Among them are the proper chemicals, heat, pressure, time and space. An aggregate will look much like an amorphous material, but internally it is composed of thousands of microscopic crystals. The most common example of this is the chalcedony family, which contains agates and jaspers. These are all members of the quartz family, so they have many characteristics in common. They will have the same density and same refractive index as a whole crystal of quartz, but considerably different appearance.
Rocks are a mixture of minerals, where crystals and amorphous materials have a single ingredient.
While not a gem material, granite is one of the most common and best known rocks. In the gem world lapis lazuli is the best known rock. Now we are getting into the heart of how gems are classified. The vast majority of gems are minerals. Chemical makeup refers to the atoms the mineral is composed of.