load-atoms#
Important
This project is under active development. Until version 1.0.0 is released, breaking changes to the API may occur.
load-atoms is a Python package for downloading, inspecting and manipulating datasets of atomic structures.
Quickstart#
Install using pip install load-atoms, and then use
load_dataset() to download an AtomsDataset (full list available here):
>>> from load_atoms import load_dataset
>>> dataset = load_dataset("QM9")
╭───────────────────────────────── QM9 ─────────────────────────────────╮
│ │
│ Downloading dsgdb9nsd.xyz.tar.bz2 ━━━━━━━━━━━━━━━━━━━━ 100% 00:09 │
│ Extracting dsgdb9nsd.xyz.tar.bz2 ━━━━━━━━━━━━━━━━━━━━ 100% 00:18 │
│ Processing files ━━━━━━━━━━━━━━━━━━━━ 100% 00:19 │
│ Caching to disk ━━━━━━━━━━━━━━━━━━━━ 100% 00:02 │
│ │
│ The QM9 dataset is covered by the CC0 license. │
│ Please cite the QM9 dataset if you use it in your work. │
│ For more information about the QM9 dataset, visit: │
│ load-atoms/QM9 │
╰───────────────────────────────────────────────────────────────────────╯
These are thin wrappers around lists of ase.Atoms:
>>> dataset[0]
Atoms(symbols='CH4', pbc=False, partial_charges=...)
view() provides interactive visualization of atomic structures:
We provide several dataset-level operations:
>>> small_structures = dataset.filter_by(lambda atoms: len(atoms) < 10)
>>> dataset.info["energy"]
array([-10.5498, -6.9933, ..., -5.7742, -6.3021])
>>> trainset, testset = dataset.random_split([0.9, 0.1], seed=42)
Contributing#
load-atoms was originally conceived and developed by me, John Gardner, as part of my PhD research at the University of Oxford within the Deringer Group.
If you are interested in contributing to the project, be that adding new functionality, suggesting a dataset or fixing a bug, please see the developer guide and feel free to open an issue or pull request on the GitHub repository.