# Instructions for each experiments in the Protocol.

Please download: 
 IC.2016_032_00_3z.nc 
 IC.2016_032_00_ssh.nc
 netcdf_eddy_levels_1-60.tar.gz
 netcdf_eddy_levels.tar.gz
 Protocol_Eddy_experiments.docx 

Configuration description:
 Gulf of Mexico domain at 4km, with closed baoundaries and no atmospheric forcing
 HYCOM grid and bathymetry are provided in:
 netcdf_eddy_levels/netcdf_eddy_levels/regional.grid.gomb4.nc
 netcdf_eddy_levels/netcdf_eddy_levels/regional.depth.gomb4.closed.nc


REF: Each group should do a nature run of 3 months with their system to compare with the HYCOM nature run.
 - initial condition file: netcdf_eddy_levels/IC.2016_001_00_3z_eddy.nc
 - if you need a ssh to start with, take the ssh of day 1 of HYCOM nature run: netcdf_eddy_levels_1-60/archm.2016_001_12_ssh.nc
 - duration 3 months (day 1 to 91)

Exp 0: 1-month run starting from flat isopycnal assimilating HYCOM nature run day 61 to 91
 - initial condition file: netcdf_eddy_levels/IC.2016_001_00_3z_flat.nc
 - ssh=0 at the start of this simulation
 - obs: HYCOM nature run files day 61 to 91 sampled 1 out 10 points for bathy deeper than 300m: 
       from files netcdf_eddy_levels/archm.2016_061_12_ssh.nc and/or netcdf_eddy_levels/archm.2016_061_12_3z.nc 
       to files   netcdf_eddy_levels/archm.2016_091_12_ssh.nc and/or netcdf_eddy_levels/archm.2016_091_12_3z.nc depending on the obs you are assimilating.
 - duration 1 month/30 days
 - case 1: assimilation SSH+profiles, case 2: SSH only, case 3: profiles only

Exp 1: 1-month run starting from day 32 if HYCOM nature run and assimilating HYCOM nature run day 61 to 91
 - initial condition file: IC.2016_001_32_3z.nc  and IC.2016_001_32_ssh.nc if needed.
 - obs:HYCOM nature run files day 61 to 91 sampled 1 out 10 points for bathy deeper than 300m: 
       from files netcdf_eddy_levels/archm.2016_061_12_ssh.nc and/or netcdf_eddy_levels/archm.2016_061_12_3z.nc 
       to files   netcdf_eddy_levels/archm.2016_091_12_ssh.nc and/or netcdf_eddy_levels/archm.2016_091_12_3z.nc depending on the obs you are assimilating.
 - duration 1 month/30 days
 - case 1: assimilation SSH+profiles, case 2: SSH only, case 3: profiles only

Exp 2: 3-months run starting from Day 1 of HYCOM nature run and assimilating Day 1 to 91 of HYCOM nature run
 - initial condition file: netcdf_eddy_levels/IC.2016_001_00_3z_eddy.nc
 - if you need a ssh to start with, take the ssh of day 1 of HYCOM nature run: netcdf_eddy_levels_1-60/archm.2016_001_12_ssh.nc
 - obs: HYCOM nature run files from Day 1 to 91 sampled 1 out 10 points for bathy deeper than 300m:
       from files netcdf_eddy_levels_1-60/ archm.2016_001_12_ssh.nc to netcdf_eddy_levels/ archm.2016_091_12_ssh.nc
 - duration 3 months (day 1 to 91)
 - assimilation: SSH only


Frequency of the outputs: 
 - Daily means 
 - Hourly snapshots

Data to provide (as of 11/8/2024):
 For spurious internal wave part:
 - 3-D Hourly netcdf data (u, v, density/pressure anomaly) from Exp 0 with SSH only - on native grid with information of the vertical grid.
 For eddy evolution part:
 - Bathymetry/grid  (if changed)
 - 3-D Daily means netcdf data (T,S,u,v,SSH) on a z-cood grid (80 levels from HYCOM netcdf files) of Exp 0 with SSH+prof, SSH only and prof only
 - 3-D Daily means netcdf data (T,S,u,v,SSH) on a z-cood grid (80 levels from HYCOM netcdf files) of Exp 1 with SSH only