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I would like to learn how different components of the Ethereum protocol are calculated. Where can see how these and other elements?

Is there a code database that a final code source that I can refer to?

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The full specification of the EVM can be found in the Yellow Paper.

The Ethereum ecosystem has many client implementations of the Yellow Paper. The most widely used client is probably Geth (this video is a good introduction to their codebase). Further there exists an execution client specs written in Python.

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