We report on the origin of fragmentation of ultracold atoms observed on a permanent magnetic film atom chip. A novel technique is used to characterize small spatial variations of the magnetic field near the film surface using radio frequency spectroscopy of the trapped atoms. Direct observations indicate the fragmentation is due to a corrugation of the magnetic potential caused by long range inhomogeneity in the film magnetization. A model which takes into account two-dimensional variations of the film magnetization is consistent with the observations.
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