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There are tons and tons of physics simulators for classical/large scale physics. I'm interested in a simulator in which you feed an input as atoms and positions and it simulates the evolution of the system. That is, it must form bonds, ions, and so on as would happen naturally. But it should be fast enough that I could be able to actually feed some huge materials into it (a full scale transistor, perhaps?) and it would be able to simulate it accurately and under reasonable times.
In other words, what I do not want is a system based on higher models such as fluid dynamics, heat transfer and so on. I want it to let those phenomena emerge.
I'm aware maybe what I am asking is too much, but is there anything at least close to it?