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This problem is known to happen when one cannot collect the entire transmitted or reflected pulses before the reflection of itself comes back to spoil the data. It can be avoided by either using longer waveguides to delay such reflection or employ a better absorbing boundary condition to eliminate the reflection, both of which are technically challenging. From our experience, if we were able to eliminate this technical error, the "correct" value tends to converge to the average between the oscillation maxima and minima.
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