About the other two issues, they did occure in your initial test didn't they?
If you man coordinates of Fs then no and I have tested that on few computers.
No, I meant:
1.the results that concern the average storey displacements (and so the drifts) that still remain different between the "normal" and the "manual" way, even if finally the coordinates of F are the same for both cases (you had said in a previous reply that: "The average displacement of the story is the weighted displacement of the center of the gravity of the ceiling of the story where the weight is the mass of the surface elements of the ceiling therefore it does not depend of the columns from the above or below").
2. the results of modal analysis that are different between these cases.
For all 3 models the geometrical matrixes and stiffness matrixes are the same. The difference is caused by the small difference in mass matrixes due to definition of mass eccentricity. The 'addition' of nodal masses is done for 'slices' of the model as defined by created stories which influences the position of the center of gravity.
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O.k, so the occurred differences in the averaged displacements of stories (and thus the drifts) are not generated because of the difference in the collection (group) of nodes in each storey but (only) because of the caused difference in the coordinates of center of mass.
I tested the results of averaged displacements and drifts for the two cases (“normal” and “manual” definition of storey) according to a load case that doesn’t involve mass (i.e wind) and they were the same indeed.
My (personal) conclusion is that the user can do these kind of manipulations in the definition of stories and he can view the results as expected. All these explanations were useful to understand the way the program works in such cases.