I've been eagerly waiting for someone's response to this.
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I'm waiting for this as well, AUSpool...
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From what I understand, the Hayward runs on a three hour cycle as you mentioned above. I just recently raised my CYA up as well.......
First off, I would check on that cycle time parameter...pentair uses a 1-hour cycle time, so that is 24 cycles/day. My understanding was that Hayward used a slightly longer cycle time so that they have 20 cycles/day. You may be confusing the 3-5 hr timing for the periodic polarity reversal of the current. For Pentair, the polarity reversal is selectable from 3, 4 or 5 hours. The ICs are programmed to start out with a reversal cycle of every 3 hours for the first 30 days and then it lengthens out to 5 hours.
As for Stenners versus SWGs, I think you guys are on the right track. Let's look at the cases -
Case #1: Manual Chlorination
Manual chlorination involves a relatively "huge" concentration of liquid chlorine all at one specific time (most people manually chlorinate at night). This method is the most sensitive to variation because first of all it relies on a person doing the chlorination. Life happens and no one is perfect so manual chlorination is subject to a lot of user error (bleach strength off, improper amount of bleach on hand, too little/too much poured in at once, etc, etc). It's also a large concentration of LC that is more apt to not fully mix if the pool pump is not running for an extended period of time after dosing. I believe manual chlorination is much more prone to developing dead spots due to poor circulation patterns and ineffectual mixing.
Case #2: Stenner Pumps
Peristaltic injection of LC attempts to get around the human factor a bit by automating the injection of chlorine. However, from a time/dose perspective, Stenner pumps still inject a "huge" dose of chlorine into the pools plumbing system over a very short period of time. Correct me if I'm wrong, but most Stenner owners program their injections to last, at most, less than hour as many people try to cut down on pump run time. Stenner injection is also going to be subject to circulation issues but it certainly has a much better chance of achieving uniform distribution. Bleach concentration, pump failures, etc, are all still a concern.
Case #3: SWG's
SWG's remove two factors - human failure and chemical variation. Also, the time/dose profile of an SWG is a lot slower than either peristaltic or manual injection of chlorine. SWG pools typically run their hydraulic systems for much longer periods of time than do manually dosed pools. So, when chlorine is generated, it is added to pool more slowly and over longer periods of time. I believe this has a tendency to create better distribution of chlorine in a pool's water volume. As you have noted, the inside of an SWG cell when it is generating chlorine is very harsh - the pH (without borates) can easily rise well above 10.5, both oxygen gas and hydrogen gas is evolved leading to an incredibly corrosive and toxic environment for biological entities. Not all of the water volume is treated to this harsh chemical effect, but none of the other chlorination methods can produce this effect. Certainly cell failure and decreased efficiency due to scaling is a concern but modern SWGs have come a long way since their initial offerings.
One other thing to keep in mind is that, as you say, there is no magic here. The FC/CYA ratio is an empirically derived value based on the equilibrium chemistry of chlorine and cyanuric acid as well as the experience of actual pools. The FC/CYA ratios used by TFP (5% and 7.5%) certainly create levels of hypochlorous acid fully capable of killing most pathogens and oxidizing organic compounds. Algae, comparatively speaking, is a slow growing nuisance (not really a pathogen, per se) and sanitized pool water has very little algae in it to start with. So even though the active chlorine levels required to kill algae are quite a bit higher (and algae, in a general sense, is all over the map in terms of chlorine sensitivity), the ratios we recommend are more than adequate too keep up with it. I believe the driving force behind the lower ratio for SWG pools is as you surmise - there is a much greater chance for variation in FC levels with a manually dosed or peristaltic-dosed pool than there is with an SWG pool. The variation is enough to warrant a higher overall dose so that accidents don't lead to cloudy water. Could a Stenner pump be set to dose in a fashion similar to an SWG? Sure, but that would defeat one of the benefits of a Stenner pump, namely the decoupling of chlorination from pump run time. So any money you save by dosing at a "low and slow" rate while using a lower FC/CYA ratio may be entirely offset by having to double, or even triple, pump run times.
Cheers,
Matt