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Natural Frequency of a Noncomposite Floor System

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I am trying to calculate the natural frequency of an existing floor system and though I've read through the appropriate portions of Design Guide 11, I'm still having a little trouble understanding a few things.

 

There is a line in the Design Guide that states that the transformed section properties are to be used if the deck is attached to the supporting beams, regardless of whether or not shear connectors are used.  The natural frequency of the beam is then estimated based upon the composite beam deflection under dead load and vibration loading.  So am I to assume that the full composite section properties (using 1.35x Ec, ...) should be used in calculating deflection, also?  My software package seems to disagree with me on that point, but then it offers no explanation as to why not.  

 

I think the actual initial deflection of the beam would be based upon the bare beam section for the weight of the beam+slab, and then possibly based upon the composite section for the equipment load.  Is it correct to look at the actual deflection in considering the natural frequency?  If so, wouldn't it be based only on the equipment load, and not on the dead load + equipment load? 

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