This phenomenon is called supercooling
To form an ice crystal the water require nucleation, something to kick start the ice forming process. This can be the water itself moving, or impurities in the water like minerals can also do that.
Because the water in your bottle is relatively pure, and the bottle is stagnant (water isn’t moving) under certain conditions the water in the bottle can cool to below the freezing point of water. This is called supercooling.
When you agitate the bottle it causes water crystals (ice) to form instantaneously
If you drink beer, this can happen quite often. You put your beer in the freezer. Take them out expecting to have a very cold beer: pour in the glass and it just turns into gooey ice. The higher than normal pressure inside the bottle lowers the freezing point. As soon as it’s in the glass under normal atmospheric pressure, it freezes.
Fun science experiment: if you want a soda slushy. Take a bottle of soda (bottle with a screw cap, not a can). Shake it up for 10-15 secs. Put it in the freezer for an hour and then pour into a glass. It will still be liquid in the bottle, but will freeze as you pour it.
The pressure in the bottle after shaking it stops it from Freezing for a short time, but it will freeze as it’s poured.
When water becomes ice, it forms crystals. These ice crystals are like any other crystal and can’t just grow anywhere, but instead require a so called “nucleation” point. This can be a tiny little particle or some other activity within the water (in this case). Ice will then form from said nucleation point.
With your bottle, it was below freezing point, but had no nucleation point and thus no ice. This is called super freezing. The way you removed it from the freezer caused a disturbance which resulted in the nucleation point being at the top of the bottle. From there on our all the water formed crystals towards the bottom.
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