When you are in the near field such as a with a helix, the phase velocity is difficult to define as such since the fields vary drastically. So in a sense, the amplitude variation comes into play. However, as a first cut you simply take the total derivative of the transient phase with respect to both time and distance. You would likely have to do numerical derivatives with the results from CST. So you need to compute the phase versus time and distance, then take the numerical derivatives. If you were looking at the helix of a BWO or TWT, then you have a more complicated problem of including the effects of the electron beam.
Model one turn of helix and define the phase difference between two end cross-sectional plane as variable, e.g. 20 - 180 deg, solve this model as eigen value problem, store the frequency (f) data for each phase difference in radian (Theta).
Theta=beta*pitch of the helix
where beta phase propagation constant
As for each frequency Theta is known, in other word beta is known (as per said formula)
you may calculate phase velocity
vp=omega/beta=2*pi*f / beta
This may not the be the answer you are looking for since it requires some processing outside CST. You could create a helix transmission line segment (the longer the better to reduce the edge effect) and connect ports at both its ends (this requires that you duplicate whatever feed mechanism you are using in a single-ended helix). Once you obtain the S11 and S21 parameters you can compute all the line parameters (characteristic impedance and complex propagation constant gamma = alpha + j beta) using the equations in the reference below. Finally you can obtain the phase velocity at every frequency using v_phase = 2*pi*frequency / beta.
[1] Eisenstadt, W.R.; Eo, Y., "S-parameter-based IC interconnect transmission line characterization," Components, Hybrids, and Manufacturing Technology, IEEE Transactions on , vol.15, no.4, pp.483,490, Aug 1992
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