Disclosing the structure of disks surrounding Herbig AeBe stars is important to expand our understanding of the formation and early evolution of stars and planets. We aim at revealing the sub-AU disk structure around the 10 Myr old Herbig Be star HD100546 and at investigating the origin of its near and mid-infrared excess. We used AMBER/VLTI observations to resolve the K-band emission and to constrain the location and composition of the hot dust in the innermost disk. Combining AMBER observations with photometric and MIDI/VLTI measurements from the litterature, we revisit the disk geometry using a passive disk model based on 3D radiative transfer. We propose a model that includes a tenuous inner disk made of micron-sized dust grains, a gap, and a massive optically thick outer disk, that successfully reproduces the interferometric data and the SED. We locate the bulk of the K-band emission at ~0.26 AU. Assuming that this emission originates from silicate, we show that micron-sized grains are required to enable the dust to survive at such a distance from the star. As a consequence, more than 40% of the K-band flux is related to scattering, showing that direct thermal emission is not sufficient to explain the near-infrared excess. In the massive outer disk, large grains in the mid-plane are responsible for the mm emission while a surface layer of small grains allows the mid and far infrared excesses to be reproduced. Such vertical structure may be an evidence for sedimentation. The observations are consistent with a model that includes a gap until ~13 AU and a total dust mass of ~0.008 lunar mass inside it. These values together with the derived scale height (~2.5 AU) and temperature (~220 K) at the inner edge of the outer disk (r=13 AU), are consistent with recent CO observations.
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