Hey everyone – bumping this after some time. We did some investigation into this behaviour (thank you @twg for helping out with some data) and we have a potential (simple) fix for this type of ‘collapsing’ or ‘squashing’ behaviour in ab-initio:
Set the parameter Enforce non-negativity to False.
We’re still investigating the root cause but it seems that this constraint biases SGD to ‘collapsed’ states in high symmetry structures. You may also need to set the parameter Center structures in real space to False if the automatic centre-of-mass adjustment results in wonky behaviour with negative density values (we found this latter change to be useful for helical structures).
Let us know if this works in your case!