Using ToposPro with CrystalGrower

ToposPro is a software package for the topological analysis of crystal structures. This software can be used to partition any crystal structure into units of growth (e.g. natural tiles or Voronoi-Dirichlet polyhedra - VDP). An interface between CrystalGrower and ToposPro has been developed to produce the input files required for CrystalGrower to grow the crystal structure from its units of growth. Due to the advanced nature of the ToposPro software, guides are provided here to familiarise CrystalGrower users with the operation of this software.

• Creating Structure and Interaction Files for Net Structures: This step-by-step guide will demonstrate how to produce a structure file for a net type structure, along with its corresponding interaction energy file (net.txt). These files are required as inputs for CrystalGrower, therefore care must be taken to ensure the structures and interactions are chosen correctly to make sense chemically.
• Creating Structure Files for Tile Structures: This step-by-step guide will demonstrate how to produce a structure file for a tile type structure. This type of partitioning is useful for cage-based framework structures e.g. zeolites. The latter parts of the guide will discuss visualising tiles with IsoCryst and 3dt.
• Setting Up and Visualising Interactions With ToposPro: This step-by-step guide will demonstrate methods to obtain and visualise an adjacency matrix for a set of interactions between molecular / ionic species for CrystalGrower using ToposPro.
• Matching Interaction Types Using ToposPro: This step-by-step guide will demonstrate how to relate the interaction types used in CrystalGrower to their real chemical counterparts. Using Isocryst within ToposPro, interactions can be visualised and labelled to allow their identification within the context of the crystal structure.
• Visualising Tiles with 3dt: This step-by-step guide will demonstrate how to visualise tile based structures using 3dt. This can only be used for frameworks where a tiling is calculated i.e. “tile” structures but not “net” structures.