Not all crystals are clear; many (probably most) are colored. Crystals are translucent (allow light to pass through them) due to the arrangement of their molecules in a crystalline form.
Crystals that are clear however are always formed under extreme heat and pressure. Adding these two elements to a specific group of molecules, like coal, forces them to realign themselves into orderly formations. This allows light to pass directly through, producing a transparent or translucent appearance, like a diamond in the case of coal. Less heat and less pressure causes stones to form into less impressive crystalline formations.
By no means are all clear crystals formed under extreme heat and pressure. Calcite and gypsum are two minerals that often form clear crystals formed at or near the earth’s surface and without especially high temperatures and pressures.
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