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Several reported bugs were corrected:

• inp_par.F: Corrected the Rad+Nud boundary conditions for passive tracer when the compact specification is used and input data is required. Many thanks to Mark Hadfield for ​reporting this bug and a solution. We just needed to add:

  #ifdef SOLVE3D
  !
  !  If processing tracers and last standard input entry (Icont=0), set
  !  unspecified tracer values to the last tracer entry.
  !
          IF ((iTrcStr.gt.0).and.(iTrcEnd.gt.0)) THEN
            IF ((Icont.eq.0).and.(ifield.lt.isTvar(iTrcEnd))) THEN
              DO i=ifield+1,isTvar(iTrcEnd)
                DO ibry=1,4
                  ...
                  S(ibry,i,igrid)%acquire   = S(ibry,ifield,igrid)%acquire
                END DO
                ic=ic+1
              END DO
            END IF
          END IF
  #endif
  

• inp_par.F: Corrected the momentum LnudgeM3CLM switch. Many thanks to ​Xueming zhu and ​Mark Hadfield for reporting this. We just need to have:

  !
  !  Set internal switch for nudging to climatology fields.
  !
  #ifdef SOLVE3D
          IF (LnudgeM3CLM(ng).or.                                         &
       &      LnudgeM3CLM(ng).or.                                         &
       &      ANY(LnudgeTCLM(:,ng))) THEN
            Lnudging(ng)=.TRUE.
          END IF
  #else
          IF (LnudgeM2CLM(ng)) THEN
            Lnudging(ng)=.TRUE.
          END IF
  #endif
  

• def_rst.F: Corrected typo when defining wetdry_psi mask. This does not affect solution. Many thanks to Kate Hedstrom for reporting this. We just need to have:

          Aval(5)=REAL(Iinfo(1,idPwet,ng),r8)
  

The other changes are for readability.

Corrected a minor bug in mod_stepping.F that was triggered when ADJUST_BOUNDARY was not activated in the 4D-Var algorithms. We need to have instead:

#if defined ADJUST_BOUNDARY || defined ADJUST_STFLUX || \
    defined ADJUST_WSTRESS
      allocate ( Lfinp(Ngrids) )
      Lfinp(1:Ngrids)=1

      allocate ( Lfout(Ngrids) )
      Lfout(1:Ngrids)=1
#endif

We were initializing Lbout instead Lfout above. A compilation error resulted if ADJUST_BOUNDARY is not activated. Many thanks to Julia Levin for bringing this to my attention.

I also corrected several comments that include ' or " in a line. Some compilers issue warnings. This is actually a bug in the compiler. It should not check commented statement like:

!    H Q(k) = Q(k) T(k) + Gamma(k) q(k+1) e'(k)                        !

The above comment was changed to:

!    H Q(k) = Q(k) T(k) + Gamma(k) q(k+1) transpose[e(k)]              !

This is an important update for the Matlab nesting scripts. The nesting grid connectivity (NGC) file has new variables and will only work with the latest version of ROMS that will be released next.

What is new:

• grid/c_contact.m: Added refined grid extraction coordinates to the output NGC NetCDF file to facilitate in ROMS the coding of mass flux conservation and two-way exchange from finer to coarser grids.

          int I_left(Ngrids) ;
                  I_left:long_name = "donor grid I-left index at PSI points used to extract refinement grid" ;
                  I_left:_FillValue = -999 ;
          int I_right(Ngrids) ;
                  I_right:long_name = "donor grid I-right index at PSI points used to extract refinement grid" ;
                  I_right:_FillValue = -999 ;
          int J_bottom(Ngrids) ;
                  J_bottom:long_name = "donor grid J-bottom index at PSI points used to extract refinement grid" ;
                  J_bottom:_FillValue = -999 ;
          int J_top(Ngrids) ;
                  J_top:long_name = "donor grid J-top index at PSI points used to extract refinement grid" ;
                  J_top:_FillValue = -999 ;
  

• grid/contact.m: Changed how the contact points interpolation weights are computed. No longer they are adjusted to take into account the land/sea mask at contact points. This is now done in ROMS routine mask_hweights to facilitate computations when wetting and drying (WET_DRY) is activated. In wetting and drying, the land/sea mask evolves at every time step and these masks cannot be use here. Only the permanent land/sea masking arrays are available for this script.

• grid/write_contact.m: Added the writing of refined grid extraction coordinates (I_left, I_right, J_bottom, J_top) to output NGC NetCDF file.

• utility/plot_nesting.m: Enhanced plotting script for nesting grids. This plotting script is good for browsing and overlaying refined nested grids. It is not intended for publication quality plots.

Updated script tile.m and ptiles.m that help debugging parallel applications.

Also added new script untexlabel.m to modify text in Matlab correctly with the TeX translator in labels. The characters ^, _, and \ are translated correctly. This script is adapted from Guiseppe Ridino script. The texlabel(f,'literal') doesn't work because it introduces blank spaces before the above symbols.

WARNING:

In order to use the newest version of ROMS, users need to recompute the input nesting grid connectivity NetCDF file!