Polymer systems are generally modeled by viscous damping, which adds a consideration of a velocity-dependent damping force. In the simplest case, a single degree of freedom system comprising a mass with a spring and dashpot in parallel (i.e. Kelvin-Voigt) the equation of motion for the system in free vibration is:
[tex]m\ddot{x} + c\dot{x} + kx = 0[/tex]
where m is the system mass, c the viscous damping coefficient and k the spring stiffness.
It's been found that damping in metallic systems is better explained by hysteretic damping, which considers a displacement-dependent force in phase with system's velocity. Here:
[tex]m\ddot{x} + k(1+i\eta)x = 0[/tex]
where [tex]\eta[/tex] is the hysteretic damping coefficient divided by the spring constant, or the ratio of hysteresis loss during a cycle.
An even better approach is to assume that damping is a mixture between the two models. This is known as a fractional damping model. All these relationships assume that damping is linear, and as a result is generally limited to small strains although there are corrections for non-linear behaviour too.
If your honeycomb were polymeric, then a viscous damping approach would be pretty good. But as it's aluminium, as mentioned you're probably better looking at the hysteretic model. A pretty simple method of doing that would be to take a solid phase sample of the honeycomb aluminium and test it in tension or compression through a series of cycles, and measure the hysteresis loss per cycle (i.e. the difference between loading and unloading curves).
With a little bit of consideration, you can plug it back into your equation of motion and see what happens.