I know this is a very old question, but since I had a lot of trouble finding any answers online, and I just worked out the pollution formula for myself through trial and error, I thought I’d share.
First, the easy one: Morale. Each farmer, worker, and scientist has a percentage multiplier to its output. This multiplier is 100%, plus your morale, plus the gravity adjustment. So if you have +20 morale, but it’s a high-gravity planet, the multiplier is 100% + 20% (morale) - 50% (gravity) = 70%. All of that planet’s farmers, workers, and scientists will be reduced to 70% of their normal output.
Some government types adjust the percentage for specific sectors. For instance, if you’re a Democracy, you get +50% to research. So your farmers and workers will still be at 70%, but your scientists will be at 120%.
Now, the complicated one: Pollution. If you have too much industry on a planet, you have to put stringent environmental regs in place so your populace doesn’t choke to death in its own toxic waste. This reduces efficiency and acts as a flat penalty to industrial output. If you’ve got 8 points of pollution on a planet, that means you’re getting 8 points knocked off your industrial output. Simple enough so far.
Where it gets tricky is the formula for calculating that pollution penalty. Several factors go into this. The first thing is your “polluting output.” This is the part of your industrial output that generates pollution.
To figure your polluting output, first add up the total output of your workers. This is the base output for the planet (1 for an Ultra Poor, 2 for Poor, 3 for Abundant, 5 for Rich, 8 for Ultra Rich), plus any modifiers from buildings (+1 for Automated Factory, +2 for Robo Miner Planet, etc.), plus your racial industry mod, times the number of workers, times the workers’ percentage multiplier for morale, gravity, and government. It does not include the bonus from a Recyclotron, nor does it include the “fixed” output of any building. So if you have a Deep Core Mine, the +3 per worker counts toward pollution, but the base +15 for the building doesn’t count. The one exception to this rule is the Robotic Factory, which does count toward polluting output.
Next, if you have a Pollution Processor, divide your polluting output by 2. If you have an Atmospheric Renewer, divide it by 4. If you have both, divide it by 8.
Then subtract the planet’s absorption capacity from the polluting output. Bigger planets can soak up more pollution, so the absorption capacity is 2 per size category: Tiny = 2, Small = 4, Medium = 6, Large = 8, Huge = 10. If you have Nano Disassemblers, absorption capacity is doubled.
Finally, take the result (polluting output minus absorption capacity) and divide by 2. Round fractions up. This is your pollution penalty.
One final wrinkle: Tolerant races and androids are immune to pollution penalties. If you have a mix of Tolerant and non-Tolerant races on a planet, the final pollution penalty is reduced in proportion to the Tolerant percentage of the population; so if 25% of the population is Tolerant, the pollution penalty is cut to 75% of normal. Again, round fractions up.