For water hammer/slug loading, a Harmonic type analysis is not possible.
There can be two solutions:
1) Use the modal analysis data and keep the lowest natural frequency to around 4.0 Hz ( or any other pre-set value). The 4.0 Hz or any number that way opens a Pandora's box as there are no "technical proofs" that they are adequate ( or "inadequate"). These have been historally used by different consultancies with proven result in most cases.
2) Do a Response Spectrum or Time History analysis. I have found many analysts perform these w/o understanding what they are doing.That is to say ,you first need to understand the authenticity and correctness of data that is used and what these methods are with respetive limitations.
Always remember CAESAR II is a structural analysis program and a complex flow induced vibration analysis cannot be done with it.
There is a special brance of vibration analysis known as Inverse Problems, which can be used to correctly perform the vibration analysis. Unfortunately this area is very complex and there are no sofwtares which can be used for this purpose.You can get wealth of information on this subject in the internet.
Regards
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anindya