  We theoretically investigate protocols based on optimal control theory (OCT)
for manipulating Bose-Einstein condensates in magnetic microtraps, using the
framework of the Gross-Pitaevskii equation. In our approach we explicitly
account for filter functions that distort the computed optimal control, a
situation inherent to many experimental OCT implementations. We apply our
scheme to the shakeup process of a condensate from the ground to the first
excited state, following a recent experimental and theoretical study, and
demonstrate that the fidelity of OCT protocols is not significantly
deteriorated by typical filters.
