@Sage_Rat, the balls-and-springs picture @Chronos described is the correct one. If you want to introduce another layer of complexity to this picture, thinking about phonons is jumping the gun. You first need to understand collective behavior – vibrational “modes”.
If we work in 2D for visualization simplicity, first imagine four unmovable objects (X) supporting a movable object (O) with identical, suitably stiff springs to keep the movable object fairly close to its home, like this:
X
|
X---O---X
|
X
(Aside: Ignore the italics in that diagram. The dashes apparently do that, which I do not want in “preformatted” text. Oh well.)
The “O” in the middle can jiggle up and down, and it can jiggle side to side, and it can do both at the same time. If it does both at the same time, it might follow a diagonal path if the up/down oscillation and the left/right oscillation are in perfect phase with one another, or it might follow an elliptical path if they aren’t. Stop me here if you want more details on this part. Else…
Now imagine that the immovable objects are themselves other movable objects connected by springs to yet more movable objects, forming a huge lattice extending in all directions:
| | | | |
--O---O---O---O---O--
| | | | |
--O---O---O---O---O--
| | | | |
--O---O---O---O---O--
| | | | |
--O---O---O---O---O--
| | | | |
Now if we look at a single object (atom) in this lattice, it sort of follows the same rules as before, except how compressed or stretched its springs are depends on what the four neighbors are up to. If those neighbors happen to be currently vibrated/displaced up and to the right, then our atom stuck in between them will be pulled that way. Or flipping the story, if our current atom vibrates right, the atoms around it will feel a push or pull from that.
So, the atoms are all still just vibrating around their little home, but the precise motion is made more complicated due to the interconnection throughout the lattice.
So looking at a single atom could lead to very complex motion given the connection to all the neighbors (and the neighbors’ neighbors, etc.), but zooming out to look at the entire lattice as a whole leads to a dramatical simplification. When you have a collection of things that individually behave in a sinusoidal way (i.e., simple oscillations), the collective behavior throughout the whole system also exhibits sinusoidal behavior, but at a macro level and with a set of system-specific frequencies possible. A 1D picture of oscillation “modes” in a vibrating string is here at Wikipedia and gives you something to visualize.
The remarkable simplification is that each mode (“harmonic”, “overtone”, whatever you want to call it) can be thought of as a separate thing now. And they can – and typically do – co-exist. You can have some vibration in mode number 17 and some vibration in mode number 138 and some vibration in mode number 2 – all at the same time. On the one hand, this is just a relabeling of the same complicated motion we would see examining individual atoms. On the other hand, since the modes each have a set frequency and spatial pattern, they provide the more relevant picture for connecting the interior motion to the outside world.
Stop me here if useful. Else…
All that is a prerequisite to worrying about phonons. In short, when you examine all this with atoms or molecules – for which quantum mechanics is relevant – you still get these oscillation modes at certain frequencies, but those modes become quantized. You can’t have arbitrary energy stored in mode number 138 or 72. You can only have discrete levels of energy. And those discrete, quantum mechanical excitations of the lattice are phonons.
I hope I have shown that phonons aren’t really a direct answer to the question “How does an atom move?” Side note: I introduced quantum mechanics only at the end, but it affects even the first “single atom” picture. I just skipped quantizing that part of the story.
In summary:
An atom is bound to its neighbors and moves in approximately a sinusoidal way in all allowed directions, and in doing so can follow various elliptical paths, except all that is subject to quantum mechanical caveats. Also, the atom’s neighbors all do the same, and thus an individual atom’s motion is made much messier by the collective behavior of all the atoms. But, that messiness can be abstracted away by thinking about vibrations across the entire lattice. Those macro vibrations have a clean interpretation as vibrational modes with specific frequencies and spatial patterns, and those are also subject to quantization, and those quantized modes are called phonons.
Unrelated to the above, but note that time crystals require a periodic perturbation (e.g., an incoming light wave). So, these aren’t standalone crystals that oscillate their structure spontaneously with time. However, in the static presence of a dynamic (and periodic) perturbation, they take on crystal properties in the time dimension.