Hi Taiko,
I will (partly) skip the first part of your message and let others reply on that, as I don't have experience with NS simulations.
Regarding the gravitational wave extraction, I think you are accessing the data correctly (your example gives the time series for one mode at one radius), and there should be more than one element in general. From your parameter file, it seems the output should go to an ascii file (it's the default), so you can double check in that file too.
However, since you have `Multipole::out_every = 128`, does your simulation reach iteration 128 and later? In particular, because you're getting nans at iteration 0, does the simulation actually go past t=0? Given what you're saying, I guess your single element of `SimDir.gws[100][(2,2)].x` is 0 (i.e t=0).
Best,
Jordan
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Taiki Makino
Graduate School of Science, Nagoya University
makino.taiki.g6@s.mail.nagoya-u.ac.jp