The method uses the following contributions for the different atoms:

These include missing or different (foreign) atoms, oxides, insulators and even stresses within the crystal.

In molecules the free electrons can reside on one atom or on different atoms.

Although the two beams are at the same frequency, they address different atoms due to natural thermal motion.

Hydrogen bonding between different atoms provides the force required.

The different atoms are joined by chemical bonds.

Could it be because of the rocks in the bottom being different and one rock attracting a different atom than another rock?

In nuclear burning, the atoms themselves are combined to create new and different atoms.

It was not long before the fusion of two different atoms was taking place beneath the surface of the planet.

When different atoms combine, they make something totally new with new properties and perhaps a new phase.