Infrared spectra are obtained by a Fourier Transform Infrared (FTIR) spectrometer (Bruker Equinox 55). The sample holder has a hole, with a diameter of 4.5 mm, which allows the infrared beam to transmit through the substrate and the sample. The infrared beam forms an angle of 45 with both the ion beam and the substrate holder. Thus, spectra can be taken in-situ before, during, and after irradiation, without tilting the sample. By illuminating the sample with an external light source it is also possible to perform reflectance spectroscopy in the 0.65-2.5 m range. Measures in the 0.4-1 m spectral range can be obtained with the CCD detector and the Triplemate SPEX spectrometer described below.