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This is an important update to facilitate the coding of the ROMS-JEDI interface. The development of the ROMS-JEDI interface is still private within JCSDA GitHub repositories. It is not ready for any application since it is still under development. However, several changes are made to improve ROMS.

• A new driver ROMS/Drivers/jedi_roms.h is added to facilitate JEDI to take direct control of the ROMS initialize, run, and finalize phases for the NLM, TLM, and ADM dynamical/numerical kernels. It is activated with new C-preprocessing option JEDI. It uses the same strategy as coupling where the ESMF/NUOPC library controls how the ROMS kernel is initialized, advanced, and terminated.

• All the ROMS modules are refactored to include a deallocation subroutine. For example, mod_ocean.F now includes allocate_ocean, deallocate_ocean, and initialize_ocean subroutines.

The destroying (deallocating) of all ROMS derived-type structures is essential in Object-Oriented Programming (OOP) for releasing memory space, avoiding memory leaks, and facilitating changing the size of the state arrays (regridding). Recall that all the ROMS derived-type objects include several pointer-variables. After a variable has been deallocated, it cannot be defined or referenced until it is allocated or assigned again.

• A new module ROMS/Utility/destroy.F is added to deallocate each variable in the derived-type structure separately. However, it is not used by default since the Fortran 2003 standard allows deallocating just the parent object to deallocate all array variables within its scope automatically. So, for example, to deallocate all the variables in the OCEAN(:) structure, we need:

       IF (ng.eq.Ngrids) THEN
         IF (allocated(OCEAN)) deallocate ( OCEAN )
       END IF
  

  We expect that all the Users of ROMS have at least a Fortran 2003 compiler. Otherwise, it is possible to activate the new C-preprocessing option SUBOBJECT_DEALLOCATION to deallocate each pointer variable within the structure object. For example:

       IF (.not.destroy(ng, OCEAN(ng)%zeta, MyFile,                      &
      &                 __LINE__, 'OCEAN(ng)%zeta')) RETURN
  
  

  Here, the ROMS function destroy deallocates the free-surface pointer variable zeta in the OCEAN(ng) structure for nested grid ng.

By the way, the DEALLOCATE Fortran statement releases the space allocated for an allocatable variable or a pointer target and nullifies the pointer.

• The modules mod_param.F, mod_parallel.F, mod_iounits.F, and mod_scalars.F were slightly modified to avoid cyclic dependencies when compiling. It required to pass the Ngrids as argument in few allocation calls in read_phypar.F:

             CASE ('Ngrids')
               Npts=load_i(Nval, Rval, 1, Ivalue)
               Ngrids=Ivalue(1)
               IF (Ngrids.le.0) THEN
                 IF (Master) WRITE (out,290) 'Ngrids', Ngrids,           &
      &            'must be greater than zero.'
                 exit_flag=5
                 RETURN
               END IF
               got_Ngrids=.TRUE.                ! Allocating variables in
               CALL allocate_param              ! modules that solely
               CALL allocate_parallel (Ngrids)  ! depend on the number 
               CALL allocate_iounits (Ngrids)   ! nested grids
               CALL allocate_stepping (Ngrids)
               ...
  

• The module mod_arrays.F is restructured into three distinct routines: ROMS_allocate_arrays, ROMS_deallocate_arrays, and ROMS_initialize_arrays. It cleans nicely the module roms_kernel_mod for all available drivers.

• Added the reporting of the river_file global attribute in output NetCDF files. In def_info.F, we have:

  #ifndef ANA_PSOURCE
          IF (exit_flag.eq.NoError) THEN
            IF (LuvSrc(ng).or.LwSrc(ng).or.(ANY(LtracerSrc(:,ng)))) THEN
              status=nf90_put_att(ncid, nf90_global, 'river_file',        &
       &                          TRIM(SSF(ng)%name))
              IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
                IF (Master) WRITE (stdout,20) 'river_file', TRIM(ncname)
                exit_flag=3
                ioerror=status
              END IF
            END IF
          END IF
  #endif
  

  Many thanks to John Wilkin for bringing this issue to my attention.

• Corrected a typo in the CPP directives in ad_get_data.F, tl_get_data.F, and rp_get_data.F. We need to have

  # if !defined ANA_PAIR       && \
       (defined ATM_PRESS      || defined BULK_FLUXES  || \
        defined ECOSIM)
  #  if !(defined FRC_COUPLING || defined FORWARD_FLUXES)
  

  a space was added before FORWARD_FLUXES. Many thanks to Raquel Toste for ​reporting this typo.

It is a minor update to correct a few things:

• Corrected a typo in module mod_arrays.F, we need to have sedbed instead of seabed. Many thanks to Jianfei Ma for ​reporting this issue. We also need to have in routine ROMS_deallocate_arrays :

  #if defined SEDIMENT || defined BBL_MODEL
          CALL deallocate_sedbed (ng)
  #endif
  

• Added JEDI C-preprocessing option to a couple of directives blocks in Compilers/defs_cmake.h to include the tangent linear and adjoint kernels in the compilation with CMake.

• Corrected documentation spellings in a couple of files.

There have been two ​reports about the AVERAGES multi-file option ​failing during restart. I looked into the debugger again, and I could not reproduce the error. I tried eight different combinations with NTIMES, NAVG, and NDEFAVG. Thus, I don't know what specific set of values makes that logic fail.

However, I examined the possibility of adding the same logic used in history files to the time-averaging files. It turns out that augmenting the OutFiles is not that harmful when all the elements of the arrays in the derived type structure (T_IO) are not filled in some cases.

#ifdef AVERAGES
        IF ((nAVG(ng).gt.0).and.(ndefAVG(ng).gt.0)) THEN
          OutFiles=ntimes(ng)/ndefAVG(ng)
          IF ((nAVG(ng).eq.ndefAVG(ng)).or.                             &
     &        (MOD(ntimes(ng),ndefAVG(ng)).ge.nAVG(ng))) THEN
            OutFiles=Outfiles+1
          END IF
          CALL edit_file_struct (ng, OutFiles, AVG)
          AVG(ng)%load=0       ! because delayed creation of NetCDF file
        END IF                 ! due to time-averaging
#endif
#ifdef DIAGNOSTICS
        IF ((nDIA(ng).gt.0).and.(ndefDIA(ng).gt.0)) THEN
          OutFiles=ntimes(ng)/ndefDIA(ng)
          IF ((nDIA(ng).eq.ndefDIA(ng)).or.                             &
     &        (MOD(ntimes(ng),ndefDIA(ng)).ge.nDIA(ng))) THEN
            OutFiles=Outfiles+1
          END IF
          CALL edit_file_struct (ng, OutFiles, DIA)
          DIA(ng)%load=0       ! because delayed creation of NetCDF file
        END IF                 ! due to time-averaging
#endif