6. geom: Global Optimization of Clusters

geom is one of the most powerful component of ABCluster. It can do global optimization of chemical clusters of both rigid and flexible structural units, including the conformation search of a single molecule. In addition, geom has integrated xTB and CHARMM computational modules internally thus the global optimization can be done in a much more simple way than isomer. Of course, it also contains the identical API as in isomer so it can connect with any computational chemistry software. In this chapter, we will introduce how to use geom to perform global optimization of clusters. In geom: Conformation Search, we will introduce how to use geom to perform conformation search and manipulate flexible molecules.

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Contents:

• 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