Radiant Ceiling System

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To answer the second part of your question first: When OpenStudio creates the EnergyPlus idf, it translates the OS:ZoneHVAC:LowTemperatureRadiant:VariableFlow object input field 'Radiant Surface Type' into the EnergyPlus ZoneHVAC:LowTemperatureRadiant:VariableFlow object input field 'Surface Name or Radiant Surface Group Name', in order to spare the user the tedium of listing all the associated radiant surfaces by name. If you read the input description for the EnergyPlus field linked above, you'll note that the surface group also defines the fraction of flow going to each surface. This translation happens here.

So why are your surfaces being referenced by more than one radiant system? I'm willing to bet that whatever measure you used applied an internal source construction not only to the ceilings of your ground floor spaces, but also to the matched floor surface of the space above (so EnergyPlus won't throw an error about matched surfaces with differing constructions). Which should be fine if you specify 'Ceilings' for 'Radiant Surface Type', which should just pick up the ceiling surfaces to add to the SurfaceGroup.

Except there's a problem: as I noted a while back (almost a year now!), there is a bug in the translation of the 'Surface Type' input, where when choosing 'Ceilings' for radiant systems serving zones whose floors also have internal source constructions applied, the floors are erroneously added to the surface group! So, if you have stacked zones with radiant ceilings in each zone, you end up with the upper zone having a SurfaceGroup that contains that zone's ceiling AND floor. But that floor is also the outside boundary condition of the lower zone's ceiling, which is the radiant surface for the lower zone's radiant system. Since matched interior surfaces aren't really seen by EnergyPlus as two surfaces, but as mirrored instances of the same construction, you end up with a surface being referenced by two radiant systems.

So what do you do about it? Well, until the translation bug is fixed, not much. There is no method in the OpenStudio API for removing surfaces from the radiant system surface list (that I know of). I suppose an EnergyPlus measure could do it, but that would be tricky. When I ran into this problem, I ended up making plenums above the spaces, so that the spaces above would have floors without internal source constructions. If this isn't an option for you, you might have to get creative, or directly edit the IDF.