NESTING TOOLS AGRIF read mbathy and NOT bathy_level for agrif_create_restart

[jharlass]

Context

1. agrif_create_restart reads bathymetry on levels from mesh_mash.nc to create all masks. In the old code it is looking for Bathy_Level, which no longer exists. Use mbathy instead.
2. add support for partial step (exisiting routines)

Fix

(a) Revision vs. (b) Working

@@ -555 +556 @@
   SUBROUTINE Init_mask(name,Grid,jpiglo,jpjglo)
     !
     USE io_netcdf
     !
     CHARACTER(*) name
     INTEGER :: nx,ny,k,i,j,jpiglo,jpjglo
     TYPE(Coordinates) :: Grid
     REAL*8, POINTER, DIMENSION(:,:) ::zwf => NULL()
     !
+    ! cjh, no Bathy_level -> mbathy from (1_)mesh_mask.nc
     IF(jpiglo == 1 .AND. jpjglo == 1) THEN
-       CALL Read_Ncdf_var('Bathy_level',name,Grid%Bathy_level)
+      CALL Read_Ncdf_var('mbathy'  ,name ,Grid%Bathy_level)
     ELSE
-       CALL Read_Ncdf_var('Bathy_level',name,Grid%Bathy_level,(/jpizoom,jpjzoom/),(/jpiglo,jpjglo/) )
+      CALL Read_Ncdf_var('mbathy',name,Grid%Bathy_level,(/jpizoom,jpjzoom/),(/jpiglo,jpjglo/) )
     ENDIF
     !
     WRITE(*,*) 'Init masks in T,U,V,F points'    
     !
     nx = SIZE(Grid%Bathy_level,1)
     ny = SIZE(Grid%Bathy_level,2)
     !      
     ALLOCATE(Grid%tmask(nx,ny,N), &
          Grid%umask(nx,ny,N), &
          Grid%vmask(nx,ny,N), &
          Grid%fmask(nx,ny,N))
+
+    ! cjh, important for correct mbathy and masks calculation
+    IF(partial_steps) THEN
+      CALL get_partial_steps(Grid)
+    END IF
+
+    ! checks for all levels for landpoints
     DO k = 1,N
-       !      
-       WHERE(Grid%Bathy_level(:,:) <= k-1 )    
+    ! nemo syntax
+       WHERE( Grid%Bathy_level(:,:) - k + 0.1 >= 0 )
+          Grid%tmask(:,:,k) = 1
+       ELSEWHERE
           Grid%tmask(:,:,k) = 0
-       ELSEWHERE
-          Grid%tmask(:,:,k) = 1
        END WHERE
-       !
     END DO
     !
     Grid%umask(1:nx-1,:,:) = Grid%tmask(1:nx-1,:,:)*Grid%tmask(2:nx,:,:)

[jharlass]

Addendum:
Subroutine Init_mask in file: agrif_readwrite.f90
Called from agrif_create_restart.f90

[jchanut]

Use the very last NESTING tool version (no correction made to the one provided with NEMO 3.6_STABLE)