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Coupling Copernicus Ocean data products (OPA-NEMO)

Hello, everyone,
I'm trying to couple a hydrodynamic model from marine.copernicus.eu to ICHTHYOP. Specifically OGCM (Ocean General Circulation Model) and MEDSEA_REANALYSIS_PHYS_006_004 product. The codes are NEMO-OPA version 3.2 and 3.4. The files are freely access and avalaible from marine.copernicus.eu. The commnon pattern filename is "sv03-med-ingv-cur-rean-d". At the end, I attach the basic information of one of these files.
I've tried coupling the models without success. I get some error messages in the NetBeans console, which I copy here. I also provide the necessary files to reproduce the error message.
So, What is the correct way to couple Copernicus' OPA NEMO with ICHTHYOP? Can someone provide a generic configuration file to manage the hydrodynamic dataset and that it is correctly associated with the hydrodynamic file and the grid/mask? 
Many thanks in advance,
Dr. Andres Ospina-Alvarez
 
NEMO_hydrodynamic_file (64,4 Mb)

The vertical grids are described in the file: MEDmeshmask_SYS4e_T.nc. This file is freely available via HTTP at this link http://gnoodap.bo.ingv.it/myocean/MEDmeshmask_SYS4e_T.nc.gz. The relevant variables described in MEDmeshmask_SYS4e_T.nc file are:

  • - tmask (3D land/sea mask);
  • - Depthlevt (3D matrix with the depth of each grid point taking into account the partial steps)
  • - e3t (3D matrix with the Δz of each grid point, taking into account the partial steps)
    netcdf MEDmeshmask_SYS4e_T { dimensions:
    x = 821 ;
    y = 253 ;
    z = 72 ;
    t = UNLIMITED ; // (1 currently)
    variables:
    floatnav_lon(y, x) ; floatnav_lat(y, x) ; floatnav_lev(z) ; doubletime_counter(t) ; bytetmask(t, z, y, x) ; floatglamt(t, y, x) ; floatgphit(t, y, x) ; double e1t(t, y, x) ; double e2t(t, y, x) ; doubleff(t, y, x) ; shortmbathy(t, y, x) ; doublehdept(t, y, x) ; double e3t(t, z, y, x) ; double gdept_0(t, z) ; double e3t_0(t, z) ; doubleDepthlevt(t, z, y, x) ;

// global attributes: :DOMAIN_number_total = 1 ;
:DOMAIN_number = 0 ; :DOMAIN_dimensions_ids = 1, 2 ; :DOMAIN_size_global = 821, 253 ; :DOMAIN_size_local = 821, 253 ; :DOMAIN_position_first = 1, 1 ; :DOMAIN_position_last = 821, 253 ; :DOMAIN_halo_size_start = 0, 0 ; :DOMAIN_halo_size_end = 0, 0 ; :DOMAIN_type = "BOX" ;
}

 

Ichthyop version: 
Ichthyop 3.3alpha
Hydrodynamic dataset: 
NEMO3D - MEDSEA_REANALYSIS_PHYS_006_004
Java version: 
Java SE 8
Operating system: 
Mac OS X

Hi

I can't download the MEDmeshmask_SYS4e_T.nc file from the URL you provided.

Nicolas

And I also need the zone files please (I found the mesh file somewhere else)

 

I updated the previous post with the link to download the grid/mask file and the release zones file.
Thanks in advance.

Hi Nicolas and Andres,
I step in here because my question is directly related to the subject,
I am also using file from Copernicus : http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw&view=details&product_id=GLOBAL_REANALYSIS_PHY_001_030
I have been running Ichthyop several times but with ROMS or MARS3D models and it is my first time using NEMO outuputs, would it be possible to get some more information about what this mask, zgr and hgr files are doing and where to find them? is using the one shared in this post would make sense?
Thanks
Boris

Hi Andres

Your problem is due to a wrong definition of the gridU file pattern parameter. It uses the grid file instead of the data file. You must modify its value to sv03-med*.nc.

However, I could not check since the mesh file I have contains 72 vertical levels, while the data file has only 47 vertical levels.

Nicolas

Hi Boris.

The mask, mesh_hgr and mesh_zgr contains some informations about the NEMO grid, which may be irregular.

The mask file contains the land-sea mask for T/U/V points, the mesh_hgr contains some informations about the 2D structure of the grid (zonal and meridional extents of the cells, longitude, latitude), the mesh_zgr contains some informations about the vertical structure of the grid (thickness of the cells, depth of the cells, etc.)

In some cases, all these files are merged together in one file, which is the case in the MEDmeshmask_SYS4e_T.nc file.

Nicolas

Hi Nicolas, thanks for fast reply,
do you usually get this file with the model outputs? is it something that I should ask from the people who run the model or can I create it myself?
thanks
Boris

Hi Boris.

You cannot generate this file yourself. Usually, this file is generated by the NEMO model and should be provided with model outputs.

Nicolas

ok thanks,
In case someone else is looking for these files,
they can can be dowloaded directly from Copernicus website (nameofthedataset-statics)
Boris