Capacitance measurement have a lot of utility in ultrasonic transducer analysis. This is because it is highly repeatable, simple, and highlights the performance of the crystals.
Measure capacitance at a frequency much lower than resonance. Let's say, at least 10x lower than your lowest resonance frequency in your structure, the minimum being 1 kHz. Measuring capacitance at too low of a frequency will (sub 1kHz) may result in contributions from space charge rather than the desired contributor to polarization.
But be careful, there are acoustic resonances in your system that may be much lower than your resonance frequencies. These will alter your capacitance and drive the loss properties way up.
In order to decide the best frequency to use for single frequency capacitance measurements, perform a slow frequency sweep from 0.8 kHz to 15 kHz (or whatever range is LOW frequency for your application) with an impedance analyzer and look for a continuous or flat change in phase - this is a stable region without subliminal resonances. Choose a nice round frequency value for testing in this region. The best practice is either to use 1 kHz or 10 kHz.
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