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Rare earth ions implanted GaN has been investigated by transmission electron microscopy versus the fluence, using Er, Eu or Tm ions at 150 keV or 300 keV and at room temperature. Point defect clusters and stacking faults are generated from low fluences (7×10^{13} at/cm^2), their density increases with the fluence up to the formation of a highly disordered layer at the surface. This highly disordered layer is observed from a threshold fluence of 3×10^{14} at/cm^2 at 150 keV and 3×10^{15} at/cm^2 at 300 keV, and appears to be composed of voids and misoriented nanocrystallites. Its thickness rapidly increases with the fluence, and then saturates. Both basal and prismatic stacking faults were observed. Basal stacking faults are I_1 in majority, but E or I_2 have also been identified. I_1 basal stacking faults propagate easily through GaN by folding from basal to prismatic planes. Channelling implantation, increasing the implantation temperature from room temperature to 500ºC, or implanting through a 10 nm thick AlN cap reduce the crystallographic damage, particularly by retarding the formation of the highly disordered layer. Implanting through the AlN cap allows the highly disordered layer formation threshold fluence to be increased by one order of magnitude, as well as the annealing at high temperature (1300ºC) which brings about a strong optical activation of the rare earths.
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