 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.