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I believe that you can capture some of these benefits, but maybe not as directly as you might be hoping for. The makeup water treatment could (**see note below) have the effect of increasing the mass diffusion and convection coefficients by increasing the interstitial area between pure H20 and air molecules. If you select the CoolingTower:VariableSpeed:Merkel tower model, then the transfer coefficients are controlled by the input of the tower UA at design conditions. One of the assumptions in Merkel's Theory is that the Lewis Number is 1, so by specifying the UA you are effectively specifying both heat and mass transfer coefficients. The tower with water treatment should have a higher UA than the current tower, but the challenge is to know by how much. I believe it will be difficult to find reliable data on the effects of mineral concentrations on transfer coefficients in cooling towers. But if you do find a delta that you're comfortable with, then you can calculate the savings by simulating the tower with different design UA values. As for the water savings, I would just caution that the EnergyPlus algorithms are fairly crude in this department. The SaturatedExit method will always over-predict water consumption, and the LossFactor method has a low precision. If you have access to Trnsys, then the Type 51 cooling tower would be a useful tool for this task. In this model, the mass flow rate through the tower is not assumed to be constant, and the water loss is calculated explicitly.
** Removing minerals might not always be a good thing. You could be removing some which have a high conductance with air, and you could be loosing more sensible potential than what you gain with the increased latent potential.