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A common approach to modeling central plants is to do your building-level modeling in separate models, then output the hourly cooling loads to individual profiles that are fed into a separate central plant model. These cooling load profiles can be added to secondary chilled water loops that represent each building in the central plant model. The downside to this approach is that the building model and the plant model are not connected, so any changes to the building model means that you have to update the profiles that are being fed into the plant model, though this is pretty easy to do and does not pose a significant inconvenience.

As to whether your chillers should be connected in parallel (what I assume you mean by "horizontal") or series (what I assume you mean by "vertical"), I can say that most chiller plants will have chillers connected in parallel, so that they can be staged on and off depending on the load, and can include a low-load chiller. However, I have heard that series configurations can be very efficient in some applications and increase the available chiller capacity. If you wan to go with a "typical" configuration, though, use parallel.