How to use two boundary conditions file in croco.in

biogeochemistry
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1

I generated boundary file for hydrodynamics and biology separately. As in the croco.in I cannot define two boundary file as it reads only the file one. What is the way to define two boundary files in croco.in. Anybody who is working can help me solve this issue.

2

Also suggestion if any on adding the boundary for biology directly into croco_bry.nc (for running inter-annual runs boundary downloaded from CMEMS) are welcome. Tried and spent lot of time but unsuccessful.

3

Hi,

For now it is not possible :

  • to use 2 differents bry file for hydro and biology
  • to use a different time axis for u,v,ubar,T,S and ssh and biology

For your case you can first try to merge the hydro and biology bry files into the same one (considering you have the same time axis). We plan to upgrade that into the code.
Cheers,
Gildas

4

Thank you Gildas,
I merged the bry files (but just appending biological parameters to the physical boundary file using ferret) but while running the model the model reads only the physical parameters and it is not reading biological parameters saying “GET_BRY_BIO - unable to find variable: NO3” even though the variable is present in the file. Initial conditions file has no problem in merging, it works absolutely fine. But boundary file I could not successfully merge and run the model. Any suggestion, thanks in advance.

5

Can you upload the ncdump output of your bry file?

6

Hi,

  • did you activate the cppkeys BIOLOGY
  • do you have the NO3 var in your bry file (OBC).
  • as say Andres, could send us a ncdump -h of the bry file and the cppkeys you are using ?

Gildas

7

I am attaching the ncdump -h of croco_bry file, croco simulation log file and the cppkeys I am using. I am studying upwelling along the coastal regions of Bay of Bengal with nutrient component. Thank you. ncdump_read croco.log cppkeys

8

I noticed two things from your ncdump output

  1. NO3_TIME = UNLIMITED ; // (35 currently)
    NO3 time as a RECORD variable, probable a harmless issue

  2. It is NO3_TIME, and not NO3_time. And the same with O2_WEST, which should be O2_west (same for all the BGQ variables)

Not sure if this is the problem, but try renaming the variables, at least, to lower case.

Mines look like this:

    double ZOO_north(zoo_time, s_rho, xi_rho) ;
            ZOO_north:long_name = "northern boundary ZOO" ;
            ZOO_north:units = "mMol N m-3" ;
    double ZOO_south(zoo_time, s_rho, xi_rho) ;
            ZOO_south:long_name = "southern boundary ZOO" ;
            ZOO_south:units = "mMol N m-3" ;
    double ZOO_west(zoo_time, s_rho, eta_rho) ;
            ZOO_west:long_name = "western boundary ZOO" ;
            ZOO_west:units = "mMol N m-3" ;
    double bry_time(bry_time) ;
            bry_time:long_name = "time for boundary climatology" ;
            bry_time:units = "day" ;
            bry_time:calendar = "360.0 days in every year" ;
            bry_time:cycle_length = 360. ;
    double chla_time(chla_time) ;
            chla_time:long_name = "time for CHLA climatology" ;
            chla_time:units = "day" ;
            chla_time:cycle_length = 360. ;
    double hc(one) ;
            hc:long_name = "S-coordinate parameter, critical depth" ;
            hc:units = "meter" ;
    double no3_time(no3_time) ;
            no3_time:long_name = "time for NO3 climatology" ;
            no3_time:units = "day" ;

Hope this helps.

Andres

9

Yes it really works, thank you sir. A big help to me.