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The first models of atoms were made by Ancient Greeks entirely based on guesswork. They were wildly wrong.

Today's models are confirmed by important tests that can show things that we cannot see by examining things that we can see. Imagine you are standing in a park and you see a very long shadow that is boxy. You then look at your shadow and see that it conforms relatively to your body, but is only half as tall as you are. You can reasonably confirm that the object casting the long shadow is also twice as tall as its shadow is very likely rectangular in shape. You do not have to turn around and see that it is a tower for you to know that it is a tower by the shadow it creates.

Some methods of verifying atomic models include: radiation testing, mass and light spectroscopy, creation of plasmas and Bose-Einstein condensates, the Theory of Relativity, particle-wave duality proofs, harmonic resonance, etc.

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