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Good question! Think about when you are designing a building, do you want all the spaces to be comfortable, or some are "very comfortable" so that the others can be less so?
I'd say you should use the maximum, and use that as a constraint in your project so that once the threshold is reached, the algorithm does not need to push any further. You have two options to do this in jEPlus+EA. The first one is defining a report variable for max of the PPDs. You can use an equation like "v1=Math.max(c2, c3, c4 ...)" - hope you don't have too many zones - and then add a constraint, say "s1=v1", and define its feasible and scaling ranges. If you have only a few zones, the alternative is to simply list them all as constraints. In this way, you can actually control the comfort level you want to provide for each zone.
Here are the relevant parts of the manual: https://www.jeplus.org/wiki/doku.php?id=docs:jeplus:v21:rvx#uservars_-_report_variables
Yi