Hello Tara,
unfortunately, there is no way at the moment to incorporate anisotropic Debye-Waller factors with qstem. The only way would be to compute the displacements yourself, generate a large model with all the atoms in the super-cell at their displaced positions and run the code in a mode that reads in a new configuration for every TDS run. This mode can also be used to incorporate accurate phonon modes, rather than using the Einstein model.
Regarding DebyeWaller factors from CIF-files: This is indeed a problem, that they get lost in the translation via the .xtl format. The only way to circumvent this problem is currently to write your own translator from CIF to .cfg.
With best regards,
Christoph Koch.
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