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The purpose is not to kill germs and germs are too small for a sieve to catch them .. kinda like irl too.
Also as Strygald said, the point of the seive is to turn PW to W (*with a side use of deletion of +40 heat)
Few things:
Sinks, Showers, Lavatories can use GERMY water, and work perfectly fine *(unlike RL), so the system can work..... HOWEVER: Germy water when used in a grill/microbmusher (for food) is not safe, and not safe for dupes to go wading through *(since it gets on their surface)
Excess water can be used in many ways, with or without the germs:
Excess GPW can be used to water peppernut plants (plants dont get germy)
*(Havent tested but assumed) If cooled, GW can be used to feed bristle berries
GPW be used to delete Heat through the sieve
OR if its the germs that are annoying you, and not the whole system, you could pour the GW into a Liquid Reservoir, submerged in chlorine gas, and watch all the germs disintegrate, Then use the CLEAN Water elsewhere :)
the loop is generating 40c heat constantly along all the pipes involved without the loop you can literally flush heat out of your base
The advantage of the closed loop toilet sieve is that you can just set and forget it. Pump some water in to start it off, cut the supply and leave it to generate a small amount of W or PW indefinitely.
Sure, the more advanced option is to send that water into a Refinery to increase its temperature and utilise the water sieve for heat deletion but it functions perfectly fine as it is.
Normally i just pump the overflow away and deal with it at a later time (when it's worth dealing with) I wanted to try and drip the overflow over a few Terrariums for a change untill i noticed all the food poisoning. thats when i went back a few saves to see where the germs were coming from.
to sum up - the water in the loop is clean, the water in the overflow generates food poisoning.
The germs are not appearing from nowhere.
Here's the good news, unless those germs somehow comes in contact with water in bottles you plan to use for food or food stuffs, the food poisoning germs won't hurt you. Also, showering and washing with germ water is perfectly legit, it will clean you. So the Advanced computer and all the non-foodie things are fine with the germs. As long as you also don't eat with surface food poisoning germs on you.
Slimelung is the same in that it can get into water and a sieve won't remoe it, but as long as the germs don't become airborne in a gas your dupes can inhale (like oxygen or polluted oxygen) you are fine. Slimelung is even safe to eat and have on your dupes as surface germs. Just be careful not to use slimelung infected water in an electrolyzer or slimelung infected algae in oxygen producing items that use algae.
In short, yellow germs are fine in air as long as it doesn't touch food or water bottles, green germs are what you want to avoid in air. Green germs are fine everywhere else as long as you don't allow them to move to the air.
-GPW, and GW do not appear out of nowwhere, it is created through lavs (possibly sinks and showers).
-Germs present in the water in a CLOSED water system for lavs/showers/sinks, do not negatively affect anything, so no your dupes would not stay sick/germy, and the germs would not go "everywhere"
-"They do get clean and they don't get sick due to the water being clean" - False. Sinks and Showers remove germs from duplicants when supplied with WATER. it does not matter if the water is germy or not.
-"Until I stick the needed overflow on" - If you are using a liquid vent to bring a closed system into the world, then you are the reason germs are being spread around, since once GPW is in the world you can contaminate anything that walks through it, or where you bottle it to send off to somewhere else.
-Dripping Germy water anywhere, sounds like s bad decision.
IF having germy water / germy Polluted Water bothers you so much to use it in showers/sinks/lavatories, then as suggested, you can kill off the germs with heat, cold, or chlorine. This makes more sense, and makes you feel good about using 'clean' water, but is unnecessary for the current state of the games mechanics.
sieved water i filter for temp anything above 30 goes i pump back out into an ice biome to melt ice and suck it back into the same sieve, anything below 30 i pump back to the base to start its sanitation.
keeps the base cool and lets you use the pwater for other things like refineries and such without much hassel
For the furance you are smelting ore to metals and producing heat, germy polluted water is perfect for it since you cook the water and destory the germs. Problem is the heat but there is a solution....
Water tubrine cooling systems use the aquatuner, a water basin, and a turbine. The aquatuner takes waterever and cools it, the basin is made of polluted water that is ethier too hot or too germy. The aquatuner vaparizes the water in the basin making steam. The steam pushes up to the turbine and cools the steam down and generates power. Now... this setup removes heat and turns it into power becuase the aquatuner produces no heat while polluted water asborbs a lot of heat while steam takes not a lot of effort to cool down.
Early early game solution for germy water? Use for watering plants mainly. The polluted water should be kept away in a basin till you can cook it in some fashion to 60-70c so the germs can die.