Non-stoichiometric monoclinic 4C pyrrhotite (Fe7S8), a ferrimagnetic monosulfide that has been intensively used as a remanence carrier to infer the magnetization of the Earth's crust and extraterrestrial materials, exhibits a characteristic low-temperature transition accompanied by complex modifications in anisotropy and magnetization. We demonstrate that the magnetic rotational symmetry of the 4C pyrrhotite is critically affected by the order of the defective Fe-sites, and this in turn is a key to decipher the physics behind the low-temperature transition. Our torque experiments and numerical simulations show an emergent four-fold rotational symmetry in the c-plane of the 4C pyrrhotite at T < 30 K. This symmetry breaking associated with the transition is caused by the competitive interaction of two inherently hexagonal systems generated by two groups of Fe-sites with different local anisotropy fields that stem from the vacancy arrangement in the 4C stacking sequence, and it is triggered by changes in the spin orbit coupling due to the overlap of Fe-Fe electron orbitals at low-temperature. This mechanism provides a new explanation for the magnetic transition in 4C pyrrhotite at low temperature and could also cast light on non-trivial magnetic phenomena in defective systems.

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