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Different minerals may have the same composition but different structures. These are called "polymorphs", and in this case, the arrangement depends upon the composition; that is, which atoms are involved and also the temperature and pressure at the time of formation of a particular mineral.

For example, there are several different varieties of silica. Silica is silicon dioxide. The most common is quartz, but there are other varieties that are formed at high pressures, and, in fact, some of these, the mineral called coesite, for example, has been identified in impact craters where meteorites smashed into the Earth, and this quartz in the rocks was reformed into a different crystal structure to form the new mineral called "coesite". Even ice, which we're all familiar with, has many different structures. The most common, of course, is the one that you find in your freezer, but under different conditions of temperature and pressure, ice can actually form several different crystal structures.

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Coesite Index
Lamproite

 

Coesite as a Quartz Polymorph

 

Above: Quartz
Top Left: Coesite
Left:Coesite Structure

Bottom: Quartz Structure