The use of common starting structural models, particularly atomic displacement parameters and occupancy, is essential for Rietveld refinement within and between laboratories performing QPA. Extensive libraries of crystal structures are available for Profex/BGMN users, transferring these models to TOPAS requires manual editing of parameters such as: space group, origin, atomic coordinates, occupancies and Beq (or conversion between different ADP formats). This process is time consuming and introduces potential for transcription errors that can have detrimental effects on QPA.
To address this problem, a Python conversion tool has been developed to automatically convert Profex crystal structure format files to TOPAS compatible crystal structure format files. The script interprets lattice parameters, atomic coordinates, site occupancies, atomic displacement parameters, Wyckoff positions, and space group meta data, generating ready to go structure files suitable for use in TOPAS. Mixed-occupancy sites and parameterised variables are output where possible. Atomic positions are converted using crystallographic symmetry information from the source structure and those contained in SPACEGRP.DAT, the space group database included with Profex.
The primary object of the script is the preservation of crystallographic intent. By enabling TOPAS users to begin refinements from the same structural descriptions used by Profex users, differences arising from manually recreated models can be reduced. This is particularly important in Round Robins, or when comparing results across laboratories, software platforms, and other studies where small differences in structural values may have larger ramifications on the final result.
Validation and reporting functions provide diagnostic information for ambiguity or errors in the starting Profex structure. This allows rapid identification of structures requiring TOPAS user review. by outputting as much of the original profex str as block comments, the TOPAS user can easily see what the issue is and also what the original intent was.
The script provides a practical framework for reproducible structure exchange and helps establish a common structural starting point for diffraction studies by TOPAS users.