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Response: The reactions include the effects of only elastic (or inelastic) forces unless links are connected at the joints in which case the damping forces from links are also included in computing the joint reactions.

What value should I set for output time-step size for time history analysis?

The output time-step size should be small enough to provide sufficient resolution for the analysis. The required resolution depends on the characteristic of applied loading and also on the characteristics (such as natural periods) of the structure itself. You can determine whether the resolution is sufficient by decreasing the time-step size until the step size is small enough that results are not longer affected by it.

What time-step size should be set for input acceleration record? And what time-step size should be set for input displacement record?

Extended Question: Say that the analysis resolution requires 0.005 sec output time-step size. What time-step size should be used for input acceleration record and what time-step size should be used for input displacement record?

Answer: The output time-step size should be small enough to provide sufficient resolution for the analysis. The required resolution depends on the characteristic of applied loading and also on the characteristics (such as natural periods) of the structure itself. You can determine whether the resolution is sufficient by decreasing the time-step size until the step size is small enough that results are not longer affected by it.