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The goal of the work is to describe the method to determine an orthonormalized basis of Josephson flux quantum bit (qubit) states under two-level approximation for systems with double-well potential. This basis was used to calculate qubit`s Hamiltonian matrix, thus allowing to verify all calculation procedures correctness by comparison of our results with other works. The calculations were carried out both for well-known three-junction and four-junction flux qubits and for perspective silent qubits. Out results for Hamiltonian matrix allow to explore qubit dynamics during logic operations, including the case of the so-called remagnetization (NOT-gate), on the picoseconds timescale.