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By repeatedly pre-cleaning the sputtering chamber with Ar gas and in-situ isochronal annealing samples, NiSi films are successfully prepared on Si (100) substrates in a radio-frequency magnetron sputtering system. A comparison between the obtained NiSi and excess oxygen-contaminated Ni/Si films has been performed by EDX analysis of oxygen atomic content in both the films. Focused ion beam milling technology is employed to make the cross-sections of the samples for characterizing the NiSi film thickness and NiSi/Si interface roughness. The influences of nickel film thickness on the NiSi-film morphology and on the NiSi/Si interface roughness are studied.