VERY IMPORTANT: Several Improvements

[arango]

This update included several enhancements:

• All the roms_*.in standard input scripts were modified to include Nsaddle parameter as the number of kernel trajectory intervals for the solution of the Saddle-Point 4D-Var (SP4DVAR). It is used to accelerate 4D-Var by parallelizing the inner loops in time. The tangent linear and adjoint models are time-stepped concurrently over short integration windows.

  ! Model iteration loops parameters.
  
         ERstr =  1
         ERend =  1
        Nouter =  1
  
        Ninner =  1
       Nsaddle =  1
    Nintervals =  1
  

• All the roms_*.in standard input scripts were modified to allow the lateral boundary conditions and climatological variables to be separate in different files, similar to the surface forcing files. For Example, the User may have different files for physical, biology, and sediment variables. The model will scan the file list and will read the needed data in the first file containing the required variable. Therefore, the order of the filenames is critical. It is also possible to split input data time records into several NetCDF files.

  ! Input lateral boundary conditions file names. The USER has the option
  ! to separate the required lateral boundary variables into individual
  ! NetCDF files (NBCFILES > 1), as in the input surface forcing.  Also,
  ! the USER may split input data time records into several NetCDF files
  ! (monthly, seasonal, or annual). See prologue instructions above. Use
  ! a single line per entry with a continuation (\) or a vertical bar (|)
  ! symbol after each entry, except the last one.
  
      NBCFILES == 1                          ! number of boundary files
  
       BRYNAME == ../Data/doppio_bry_Mercator2007_corr.nc
  
  ! Input climatology file names. The USER has the option to separate the
  ! climatology variables into individual NetCDF files (NCLMFILES > 1),
  ! as in the input surface forcing.  Also, the USER may split input data
  ! time records into several NetCDF files (monthly, seasonal, or annual).
  ! See prologue instructions above. Use a single line per entry with a
  ! continuation (\) or a vertical bar (|) symbol after each entry, except
  ! the last one.
  
     NCLMFILES == 1                          ! number of climatology files
  
       CLMNAME == ../Data/doppio_clm_Mercator2007_corr.nc
  

That is, we can have:

    NBCFILES == 2                            ! number of boundary files

     BRYNAME == my_physics_bry_year1.nc |    ! physical kernel variables
                my_physics_bry_year2.nc \
                my_biology_bry_year1.nc |    ! biological tracers
                my_biology_bry_year2.nc


    NCLMFILES == 2                           ! number of climatology files

      CLMNAME == my_physics_clm_year1.nc |   ! physical kernel variables
                 my_physics_bry_year2.nc \
                 my_biology_bry_year1.nc |   ! biological tracers
                 my_biology_bry_year2.nc

• The routine metrics.F was updated to include some of the statistics to exclude the land values when MASKING is activated:

  Metrics information for Grid 01:
   ===============================
  
   Minimum X-grid spacing, DXmin =  6.88663955E+00 km    Water points =  6.90302997E+00 km
   Maximum X-grid spacing, DXmax =  7.03257515E+00 km    Water points =  7.03257508E+00 km
   Minimum Y-grid spacing, DYmin =  6.86772676E+00 km    Water points =  6.88396066E+00 km
   Maximum Y-grid spacing, DYmax =  7.01314814E+00 km    Water points =  7.01314814E+00 km
   Minimum Z-grid spacing, DZmin =  1.22555380E-01 m     Water points =  1.23127234E-01 m
   Maximum Z-grid spacing, DZmax =  3.61224935E+02 m     Water points =  3.61224935E+02 m
  
   Minimum barotropic Courant Number =  1.69968839E-02
   Maximum barotropic Courant Number =  5.37936938E-01
   Maximum Coriolis   Courant Number =  3.77305364E-02
  
   Horizontal mixing scaled by grid area squared root, MAXVAL(grdscl) =  7.02285483E+00 km  (Water Points)
  

• All the batch, csh, and perl scripts were updated to acceptable Standards to include:
  • The csh scripts need to have extension .csh (we were using .sh)
  • The batch scripts need to have extension .sh (we were using .bash)
  • The perl scripts need use strict, variables declared via my or our, avoid overriding the $a built-in, and require version 5.6 or newer.

---

WARNING:

• All the ROMS standard input scripts roms_*.in were modified.
• All the ROMS build scripts were updated and renamed to have the proper extension according to the Standard.
• All the csh and bash scripts were renamed so they have proper extension.