Input and output indices convention

[ChenZhao44]

Avoid using the first 2n indices for inputs and outputs as a pattern.

[exAClior]

I added commit dc3a3aa430cc210fbaa39e509bbf6554cf1680b2 for accessing the index in multigraph that represents output and input for a certain qubit. It seemed safer. I don't see anywhere else where this problem appears.