From 7b5ff289dd2747a95c2d61e8d35c058a8692cc3d Mon Sep 17 00:00:00 2001 From: Michelle Richer Date: Mon, 13 May 2024 10:54:09 -0400 Subject: [PATCH] Update readme --- README.rst | 113 +++++++++++++++++++++++++++++------------------------ 1 file changed, 62 insertions(+), 51 deletions(-) diff --git a/README.rst b/README.rst index 06b572b6..2b6c85e9 100644 --- a/README.rst +++ b/README.rst @@ -14,79 +14,90 @@ : You should have received a copy of the GNU General Public License : along with AtomDB. If not, see . +|Documentation| |Github| + AtomDB ====== -|Python3.9| |Github| About ----- -AtomDB is a database of atomic and ionic properties. - -Installation ------------- +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. -.. code-block:: +AtomDB is a `QC-Devs `_ project. - python -m pip install -e . - -Usage ------ +Documentation +------------- -.. code-block:: +AtomDB's documentation, including installation and usage instructions, as well as API documentation, +is available at `atomdb.qcdevs.org `_. - ~/git/atomdb % python -m atomdb -h - usage: python -m atomdb [-h] [-c] [-q] [-e E] dataset elem basis charge mult +Functionality +~~~~~~~~~~~~~ - Compile and/or query an AtomDB entry +* **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** - positional arguments: - dataset name of dataset - elem element symbol - basis basis set - charge charge - mult multiplicity +* **Point dependent properties** + AtomDB provides functions to calculate point-dependent properties, such as: + **Electron density** :math:`\rho(r)`, **Electron density gradient** :math:`\nabla \rho(r)`, + **Electron density Laplacian** :math:`\nabla^2 \rho(r)`, **Electron density Hessian** :math:`\nabla^2 \rho(r)` + (for these properties, only the radial part is provided), and **Kinetic energy density** :math:`ked(r)` - optional arguments: - -h, --help show this help message and exit - -c compile the specified entry - -q query the specified entry - -e E excitation level + The computation of contributions per orbital, set of orbitals or spin to these properties is also supported. -If AtomDB is installed in a directory for which you do not have write permissions, or if you'd -rather store your AtomDB database in another directory (or you already have one), then you -can set the ``ATOMDB_DATAPATH`` environment variable to the directory of your choice; either -a non-existing directory, or an existing AtomDB database. +* **promolecular properties** + AtomDB provides the capabilities to create promolecular models, and then estimate molecular properties + from the atomic properties. -On release, AtomDB should come with compiled database files pre-installed in the default -``ATOMDB_DATAPATH``. Raw data files containing the output of electronic structure computations -will be hosted in another Git repo (AtomDB-Data) via LFS. If you are a developer working on compiling new -database entries or writing new datasets, then you can set ``ATOMDB_DATAPATH`` to the location -of the AtomDB-Data repo on your computer. +* **Dumping and loading** + AtomDB provides the capability to dump and load atomic properties to and from json files. -Send Michael your SSH public key and ask him for the current URL for the AtomDB-Data repo. +For a complete list of available properties, see +`this table `_. Contributing ------------ -You can help by writing features, properties, and datasets, or by running computations! 🙂 +We welcome any contributions to the AtomDB library in accordance with our +`Code of Conduct `_; please see our +`Contributing 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 `_. + +Citing AtomDB +------------- + +Please use the following citation in any publication using AtomDB: + +.. code::bibtex -TODO -~~~~ -- Add functions for dealing with multiple database entries at once -- Add more properties (C-DFT, SP-CDFT, etc.) See the [properties list](https://docs.google.com/spreadsheets/d/1_N-wvdiSEjHuCrhf9t14a114BRIzcugmE8sRww5XUTY/edit?usp=sharing) -- Add more datasets (Hartree-Fock, some useful DFT calcs...?) -- Get the NIST dataset, and add those dataset-independent fields to the DB entries -- Make all field names consistent with IOData -- See Issues tab + @Article{atomdb, + author = {S{\'a}nchez D{\'\i}az, Gabriela and Richer, Michelle and + Mart{\'\i}nez Gonz{\'a}lez, Marco and {v}an Zyl, Maximilian and + Pujal, Leila and Tehrani, Alireza and Bianchi, Julianna 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/}, + } +License +------- -Citations ---------- +AtomDB's source code is hosted on GitHub and is released under the GNU General Public License v3.0. -2021 QuantumElephant 🐘 AtomDB ⚛ +.. |Documentation| image:: https://img.shields.io/badge/documentation-blue.svg?logo=Sphinx + :target: https://atomdb.qcdevs.org/ -.. |Python3.9| image:: http://img.shields.io/badge/python-3.9-blue.svg - :target: https://docs.python.org/3/ -.. |Github| image:: https://img.shields.io/badge/quantumelephant-black.svg?logo=GitHub - :target: https://github.com/quantumelephant/atomdb/ +.. |Github| image:: https://img.shields.io/badge/theochem-black.svg?logo=GitHub + :target: https://github.com/theochem/AtomDB/