How to handle atomic overlap in CIF → Quantum ESPRESSO pipeline for periodic crystal DFT

I’m running into atom overlap errors when converting a CIF (halide perovskite, partial B-site occupancy, pm3̄m) to a pw.x input for a vc-relax + SCF workflow with PAW/standard solid state pseudopotentials.

The structure looks fine in VESTA, but symmetry expansion of the asymmetric unit duplicates sites at high-symmetry Wyckoff positions, and QE rejects the input before SCF even starts.

I’ve tried loosening site_tolerance in pymatgen’s CifParser, SpacegroupAnalyzer.get_primitive_standard_structure(), and manually merging via StructureMatcher, with only partial success.

Im wondering if there is a clean canonical pipeline for CIF → valid QE input that handles special position duplication and partial occupancy robustly and should I just be using ibrav=0 with explicit cell parameters throughout to rule out any lattice parameterization weirdness on QE’s end?