DOMcfg: improve reproducibility of the domcfg.nc

[mathiot]

Context

When you found a domaincfg.nc, it is difficult to know how it has been built and how to reproduce it. MEOM/DRAKKAR build a script to add a specific the namelist_cfg in it as netcdf variable and input file name as attribute. A script to generate the namelist from the domcfg.nc is also available.

Analysis

To partially fix this, namelist_cfg should be introduced in the domcfg.nc output file AND bathymetry, coordinate (...) files name used to generate the input file should be added to the namelist_cfg (default name being the one specified in namelist_ref of the domain_cfg).

Steps

• Introduced in the namelist the ability to use non generic name for coordinates, bathy, isf draft:

   cn_fcoord   =  'coordinates.nc'             ! external coordinates file (jphgr_msh = 0)
   cn_topo     =  'bathy_meter.nc           '  ! external topo file (nn_bathy =1/2)
   cn_topolvl  =  'bathy_level.nc           '  ! external topo file (nn_bathy =1) 
   cn_fisfd    =  'isf_draft_meter.nc'         ! external isf draft (nn_bathy =1 and ln_isfcav = .true.)
   cn_bath     =  'Bathymetry'                 ! topo name in file  (nn_bathy =1/2)
   cn_bathlvl  =  'Bathy_level'                ! lvl name in file   (nn_bathy =1) 
   cn_visfd    =  'isf_draft'                  ! isf draft variable (nn_bathy =1 and ln_isfcav = .true.)

• Add the sript to include the namelist_cfg.nc into the domcfg.nc netcdf:

  ./dom_doc.exe -h
    usage : dom_doc -n NAMELIST-file 
                          -d DOMAIN_CFG-file
         
        PURPOSE :
           Add information in the domain_cfg.nc file after its creation for
           NEMO4. The additional information consists in a new netcdf variable
           called namelist_cfg, holding the content of the used namelist_cfg.
         
        ARGUMENTS :
           -n NAMELIST-file : name of the namelist_cfg. file required
           -d DOMAIN_CFG-file : name of the domain_cfg file to document. file requ
   ired
         
        OUTPUT : 
            input DOMAIN_CFG-file is modified on output.
  

• Add the reverse script (ie to generate the namelist from the namelist_cfg netcdf variable):

  ./xtrac_namelist.bash domain_cfg.nc namelist_output
  (base) mathiotp@f-dahu:.../test_trunk$ cat namelist_output 
  !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
  !! NEMO/OCE :   Reference namelist_ref                                !!
  !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
  !! NEMO/OCE  :  1 - Domain & run manager (namrun, namcfg, namdom, namzgr, namzgr_sco )
  !!              8 - diagnostics      (namnc4)
  !!             10 - miscellaneous    (nammpp, namctl)
  !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
  !-----------------------------------------------------------------------
  &namrun        !   parameters of the run
  !-----------------------------------------------------------------------
  ...
  /
  !-----------------------------------------------------------------------
  &namdom        !   space and time domain (bathymetry, mesh, timestep)
  !-----------------------------------------------------------------------
     ln_read_cfg = .false.   !  Read from a domain_cfg file
     nn_bathy    =    1      !  compute analyticaly (=0) or read (=1) the bathymetry file
                             !  or compute (2) from external bathymetry
     nn_interp   =    1                          ! type of interpolation (nn_bathy =2)
     cn_domcfg   = ' '       ! Name of the domain_cfg input file
     cn_fcoord   =  'coordinates.nc'             ! external coordinates file (nn_bathy =2)
     cn_topo     =  'bathy_meter.nc'             ! external topo file (nn_bathy =2)
     cn_topolvl  =  'bathy_level.nc'             ! external topo file (nn_bathy =2)
     cn_fisfd    =  'isf_draft_meter.nc'         ! external isf draft (nn_bathy =2 and ln_isfcav = .true.)
     cn_bath     =  'Bathymetry_isf'             ! topo name in file  (nn_bathy =2)
     cn_visfd    =  'isf_draft'                  ! isf draft variable (nn_bathy =2 and ln_isfcav = .true.)
     cn_lon      =  'nav_lon'                    ! lon  name in file  (nn_bathy =2)
     cn_lat      =  'nav_lat'                    ! lat  name in file  (nn_bathy =2)
     rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
     nn_msh      =    1      !  create (=1) a mesh file or not (=0)
     rn_hmin     =   10.     !  min depth of the ocean (>0) or min number of ocean level (<0) (out of ice shelf cavity)
     rn_e3zps_min=   20.0     !  partial step thickness is set larger than the minimum of
     rn_e3zps_rat=    0.1    !  rn_e3zps_min and rn_e3zps_rat*e3t, with 0<rn_e3zps_rat<1
                             !
     rn_rdt      =  720.0    !  time step for the dynamics (and tracer if nn_acc=0)
     rn_atfp     =    0.1    !  asselin time filter parameter
     ln_crs      = .false.      !  Logical switch for coarsening module
     jphgr_msh   =       2               !  type of horizontal mesh
    ...
  

[mathiot]

In 13339:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[mathiot]

In 13345:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[davestorkey]

I had a go with this and it all seems to work for eORCA025.

[mathiot]

In 13390:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[mathiot]

In 13391:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[mathiot]

Thank you Dave for the external testing.