Atom's 3D visualization has a safeguard in place to prevent your system from running out of resources when using the plugin.
If you open many instances of Atom inside your DAW the plugin new instances will eventually open with the 3D Animation turned off.
To turn it on you'll need to delete some instances of Atom to free up some system resources, or turn of the Animation in other instances to achieve the same result.
if the animation is still off even using very few instances of Atom you might accidentally have the animation set to "off," in the menu. To check this click the top right gear icon of the Atom GUI, and ensure the Animation is set to "on."
Please note that if it was set to "off," you'll need to close the plugin and re-open it to see the animation once again.