Here are my two cents:
Amorphous structures is an advanced topic, but not impossible. Our group has 
calculated the electronic structure of amorphous Se in the past with WIEN2k 
(https://olegrubel.mcmaster.ca/publications/2012/Darbandi_JPCM_24_2012.pdf), 
but we had to construct the structural model ourselves using a pre-existing 
recipe (see Refs. 21-23 therein). This recipe is not universal though. 
Alternatively, there should also be literature on the phase-change GST 
compound. I have seen amorphous structures created using ab initio MD by 
heating up (melting) and slowly cooling down, which is a more "universal" 
method.

In summary: I do not think WIEN2k has tools that are dedicated to facilitate 
creation of an amorphous structure. But if you manage to generate a reasonable 
structure somehow, it should be possible to calculate its electronic structure 
with WIEN2k.

I hope it will help
Oleg


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