Welcome to ABCluster’s tutorial!
I understand that most readers (including me) hate reading lengthy software manual. Thus:
This tutorial is composed of many realistic cases. In each case, you can finish a real global optimization 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!
ABCluster has a very low study-curve: it is developed as a black-box program, so you can quickly start you scientific research without being distracted by uninterested details!
The best way to support the development of ABCluster is that in any published works using ABCluster, please include the following references:
Zhang, J.; Dolg, M. ABCluster: The Artificial Bee Colony Algorithm for Cluster Global Optimization. Phys. Chem. Chem. Phys. 2015, 17, 24173-24181.
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 a review of recent development of global optimization algorithms for chemical clusters, including many applications of ABCluster:
Zhang, J.; Glezakou, V.-A. Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges. Int. J. Quantum Chem. 2021, 121, e26553.
Below is the graph representation learning-enabled automatic atom typing algorithm used in ABCluster:
Zhang, J. Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? J. Chem. Phys. 2022, 156, 204108.
Other relevant references are also welcomed to be cited:
Zhang, J.; Glezakou, V.-A.; Rousseau, R.; Nguyen, M.-T. NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems. J. Chem. Theory Comput. 2020, 16, 3947-3958.
- 1. Introduction
- 2. Theoretical Background
- 2.1. Global Optimization
- 2.2. Conformation Search
- 2.3. Energy Evaluation
- 2.4. The Artificial Bee Colony Algorithm
- 2.5. Automatic Atom Typing
- 3. atom: Atomic Clusters Using Force Fields
- 4. rigidmol: Rigid Molecular Clusters Using Force Fields
- 4.1. CHARMM Force Field
- 4.2. Example: (H2O)6
- 4.3. Example: Build Parameter File for (NHCH3)2CO
- 4.4. Example: Pincer and Water Using topgen and Multiwfn
- 4.5. Example: Li+, Na+, and Cs+ in (C6H6)6
- 4.6. Example: HNO3(H2O)10 in Electric Field
- 5. isomer: Atomic Clusters Using General Methods
- 5.1. isomer with Gaussian
- 5.2. isomer with xTB
- 5.3. Interfaces to External Programs
- 5.4. Clusters with Specific Point Group Symmetry
- 6. geom: Global Optimization of Clusters
- 6.1. Input File for geom
- 6.2. Restart or Continuation
- 6.3. Control the Cluster Shape
- 6.3.1. General Input
- 6.3.2. Example: box, (C6H6)512(H2O)2048
- 6.3.3. Example: random, (H2O)50
- 6.3.4. Example: fix, H2O in SSZ-13
- 6.3.5. Example: droplet, NaCl in water droplet
- 6.3.6. Example: absorb, (CO)10@Ag38
- 6.3.7. Example: shell, (CH3CN)10
- 6.3.8. Example: layer, (C4H2)30
- 6.4. geom with Gaussian
- 6.5. geom with xTB
- 6.6. geom with CP2K
- 6.7. geom with CHARMM
- 6.8. geom with VASP
- 7. geom: Conformation Search
- 8. Appendix