I've got an O'Neill Cylinder that's virtually identical to Gerard O'Neill's original design, only scaled up a bit to allow for more surface area. The cylinder is divided into 6 sections, 3 windows and 3 "valleys," long stretches of habitable surface area. Mirrors reflect sunlight into the habitat, so each window directly lights one valley. The mirrors rotate to simulate a day-night cycle roughly the same as Earth's. The central axis experiences no gravity, and the atmospheric pressure there is roughly 0.8 atm.
The idea is for the cylinder to be an ecosystem as self-sustaining as possible on the long term, with large forests and bodies of water located on the valleys. My idea for the moment is for the edges of the valleys to be essentially tall mountain chains some 8 km tall, so as to keep the biomass in the valleys from "spilling" into the windows (I just assumed that would happen without some sort of barrier). General type of environment I'm going for is that of a tropical rainforest, similar to the Amazon, so high temperatures, high humidity and no seasonal variation (since the cylinder has no tilt like Earth does, that'd have to be simulated anyway).
So basically I'm scratching my head trying to figure out how the climate would work. I'm fairly certain the alternated layout of land and windows, plus the zero-g centre with slightly lower pressure, would have at least some consequence, but I don't know nearly enough physics or metereology to work that out. Would it rain on the windows? Would that disturb the water cycle or the illumination? How would air circulate? These are all smaller questions I've been having that relate to the general problem.
I also understand there's no way to answer this with any certainty, as no one's ever built this thing to test it -- all I need are some points to consider, and possible solutions to any problems that might arise from such a configuration.
Also, I'd like as little artificial climate control as possible. If things are different from Earth, but wouldn't doom life inside, then it's actually a good thing -- I like a bit of uniqueness or weirdness as long as it's harmless.
I've scoured this site and others for some sort of guidance but it seems the windowed cylinder really has gone out of fashion, because all I've found assumes a closed, windowless design with artificial lighting. Yes, I know it's better for radiation shielding, but I'm not giving up windows -- they're pretty and fit the vibe of my setting better. Thanks in advance.