NESTING TOOLS AGRIF create restart files

[jharlass]

Context

AGRIF NESTING TOOLS: agrif_create_restart.exe does not work with current NEMO 3.6 version

Analysis

Create restart file for AGRIF NEST from base model restart (global file).

1. Restart variables of current NEMO version were unknown to nesting tools.
2. The nest grid can have deeper values than the base grid, if e.g. bathymetry created with ETOPO. Happens in the near bottom levels in ragged bathymetry. Since there are no vlaues to inter/extrapolate they remain zero which causes the model to crash after a few time steps as e.g. zero salinity causes huge gradients, creating instabilty and so on ...

Fix

1. Add all variables needed.
2. New routine ("check_interpextrap") that checks for such missing values and replaces them with values from 1 level above.

CHANGES IN: NESTING/src/agrif_create_restart.f90:

(a) Revision vs. (b) Working

@@ -436 +458 @@
         ENDIF
         !
         ! Variable interpolation according to their position on grid
-        !                                   
-     CASE('un','ub')  
+        !
+        ! grid U
+        ! 3D 
+     CASE('un','ub','avu','avmu')  
+        ! irec only for DIMG format !
         varname = Ncdf_varname(i)
-
         IF(TRIM(varname)=='un') irec = 6 * z + 2
         IF(TRIM(varname)=='ub') irec = 2
-
-        WRITE(*,*) TRIM(varname),'interpolation ...'    
+!        WRITE(*,*) TRIM(varname),'interpolation ...'    
         vert_coord_name = 'z'             
         posvar='U'
         Interpolation = .TRUE.  
-        !
-     CASE('u_io')  
+        ! 1D                                  
+     CASE('u_io','ssu_m','utau_b')
         varname = Ncdf_varname(i)  
-        WRITE(*,*) TRIM(varname),'interpolation ...'    
+!        WRITE(*,*) TRIM(varname),'interpolation ...'    
         vert_coord_name = 'z_b'             
         posvar='U'
         Interpolation = .TRUE. 
-        !                          
-     CASE('vn','vb')
+        !
+        ! grid V
+        ! 3D
+     CASE('vn','vb','avmv')
         varname = Ncdf_varname(i)
-
         IF(TRIM(varname)=='vn') irec = 7 * z + 2
         IF(TRIM(varname)=='vb') irec = 2 + z
-
-        WRITE(*,*) TRIM(varname),'interpolation ...'      
+!        WRITE(*,*) TRIM(varname),'interpolation ...'      
         vert_coord_name = 'z'
         posvar='V'
         Interpolation = .TRUE.     
-        !              
-     CASE('v_io')
+        ! 1D             
+     CASE('v_io','ssv_m','vtau_b')
         varname = Ncdf_varname(i)
-        WRITE(*,*) TRIM(varname),'interpolation ...'      
+!        WRITE(*,*) TRIM(varname),' interpolation ...'      
         vert_coord_name = 'z_b'
         posvar='V'
         Interpolation = .TRUE.
-        !             
-     CASE('gcx','gcxb','sshb','sshn','sst_io','sss_io','gsst')
-        varname = Ncdf_varname(i)    
-
-        IF(TRIM(varname)=='gcx') irec = 12 * z + 2
-        IF(TRIM(varname)=='gcxb')  irec = 12 * z + 3
-        IF(TRIM(varname)=='sshb') irec = 12 * z + 4
-        IF(TRIM(varname)=='sshn') irec = 12 * z + 5
-
-        WRITE(*,*) TRIM(varname),'interpolation ...' 
-        vert_coord_name = 'z_b'             
-        posvar='T'
-        Interpolation = .TRUE.     
-
-        !  
-     CASE ('tb','sb','sn','tn')
+        !
+        ! grid T
+        ! 3D
+     CASE ('tb','sb','tn','sn','en','avt','avm','dissl','rhop','qsr_hc_b')
         varname = Ncdf_varname(i) 
-
         IF(TRIM(varname)=='sn') irec = 9 * z + 2
         IF(TRIM(varname)=='tn') irec = 8 * z + 2
         IF(TRIM(varname)=='sb') irec = 3 * z + 2
         IF(TRIM(varname)=='tb') irec = 2 * z + 2
-
-        WRITE(*,*) TRIM(varname),'interpolation ...'     
+        IF(TRIM(varname)=='tb') irec = 2 * z + 2
+        IF(TRIM(varname)=='en') irec = 12* z + 6
+ !       WRITE(*,*) TRIM(varname),' interpolation ...'     
         vert_coord_name = 'z'
         posvar='T'
         Interpolation = .TRUE.            
-
-     CASE('en')
-        varname = Ncdf_varname(i) 
-        irec = 12 * z + 6
-        WRITE(*,*) TRIM(varname),'interpolation ...'     
-        vert_coord_name = 'z'
+        ! 1D
+     CASE('gcx','gcxb','sshb','sshn','sst_io','sss_io','gsst','sss_m','sst_m','ssh_m','frq_m','qns_b','emp_b','sfx_b','sbc_hc_b','sbc_sc_b','fraqsr_1lev')
+        varname = Ncdf_varname(i)    
+        IF(TRIM(varname)=='gcx')  irec = 12 * z + 2
+        IF(TRIM(varname)=='gcxb') irec = 12 * z + 3
+        IF(TRIM(varname)=='sshb') irec = 12 * z + 4
+        IF(TRIM(varname)=='sshn') irec = 12 * z + 5
+ !       WRITE(*,*) TRIM(varname),' interpolation ...' 
+        vert_coord_name = 'z_b'             
         posvar='T'
-        Interpolation = .TRUE.             
-
+        Interpolation = .TRUE.     
+        !
+        ! NO interpolation
+        !
      CASE ('rotb','rotn','hdivb','hdivn')
         Interpolation = .FALSE.
         !

FULL COURCE CODE ATTACHED:

NESTING/src/agrif_create_restart.f90
and
NESTING/src/agrif_extrapolation.f90 with new routine: "check_interpextrap"

[jharlass]

routine checking for missing values: check_interpextrap

[mdunphy]

Hi Jan,

Thanks for this, it eliminates a bunch of post-processing work to fix up the partial steps. There's a typo in the allocations in check_interpextrap (see attached patch), but otherwise it looks good!

[mdunphy]

Fix for the allocations in check_interpextrap(). This patch is for agrif_extrapolation.f90 attached to this ticket (#1870), not for the version under SVN.