I can't visualizate the motion of atoms? How can it be so weird? It can be weird, but it must follow a rule.
bp_psy, why? This is easy I guess? Planets orbiting: 3d spheres as planets, position vectors atracting themselves every tick following the laws of gravitation, initial conditions to match the centripetal equilibrium. Charges iterating: basically the same. I even did a color mapping stuff when I was trying to understand eletrodynamics. This also made me understand a little better how electrons could oscilatte though a nuclei without falling on it or needing circular motion (I still don't understand many things, though). Springs oscillating: once I made several small balls glued together by a force. Then I noticed it acted as a string. Then I suddenly understood how springs works. It was beautiful. I had no idea of what I was doing. As I said, it was nothing serious or precise, yet I'm sure it followed the intuitive principles. And was fun.