Question-and-Answer Resource for the Building Energy Modeling Community
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... this may only be a partial answer - others might have additional or better suggestions.
It depends on what you're after. If you're interested in modelling stack effects in tall buildings in cold climates (for instance), then EnergyPlus' Airflow Network (AFN) Model is well suited. Note that the AFN doesn't generate stratified air layers within zones (only between zones). If instead you're interested in buoyancy effects linked to displacement ventilation, then EnergyPlus' in-house 3-node solution is pretty handy. There's a nice explanation here. More complex cases will push you towards CFD-coupled solutions, such as described here.
If you search for "CFD", "displacement", etc. using UnmetHours' search bar, you'll find plenty of past discussions on the topic.
