The control of CGI for film is vital for artists seeking to achieve accurate and realistic motion.
Animation used to be a matter of frame by frame capture, 3D modeling and animation aplications can "tween" and plot paths for objects according to a vast range of variable inputs available.
So I'll go through the methods of input involved for digital animation of effects and general CGI
Manual keyframe input - this kind of process is my level of understanding at the moment, I am able to animate models in 3D through manual input, telling the program at what point in time and at what rate certain models should have their attributes modified, this can be anything from movement to a specific effect. The software will then tween the values and through a gradient/rate of your choice will integrate movement between the points in time identified.

Motion capture (wiki link) - This process can be carried out in a few different ways and has advanced considerably through time, here is an example of a non-optical process shown in this video:
I was very interested to find out that technology now permits 3D motion to be captured just using a small array of cameras (even just 2) to interpret and record motion.
Simulation and Generation - This method can be used for particle based simulations and other large character group animations for example swarms of birds or bees ect. (wiki)
A good example you may not have seen which involves computer generated animation:

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