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In BEopt 2.8, we switched to a new foundation heat transfer model (Kiva). Unfortunately, there's an issue that occasionally crops up where the radiation heat transfer in EnergyPlus causes temperature oscillations when using Kiva. This issue is being worked on right now.

Long story short, the easiest way to workaround this issue is to revert to the old foundation heat transfer model that was used in BEopt 2.7. To do this, go to C:\Program Files (x86)\NREL\BEopt_2.8.0\Modeling\sim.py, search for the line that says self.use_kiva = True and change it to self.use_kiva = False. Then re-run your simulation(s).

It would also help if you could email your project file to beopt@nrel.gov.