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When only a single composition sensor is available for a multi-zone co-evaporation process, it can be difficult to determine the relative amount of material deposited in each zone. In this paper, a method of estimating the deposition-rate ratio between zones using small signal perturbation sequences is presented that exploits the exponential dependence of deposition rate on the temperature of the molten metal. A quality metric for the ratio estimate is presented, which can be easily calculated. Then, in order to determine the best perturbation sequence that meets all manufacturing constraints, a constrained optimization problem is described that is shown to be convex. An interesting feature of the solution is the importance of correlations between purturbation inputs. Experimental and simulation results are presented to validate the method.