Welcome to ABCluster’s tutorial!

Tip

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!

Attention

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, if you use topgen:

• Zhang, J. Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? J. Chem. Phys. 2022, 156, 204108.

If you use Qbics and many-body energy decomposition analysis (MB-EDA) to analyze the cluster formation processes, please cite:

• Zhang, J.; Tang, Z.; Zhang, X.; Zhu, H.; Zhao, R.; Lu, Y.; Gao, J. Target State Optimized Density Functional Theory for Electronic Excited and Diabatic States. J. Chem. Theory Comput. 2023, 19, 1777-1789.

• Tang, Z.; Zhu, H.; Pan, Z.; Gao, J.; Zhang, J. A Many-Body Energy Decomposition Analysis (MB-EDA) Scheme based on a Target State Optimization Self-Consistent Field (TSO-SCF) Method. Phys. Chem. Chem. Phys. 2024, 26, 17549-17560.

Attention

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.

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Contents:

• 1. Introduction
  • 1.1. What is ABCluster?
  • 1.2. ABCluster Information
  • 1.3. ABCluster Citation
  • 1.4. Support ABCluster
  • 1.5. Installation of ABCluster
    • 1.5.1. For Windows Users
    • 1.5.2. For Linux Users
    • 1.5.3. For xTB Crash Bug
    • 1.5.4. For OpenMP
    • 1.5.5. For GPU Acceleration
  • 1.6. Compilation of ABCluster
    • 1.6.1. System requirement
    • 1.6.2. One-key Compilation
    • 1.6.3. Lean Source Code
  • 1.7. ABCluster Files
• 2. Theoretical Background
  • 2.1. Global Optimization
  • 2.2. Conformation Search
  • 2.3. Energy Evaluation
    • 2.3.1. Rule of Thumb
    • 2.3.2. When does CHARMM Force Field Perform Well?
    • 2.3.3. When Must Quantum Chemistry Method be Used?
    • 2.3.4. Be Cautious with Model Potentials!
  • 2.4. The Artificial Bee Colony Algorithm
  • 2.5. Automatic Atom Typing
  • 2.6. Many-Body Energy Decomposition Analysis
• 3. atom: Atomic Clusters Using Force Fields
  • 3.1. Supported Model Force Fields
  • 3.2. Example: 38 Lennard-Jones Particles
  • 3.3. Build atom Input
  • 3.4. Example: (MgO)₂₀
  • 3.5. Example: Silver and Copper Clusters
    • 3.5.1. Ag₃₈ and Cu₃₈
    • 3.5.2. Ag₃₂Cu₆
  • 3.6. Example: (CaTiO₃)₅
  • 3.7. Example: C₁₆ and Ge₁₆
• 4. rigidmol: Rigid Molecular Clusters Using Force Fields
  • 4.1. CHARMM Force Field
  • 4.2. Example: (H₂O)₆
    • 4.2.1. Global Optimization
    • 4.2.2. Many-Body Energy Decomposition Analysis
  • 4.3. Example: Build Parameter File for (NHCH₃)₂CO
    • 4.3.1. New Way: Automatically Building
    • 4.3.2. Old (and out-of-date) Way: Manually Building
  • 4.4. Example: Pincer and Water Using topgen and Multiwfn
    • 4.4.1. Calculate Parameters
    • 4.4.2. Global Optimization
  • 4.5. Example: Li⁺, Na⁺, and Cs⁺ in (C₆H₆)₆
    • 4.5.1. Global Optimization
    • 4.5.2. Many-Body Energy Decomposition Analysis
  • 4.6. Example: HNO₃ (H₂O)₁₀ in Electric Field
  • 4.7. Example: Performance Comparison Using (Camphor)₁₀
  • 4.8. rigidmol Accelerated by GPU
    • 4.8.1. Enable GPU Acceleration
    • 4.8.2. Single GPU Performance
    • 4.8.3. Multiple GPUs Performance
• 5. isomer: Atomic Clusters Using General Methods
  • 5.1. isomer with Gaussian
    • 5.1.1. Configuration of Gaussian
    • 5.1.2. Example: Al₃O₄⁺
    • 5.1.3. Example: Au₆
  • 5.2. isomer with xTB
    • 5.2.1. Example: Au₈
    • 5.2.2. Example: Li₅F₅ and Li₅F₅^-
  • 5.3. Interfaces to External Programs
  • 5.4. Clusters with Specific Point Group Symmetry
    • 5.4.1. Point Group Input
    • 5.4.2. Example: Au₂₀ under Point Group Symmetries
    • 5.4.3. Example: B₆N₆
• 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
      • 6.3.2.1. Mixture
      • 6.3.2.2. Bi-phase
    • 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
    • 6.4.1. Example: (H₂O)₄^-
    • 6.4.2. Example: (CF₃)₄@C₂₀
  • 6.5. geom with xTB
    • 6.5.1. Example: NaCl(H₂O)₁₀
    • 6.5.2. Example: Co₆Te₈(PEt₃)₆
      • 6.5.2.1. Co₆Te₈
      • 6.5.2.2. Co₆Te₈(PEt₃)₆
  • 6.6. geom with CP2K
    • 6.6.1. Example: Graphene oxide-supported Cu₈
    • 6.6.2. Example: (H₂S)₅@SSZ-13
  • 6.7. geom with CHARMM
    • 6.7.1. Example: Decaalanines
      • 6.7.1.1. Packing
      • 6.7.1.2. Layer
  • 6.8. geom with VASP
    • 6.8.1. Example: Se₃ on C₂N
• 7. geom: Conformation Search
  • 7.1. Flexibility
    • 7.1.1. topgen
    • 7.1.2. Set up Flexibility in Input Files
    • 7.1.3. Some Examples
  • 7.2. Example: C₆H₁₂
  • 7.3. Example: AIP (C₃₇H₅₉O₈N₈S⁺)
• 8. New Quantum Chemistry Methods for Clusters
  • 8.1. For Molecular Clusters: Many-Body Energy Decomposition Analysis
    • 8.1.1. TSO-EDA
    • 8.1.2. Many-Body TSO-EDA
    • 8.1.3. Input Examples
      • 8.1.3.1. Example: EDA for GeH₃F-NCH Complex by B3LYP-D3BJ/def2-SVP
      • 8.1.3.2. Example: MB-EDA for Molecular Cluster (NH₄⁺)₂(H₂SO₄)(HSO₄^-)₂
• 9. Appendix
  • 9.1. Update History
  • 9.2. Acknowledgement