aton 0.0.1rc36

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.

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.

Just like its ancient Egyptian deity counterpart, this all-in-one Python package contains a range of tools from spectra normalisation to deuteration estimations. 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 calculation files. In particular, it contains interfaces for Quantum ESPRESSO, Phonopy and CASTEP.

The source code is available on GitHub.
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

To upgrade to a newer version,

pip install aton -U

From source

Optionally, you can install ATON from the GitHub repository.

First install the dependencies:

pip install pandas numpy scipy matplotlib

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 ATON/examples/ folder.

Interfaces for ab-initio codes

The interface module contains interfaces for several ab-initio codes. These are powered by the aton.txt module and can be easily extended.

aton.interface

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

Physico-chemical constants

The phys module contains physico-chemical definitions. Values are accessed directly as phys.value or phys.function().

aton.phys

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, and to update the atoms dictionary

Quantum rotations

The QRotor module is used to study the energy levels of quantum rotations, such as methyl and amine groups.

aton.qrotor

qrotor.classes	Definition of the QSys and QExp classes
qrotor.constants	Bond lengths and inertias
qrotor.rotate	Rotate specific atoms from structural files
qrotor.potential	Potential definitions and loading functions
qrotor.solve	Solve rotation eigenvalues and eigenvectors
qrotor.plot	Plotting functions

Spectra analysis

The spx module includes tools for spectral analysis from Inelastic Neutron Scattering, Raman, Infrared, etc.

aton.spx

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

General text edition

The text module handles text files. It powers more complex subpackages, such as aton.interface.

aton.txt

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

System tools

The st module contains System Tools for common system tasks across subpackages.

aton.st

st.file	File manipulation
st.call	Run bash scripts and related
st.alias	Useful dictionaries for user input correction

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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 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.

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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.