Advice on modelling nine story atrium across shells

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I've modeled a nine story office building which requires different
shells for several of the levels in the building. It also has a nine
story (full height) atrium that will be used to extract all of the
exhaust air (i.e. supply OA to the floors and condition via FC units
and pull exhaust air out of the top of the atrium). I'm aware that
eQuest doesn't track air flows but I'd like to best approximate the
atrium effects on the overall energy use of the building.

Current approach: I've modeled each floor as a separate zone and I'm
going to delete the floors and turn the ceilings into air-walls and
link them to the zone above. Currently I'm conditioning all of the
zones that make up the atrium but at some point I'd like to explore
not conditioning these zones to more accurately approximate how we'd
run the building.

Comments?

One alternate approach I've seen proposed is to replace all nine zones
in the atrium with one full height zone - the advantage is the glass
on the roof and upper walls can "see" the floor and walls in all of
the zones of the atrium. However this won't let me later go back in
and explore any variation of temperature with height. I think this
might be important as I would expect the air at the top of the atrium
to be warmer and cause more load on the top floor zones next to the
atrium.

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Jason Quinn

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