For best filtering it really doesn't matter. If you have a SWCG it is recommended that you run it during daylight hours to keep the chlorine level up. If you have different electric rates run it when the rates are cheaper.
I would suggest that you run the filter at the time of day that you test and add chemicals. This allows for the ater to mix well which makes more accurate testing and also allows for chemical addtions to mix well in the water after you have added them. You shouldn't add chemicals or draw samples from the water with your pump off.
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