https://github.com/theochem/atomdb
An Extended Periodic Table of Neutral and Charged Atomic Species
https://github.com/theochem/atomdb
Last synced: about 1 year ago
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An Extended Periodic Table of Neutral and Charged Atomic Species
- Host: GitHub
- URL: https://github.com/theochem/atomdb
- Owner: theochem
- License: gpl-3.0
- Created: 2022-02-27T18:36:41.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2025-04-11T20:21:05.000Z (about 1 year ago)
- Last Synced: 2025-05-06T00:49:25.605Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage: http://atomdb.qcdevs.org/
- Size: 172 MB
- Stars: 24
- Watchers: 6
- Forks: 15
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# AtomDB
## About
AtomDB is a versatile, free, and open-source Python library for accessing and managing atomic and
promolecular properties. It serves as an extended database or periodic table of neutral and charged
atomic properties, offering accurate experimental and computational data for various atomic
charge/multiplicity states. AtomDB is a [QC-Devs](https://qcdevs.org/) project.
## Documentation
AtomDB's documentation, including installation and usage instructions, as well as API documentation, is available at [atomdb.qcdevs.org](https://atomdb.qcdevs.org/).
### Functionality
- **Atomic scalar properties**
AtomDB provides a wide range of atomic properties for neutral and charged atoms, including: **Atomic number**, **Atomic symbol**, **Atomic mass**, **Atomic radius**, **van der Waals radius**, **Covalent radius**, **Ionization potential**, **Electron affinity**, **Electronegativity**, **Atomic polarizability**.
- **Point dependent properties**
AtomDB provides functions to calculate point-dependent properties, such as:
**Electron density** $\rho(r)$,
**Electron density gradient** $\nabla \rho(r)$,
**Electron density Laplacian** $\nabla^2 \rho(r)$,
**Electron density Hessian** $\nabla^2 \rho(r)$ (for these properties, only the radial part is provided),
and **Kinetic energy density** $ked(r)$.
The computation of contributions per orbital, set of orbitals, or spin to these properties is also supported.
- **Promolecular properties**
AtomDB provides the capabilities to create promolecular models, and then estimate molecular properties from the atomic properties.
- **Dumping and loading**
AtomDB provides the capability to dump and load atomic properties to and from JSON files.
For a complete list of available properties, see [this
table](https://atomdb.qcdevs.org/api/index.html#properties).
## Installation
We recommend using Python 3.9 or later. The `qc-grid` is need to run `AtomDB`. You can install it
from source for now:
```bash
pip install git+https://github.com/theochem/grid.git
```
Then,
`qc-AtomDB` can be installed using `pip`:
```bash
pip install qc-AtomDB
```
## Contributing
We welcome any contributions to the AtomDB library in accordance with our [Code of Conduct](https://qcdevs.org/guidelines/qcdevs_code_of_conduct/). Please see our [Contributing Guidelines](https://qcdevs.org/guidelines/).
Please report any issues you encounter while using AtomDB on GitHub Issues.
For further information and inquiries, please contact us at [qcdevs@gmail.com](mailto:qcdevs@gmail.com).
## Citing AtomDB
Please use the following citation in any publication using AtomDB:
```bibtex
@Article{atomdb,
author = {S{\'a}nchez D{\'i}az, Gabriela and Richer, Michelle and
Mart\'{i}nez Gonz\'{a}lez, Marco and van Zyl, Maximilian and
Pujal, Leila and Tehrani, Alireza and Bianchi, Julianna and
Chuiko, Valerii and Erhard, Jannis and Ayers, Paul W. and
Heidar-Zadeh, Farnaz},
title = {{AtomDB: A Python Library for Atomic and Promolecular Properties}},
journal = {-},
year = {2024},
url = {https://atomdb.qcdevs.org/},
```