Removed obsolete option NUDGING_SSH

[arango]

The issue of nudging free-surface, as an assimilation option NUDGING_SSH, has come-up several times in the ROMS forum. This option is very old and part of the legacy code. I am cleaning this option because it doesn't make sense within ROMS kernel. I tried this many years ago and it was not a good idea because it affected the volume and mass conservation. The nudging scales are very difficult since we need to constraint the free-surface at every barotropic time-step. If you change zeta during nudging, you need to change ubar and vbar accordingly. Then, the very direct (and best) problem is to constrain (nudge) only ubar and vbar.

However, the assimilation of SSH (altimetry) is possible in ROMS via OI or 4D-Var. The OI is intermittent and not part of the time-step and forces a cold start. This allows such assimilation to be consistent with ROMS governing equations and its discretization. In 4D-Var everything is consistent with the adjoint-based increment (adjustment). Notice that in 4D-Var we cannot assimilate ubar and vbar. Everything has to be done in terms of u and v. Then, the ubar and vbar are computed by the vertical integral of the estimated u an v. This implies that we need to be very careful with the assimilation strategy and ROMS kernel.

In ROMS, the free-surface (zeta) is is an statement of the vertical integrated continuity equation, which is a function of the vertically integrated velocity (ubar, vbar) divergence. That is, ubar and vbar are the real prognostic variables in ROMS. The free-surface zeta is kind of a diagnostic quantity since it is computed from the vertically integrated continuity equation. Any change in zeta at every time-step needs to be consistent with changes in ubar and vbar.

[arango]

I also updated the file Data/ROMS/forcing/bio_toy_frc.nc. I just forgot to update the version of this file in the other repositories. The version in my branch was up to date. The change is the time-coordinate to allow time cycling.