crystal sim

 
Crystals are formed when atoms and molecules arrange themselves in patterns. You can set up a demonstration which shows a similar situation. Place several hundred BBs on a flat surface which has a raised edge that holds the BBs from rolling away. The underside of a paint can lid is ideal. The top of a cottage cheese container will do. Shake the surface slightly and the BBs will align themselves in rows.
 
The rows tend to be very orderly and symmetrical.
 
But several interesting imperfections can occur just as imperfections occur in real crystals. Holes can occur where one or more BBs are missing. There can be sections which are correctly arranged but the boundaries between sections contain misaligned BBs. BBs of different size, shape or composition could be put into the pattern in place of regular BBs. This corresponds to an impurity in a crystal. It is impurities which give color and other desirable characteristics to some natural and manmade crystals such as gems and semiconductors.