How often to flood (flood frequency) is determined by three factors.
1.How long it takes for the plants to show drooping or wilting between floods.
2.How large the planter of rocks is (wether or not the roots are drying out too much).
3.The dryness of the root mat in the tray outside of the planters must also be considered, you cannot allow it to get too dried out between floods.
A good rule of thumb, with expanded clay in planters is to begin with floods every four hours while the lights are on and watch the plants for any signs of wilting just before the next flood. If 4 hours between floods causes the plants to droop, than shorten the time between floods by a half hour to 3-1/2.
As the plants grow larger, a mat of roots will grow out of the planters, onto the tray between the planters. The floods should be often enough to keep this root mat from becoming too dried out between floods, including the long dry spell overnight during the 12/12 flowering stage. You should monitor the condition of the root mat to make sure the roots stay semi-moist.
A good way to check this is to have the first flood start a few minutes after the lights come on, if the roots are dry before the first flood, you will need to have one fast flood at night. Otherwise the drying can cause stunted growth and reduced yield.
Keeping the tray covered with plastic wrap will help keep the root mat moist and help to slow down evaporation, thus preventing the need for a night flood and helping to keep the rooms relative humidity controlled.
A better solution is to build a cover plate for the tray which holds the planters slightly suspended above the tray to encourage a thick and healthy root mat growing in the tray, which will also cure the problem of roots getting too dry overnight.
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Remember to check the trays drains often to make sure they're not getting clogged by roots or loose medium (small grow rocks).