.. ABCrystal documentation master file, created by
   sphinx-quickstart on Sat Aug 22 13:28:52 2020.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to ABCrystal's tutorial!
=====================================

.. tip::
    I understand that most readers (including me) **hate** reading lengthy software manual. Thus:

    - This tutorial is composed of many **practical examples**. In each case, you can finish a crystal structure predction under step-by-step instructions. 
    - You can just go over the Contents below, see which "Example" subsection is the most relevant to your interested problems and then go there!

.. attention::
    The best way to support the development of ABCrystal is that in any published works using ABCrystal, please **include the following references**:

    - Zhang, J. `ABCrystal <https://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/C5CP04060D>`_ *XX* **2024**, *XX*, XX-XX.
    - Zhang, J.; Dolg, M. `Global Optimization of Clusters of Rigid Molecules Using the Artificial Bee Colony Algorithm. <https://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/C5CP06313B>`_ *Phys. Chem. Chem. Phys.* **2016**, *18*, 3003-3010.

    Below is the **graph representation learning**-enabled automatic atom typing algorithm used in ABCrystal:

    - Zhang, J. `Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? <https://aip.scitation.org/doi/10.1063/5.0095008>`_ *J. Chem. Phys.* **2022**, *156*, 204108.

.. attention::
    ABCrystal has included `spglib <https://spglib.readthedocs.io/en/latest/index.html>`_ for space group manipulation. Please also **cite spglib** if you have used ABCrystal:

    - "Spglib: a software library for crystal symmetry search", Atsushi Togo and Isao Tanaka, https://arxiv.org/abs/1808.01590 (written at version 1.10.4).

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.. toctree::
   :numbered: 5
   :maxdepth: 4
   :caption: Contents:

   introduction.rst
   theory.rst
   usage.rst
   appendix.rst