In the case that I have CPT data, when calculating total and effective stress, should I be taking u=9.81*z or u=u2 (pore water pressure from CPT)?
You should be looking at the pore pressure dissipation tests. Then calculating u=9.81 x z. If there are downward or upward gradients the dissipation tests completed at multiple depths and in all strata should estimate the phreatic surface throughout the profile.
The pore pressure measurements during penetration is an indication of whether the material will generate positive or negative pore pressures during compression shearing.
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