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Restart does not take into account initial topography of the mesh. #3254
When restarting a model that had initial topography added to the mesh, this topography is not taken into account and thus you'll have a different mesh upon restart. See the figure of a model with an initial hill that is or is not restarted at the second timestep. I have a PR coming up to remedy this that adds the initial topography to the stored mesh displacements.