HA! I think I know what it is: the ML guide on p 16 says in footnote 11: "Note that the hierarchy produced by ReComputePreconditioner() can differ from that produced by ComputePreconditioner() for non-zero threshold values." So when the matrix changes too much, the const double aggregation_threshold in PreconditionAMG::AdditionalData would lead to different matrix entries being considered. That is why it was also working for (constant) Laplace and (almost constant Hyper-) Elasticity, but not so well for Navier-Stokes, since I initialized the AMG in the first timestep, where convective terms are completely zero starting from the quiescent state. Hope someone finds this in the future and updates their AMG every few timesteps as well! Best Richard
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