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Alright. I’ve poked things a bit and ran a bunch of tests and talked to people and I think the answer is that EnergyPlus is not modelling heat transfer from interzonal air exchange properly, and you are right to be concerned. This appears to particularly be an issue when you have two-way exchange between zones.
The first thing I did was grab an old two-zone test model I had to make sure I could replicate your results, which I did. In my case, my model had a large main zone with windows, and a much smaller zone attached to it. In this case we would expect that putting a large opening between the two zones would result the temperatures converging to that of the main zone.
This may also apply when using the AirflowNetwork as well. It’s harder to test, since I can’t easily force air exchange between the zones, but just setting up a 27m2 permanent opening between the zones and some leakage produced results similar to what we get if we use cross-mixing to exchange a similar amount of air (here ~0.75 m3/s roughly lined up with what was happening in the AFN):
I then looked at what happens with two identical zones. Theoretically, this should provide a very clean test since if the zones are identical then exchanging air between them shouldn’t do anything since they have the same temperature and loads. Again, however, we see EnergyPlus produce this bizarre result. Indeed, rather than mixing the two zones we can even have one zone cross-mix with itself, which should definitely have no effect. Again though we see it act as if it has more mass.
Finally, to check whether or not this is an issue with EnergyPlus specifically, I re-ran these tests with AccuRateNZ using CSIRO’s Chenath engine.
AccuRate does not agree with EnergyPlus, and instead produces the results we would expect. With a big zone and a small zone, adding a large opening between them results in the temperatures converging to that of the big zone (and a small reduction in mass because we’ve removed most of the internal wall). When we connect to identical zones to each other, it results in no change in temperature as we would expect.
So at this point with Energyplus producing bizarre results that aren’t corroborated by another tool, I think there’s fairly good reason to suspect that there’s something wrong.