Atom struture : opaque and Transparent

A solid has a network of ions and electrons fixed in a "lattice". Think of this as a network of balls connected to each other by springs. Because of this, they have what is known as "collective vibrational modes", often called phonons. These are quanta of lattice vibrations, similar to photons being the quanta of EM radiation. It is these vibrational modes that can absorb a photon. So when a photon encounters a solid, and it can interact with an available phonon mode (i.e. something similar to a resonance condition), this photon can be absorbed by the solid and then converted to heat (it is the energy of these vibrations or phonons that we commonly refer to as heat). The solid is then opaque to this particular photon (i.e. at that frequency). Now, unlike the atomic orbitals, the phonon spectrum can be broad and continuous over a large frequency range. That is why all materials have a "bandwidth" of transmission or absorption. The width here depends on how wide the phonon spectrum is.

On the other hand, if a photon has an energy beyond the phonon spectrum, then while it can still cause a disturbance of the lattice ions, the solid cannot sustain this vibration, because the phonon mode isn't available. This is similar to trying to oscillate something at a different frequency than the resonance frequency. So the lattice does not absorb this photon and it is re-emitted but with a very slight delay. This, naively, is the origin of the apparent slowdown of the light speed in the material. The emitted photon may encounter other lattice ions as it makes its way through the material and this accumulate the delay.

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Edit: Dammit Zz

Well, you also missed the most important message in that FAQ. :)

Moral of the story: the properties of a solid that we are familiar with have more to do with the "collective" behavior of a large number of atoms interacting with each other. In most cases, these do not reflect the properties of the individual, isolated atoms.

yeah i know its not the atom that makes the color, its the molecule