This has come up a number of times. The current Set Window to Wall Ratio by Facade Measure does only let you select the scope of the measure by orientation. We don't currently have a way in OpenStudio to pass a selection to the measure like user scripts in the SketchUp plugin can. One solution would be for us or someone else to add a new argument to the measure to select a measure to include or exclude from the measure. You could also filter by story, surface size, construction etc. If you want to use this today, below is a quick fix.
First, download the measure from BCL, and make a copy of it, so it is in the "My Measures" directory.
Next open up the measure.rb file and look for the following code.
new_window = s.setWindowToWallRatio(wwr, sillHeight_si.value, true)
This is inside of a loop through surfaces where "s" is the surface. If you add the lines below prior to the "new_window" line you can hard code it to follow this logic. "If the parent space for this surface has a space type assigned, and if the name of that space type is Atrium then go to the next surface in the model, don't do anything to this one".
if space.get.spaceType.is_initialized and space.get.spaceType.get.name.to_s == "Atrium"
runner.registerInfo("Skipping this surface because it belongs to a hard coded space type that I want to skip")
next
end
You may want to skip the "info" message if you have a lot of these. I just put it in the example code for demonstration. The "new_window" line should be on the line after "end". Congratulations! you are a ruby programmer now.