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Yes, the problem certainly seems to have something to do with the vertical velocity field, since it only occurs with method 0. But at the same time it is very specific to trajectories re-entering from a lower resolution domain to a higher resolution domain. I have run thousands trajectories with this setup and this only happens for trajectories re-entering a higher resolution domain. This leads me to think that there might be something wrong with how the code treats vertical velocity fields in those cases. If there was something more generally wrong with the vertical velocities in the met data files, I would have expected it to show up in a lot of other cases too. If the vertical velocity fields in the met data files were wrong specifically in the domain edges, I would have expected it to show up much more frequently for trajectories exiting a higher resolution domain.