initializeOutputFile

tells the output groups to initialize themselves in the NetCDF file

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Discussion

One noteworthy piece of logic handle by this function: we want all files to able to re-initialize the model, so we make sure that the NetCDFFile has all the required properties of the transform. However, we are writing time series data, so we need to exclude t. Additionally, if we happen to also be writing the wave-vortex coefficients, we can neglect writing those to file.