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Humboldt-Universität zu Berlin - Faculty of Mathematics and Natural Sciences - Strukturforschung / Elektronenmikroskopie

How to convert crystal structure files to the CFG format

The QSTEM software for simulating TEM and STEM images uses the .cfg file format because this format is compact, easy to read and write, easily extendable, and allows all the atomic structure parameters relevant toQSTEM to be defined, such as fractional atom coordinates, occupancy, charge, and Debye-Waller factor.

However, since this format is not commonly used by other software packages (except for, e.g., AtomEye) one may want to convert crystal structures defined in another format to the .cfg format.

This can easily be achieved in by

  1. First loading your atomic configuration into a software that can both read your format and also save it in the .xtl format (e.g. Vesta).
  2. Call the program Convert2CFG (part of the QSTEM package) and open the .xtl file. This will automatically create a file with the same name but a .cfg extension and the converted structure.

Alternatively, you may also load files in the .xyz format. However, the .xyz format does not specify any unit cell parameters, so that this format only makes sense for super cells. The ‘unit cell’ will, in this case, be assumed to be the extension of the model.
I want to give credit to Dr. Yaron Kaufmann for writing the xyz->cfg porting routine.