Iterative approaches to quantum computation are described. Incongruities in the behavior of the various individual elements in a quantum processor may be managed by establishing a set of equivalent configurations for the elements of the quantum processor. The quantum processor is programmed and operated using each equivalent configuration to determine a set of solutions. The solutions are evaluated to determine a preferred solution that best satisfies at least one criterion. Furthermore, thermodynamic effects from operating a quantum processor at non-absolute zero temperature can cause the ground state to be the most probable state into which the system will settle. By running multiple iterations the ground state may be identified as the state with the most frequent reoccurrences. Alternatively, the energy of each unique state may be calculated and the state that corresponds to the lowest energy may be returned as the solution to the problem.