aton
Welcome to ATON
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. Designed to bridge the gap between theoretical modeling and experimental validation, ATON allows researchers to streamline and simplify workflows in the study of advanced materials.
Just like its ancient Egyptian deity counterpart, this all-in-one Python package comprises a range of utility 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.
Installation
As always, it is recommended to install your packages in a virtual environment:
python3 -m venv .venv
source .venv/bin/activate
With pip
Install ATON with
pip install aton
Or upgrade to a new version as
pip install aton -U
From source
Optionally, 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 .
Documentation
The full ATON documentation is available online.
An offline version is found at docs/aton.html.
Code examples are included in the examples/ folder.
Interfaces for ab-initio codes
The api module contains Python interfaces for several ab-initio codes and related. These are powered by the aton.txt module and can be easily extended.
aton.api
aton.api.qe |
Interface for Quantum ESPRESSO's pw.x module |
aton.api.phonopy |
Interface for Phonopy calculations |
aton.api.castep |
Interface for CASTEP calculations |
aton.api.slurm |
Batch jobs via Slurm |
Physico-chemical constants
The phys module contains physical constants and conversion factors,
as well as chemical information from all known elements.
Values are accessed directly as phys.value or phys.function().
aton.phys
aton.phys.units |
Physical constants and conversion factors |
aton.phys.atoms |
Megadictionary with data for all chemical elements |
aton.phys.functions |
Functions to sort and analyse element data |
Quantum rotations
The QRotor module is used to study energy excitations and tunnel splittings from molecular rotations, such as those of methyl and amine groups.
aton.qrotor
aton.qrotor.system |
Definition of the quantum System object |
aton.qrotor.systems |
Functions to manage several System objects |
aton.qrotor.rotate |
Rotate specific atoms from structural files |
aton.qrotor.constants |
Common bond lengths and inertias |
aton.qrotor.potential |
Potential definitions and loading functions |
aton.qrotor.solve |
Solve rotation eigenvalues and eigenvectors |
aton.qrotor.plot |
Plotting functions |
Spectra analysis
The spx module includes tools for spectral analysis from Inelastic Neutron Scattering, Raman, Infrared, etc.
aton.spx
aton.spx.classes |
Class definitions for the spectra module |
aton.spx.fit |
Spectra fitting functions |
aton.spx.normalize |
Spectra normalization |
aton.spx.plot |
Plotting |
aton.spx.deuterium |
Deuteration estimations via INS |
aton.spx.samples |
Sample materials for testing |
General text edition
The txt module handles text files. It powers more complex subpackages, such as aton.api.
aton.txt
aton.txt.find |
Search for specific content in text files |
aton.txt.edit |
Manipulate text files |
aton.txt.extract |
Extract data from raw text strings |
System tools
Additional utility tools are available for common system tasks across subpackages.
aton.file |
File manipulation |
aton.alias |
Useful dictionaries for user input correction |
aton.call |
Run bash scripts and related |
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 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).
Automated testing
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 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
This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the css/ folder.
Citation
ATON development started for the following paper, please cite if you use ATON in your work:
Cryst. Growth Des. 2024, 24, 391−404
License
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.