The Crystalarium will replicate any inserted gem or mineral except Prismatic Shards. (In the Museum there is a book that states: "For some reason, the EMF from the shard interacts negatively with the crystalarium"). Once inserted, it will replicate that item an infinite number of times. Once a gem or mineral has been inserted into the Crystalarium it cannot be removed, only replaced with another. The original item is lost and so it is best to let it finish at least once to avoid loss.
No one knows how these form. Some scientists claim that the microscopic structure displays unnatural regularity.
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Trivia
The most profitable gem to grow for money is Diamond at 150 gold per day assuming the player harvests the gem as soon as it is ready (5 days).
A strong second contender is a gold star-quality Fire Quartz, which sells for 150 gold and takes only 22 hours to grow, ensuring that the player will be able to harvest a new Fire Quartz at the same time each day.
Putting Quartz in several Crystalariums is one of the most efficient ways to obtain Refined Quartz, due to it only taking 7 hours to produce.