Tools

This section describes miscellaneous functions available within ChemShell.

• Cutting clusters
  • Setting up clusters with construct_cluster
    • construct_cluster()
    • crystal_type
    • origin
    • radius_cluster
    • radius_active
    • bq_margin
    • bq_density
    • bq_symbol
    • adjust_charge
    • valence_matrix
  • Setting up QM/MM based on cut cluster
    • partition()
    • label_qm
    • label_interface
    • label_active
    • label_inactive
    • label_bq
    • bq_symbol
    • cutoff_boundary
    • interface_exclude
    • interface_rigid
    • origin
    • qmmm_interface
    • radius_active
• Fragment Conversion
  • Overview
  • Convert Fragment to Atoms
  • Convert Atoms to Fragment
• MD analysis
  • Plotting trajectories
  • Trajectory analysis
  • Taking snapshots
• Collection of Utility Tools
  • takeSnapshots()