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 XX 2024, XX, XX-XX.

• Zhang, J.; Dolg, M. Global Optimization of Clusters of Rigid Molecules Using the Artificial Bee Colony Algorithm. 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? J. Chem. Phys. 2022, 156, 204108.

Attention

ABCrystal has included spglib 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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Contents:

• 1. Introduction
  • 1.1. What is ABCrystal?
  • 1.2. ABCrystal Information
  • 1.3. ABCrystal Citation
  • 1.4. Installation of ABCrystal
    • 1.4.1. For Windows Users
    • 1.4.2. For Linux Users
    • 1.4.3. For OpenMP
  • 1.5. ABCrystal Files
• 2. Theoretical Background
  • 2.1. The Artificial Bee Colony Algorithm
  • 2.2. Automatic Atom Typing
• 3. How to Use ABCrystal
  • 3.1. CHARMM Force Field
  • 3.2. Example: CO2 Crystal
    • 3.2.1. Run the Search
    • 3.2.2. Check the Output
    • 3.2.3. Visualization of Structures
    • 3.2.4. DFT Calculations
• 4. Appendix
  • 4.1. Update History