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SImple rigidbody physics - stacking

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I am developing a little simple rigidbody physics engine just for fun and I ran into a problem. It runs rather fast when I add small amount of objects (I use just while and for loops in my code and I check if rigidbody was simulated or not), but when I create a pyramid (or whatever where bodies are on each other) it runs slow, because onto every object gravity and reaction force is added. Thus a little move of any object in pyramid will result in huge iteration of all objects in pyramid. I see some engines (like Tomakak) uses a little trick - stacking. I would like to implement that too, but I can't find any suitable tutorial for it. Can somebody help me to discover how does this work and how to implement it?

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