Data Flow
Atoms computes all the simulation outside any 3D application. Maya, Houdini and Unreal send data to Atoms which is then used for initializing and modifying the simulation, Atoms then displays the simulated characters in OpenGL or using Unreal render interface. There's no actual live geometry in the viewport at any time.
Usually the user will export assets from his favorite 3D package (i.e. character definitions, clips, etc.), Atoms will use those during the simulation. The user will then be able to export the simulation in Atoms Caches. Atoms Caches are useful for speeding up the your levels, you might also re-simulate on top of them.
Core
Atoms can handle more than one Agent Simulation at the same time, but typically you will have only one running on your 3D application.
An Agent Simulation contains a set of Agent groups and Simulation events of different types. They all contain methods that will get triggered at different stages of the simulation.
Each Agent group contains a list of agents, while each agent has a independent dependency graph computing its pose at every frame.
