Add ECCC driver for coupling with NEMO, update 'hadgem3' driver (#605)

* drivers/hadgem3: add missing 'subname' and use existing 'subname's

* drivers/hadgem3/CICE_InitMod: update 'init_lvl' call

Add the required 'iblk' argument.

* drivers/hadgem3/CICE_RunMod: remove uneeded 'dt' arguments

The subroutines 'prep_radiation', 'zsal_diags', 'bgc_diags' and 'hbrine_diags'
do not take a 'dt' argument anymore, so remove it.

* drivers/hadgem3/CICE_RunMod: get 'Lsub' from Icepack

* drivers/hadgem3/CICE_RunMod: remove 'da_state_update' subroutine

This subroutine is inside an 'ICE_DA' CPP, which is not used in
any configuration. Remove it.

* drivers/hadgem3/CICE_RunMod: remove stray '+'

This '+' sign was copy-pasted there in error in 29b99b6 (CICE: Floe size
distribution  (#382), 2019-12-07). Remove it.

* drivers/hadgem3: remove obsolete 'check_finished_file' subroutine

Remove the call to 'check_finished_file' as well as the definition
of the subroutine, as the 'hadgem3' driver is not used on machine 'bering'
and it's unclear if machine 'bering' still exists.

* drivers/hadgem3: fix cice_init so it calls 'count_tracers'

This was forgotten back in 8b0ae03 (Refactor tracer initialization (#235), 2018-11-16)

* drivers/hadgem3/CICE_RunMod: add call to 'save_init'

The hadgem3 driver was not updated when 'save_init' was added in 83686a3
(Implement box model test from 2001 JCP paper (#151), 2018-10-22). As
this subroutine is necessary to ensure proper initialization of the
model, add it now.

* drivers/hadgem3/CICE_RunMod: tweak loop indices in 'coupling_prep'

Other drivers use 'ilo,ihi' and 'jlo,jhi' here. Do the same.

* drivers/hagdem3: update driver to new time manager

* drivers/hadgem3: pass 'mpi_comm_opa' explicitely to init_communicate

In 066070e (Fix minor issues in documentation, key_ CPPs, bfbcomp return
codes (#532), 2020-11-23), the 'ice_communicate' module was updated to
remove CPP macros relating to the OASIS coupler (key_oasis*) and to the
NEMO ocean model (key_iomput). These CPPs were used to make the correct
MPI communicator accessible to the 'init_communicate' subroutine.
However, that subroutine already accepts an optional MPI communicator as
argument and it was deemed cleaner to require the driver layer to
explicitely pass the communicator instead of making it accessible
through 'use' statements.

Update the 'hadgem3' driver, used for coupling with NEMO, to explicitely
pass the NEMO MPI communicator 'mpi_comm_opa' to 'init_communicate'.

* drivers: add 'nemo_concepts' driver

Historically the 'hadgem3' driver has been used when compiling a single
NEMO-CICE executable at ECCC.

Going forward, all driver-level adjustements will be done in our own
driver, 'nemo_concepts', 'CONCEPTS' being the name of the
multi-departmental collaboration around using the NEMO ocean model.

Copy CICE_InitMod, CICE_RunMod and CICE_FinalMod from the 'hadgem3'
directory to a new 'nemo_concepts' directory under 'drivers/direct'.

The following commits will clean up this new driver and port over some
in-house adjustments.

* drivers/nemo_concepts: remove unused 'writeout_finished_file' subroutine

This subroutine was only called on machine 'bering', which is not an
ECCC machine and probably does not exist anymore anyway. Remove it.

* drivers/nemo_concepts: call 'scale_fluxes' with 'aice_init'

Since 'merge_fluxes' is called with aice_init, it is more consistent to
also call 'scale_fluxes', in 'coupling_prep' with 'aice_init'
instead of 'aice'.

Copy this in-house change to the new 'nemo_concepts' driver.

cicecore/drivers/direct/hadgem3/CICE_FinalMod.F90

@@ -39,7 +39,7 @@ subroutine CICE_Finalize
    !-------------------------------------------------------------------
 
       call icepack_warnings_flush(nu_diag)
-      if (icepack_warnings_aborted()) call abort_ice(error_message="subname", &
+      if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
           file=__FILE__,line= __LINE__)
 
       call ice_timer_stop(timer_total)        ! stop timing entire run

cicecore/drivers/direct/hadgem3/CICE_InitMod.F90

@@ -64,8 +64,8 @@ subroutine cice_init
           ocean_bio_all, ice_bio_net, snow_bio_net, alloc_arrays_column
       use ice_arrays_column, only: floe_rad_l, floe_rad_c, &
           floe_binwidth, c_fsd_range
-      use ice_calendar, only: dt, dt_dyn, time, istep, istep1, write_ic, &
-          init_calendar, calendar
+      use ice_calendar, only: dt, dt_dyn, write_ic, &
+          init_calendar, advance_timestep, calc_timesteps
       use ice_communicate, only: init_communicate, my_task, master_task
       use ice_diagnostics, only: init_diags
       use ice_domain, only: init_domain_blocks
@@ -83,17 +83,18 @@ subroutine cice_init
       use ice_history, only: init_hist, accum_hist
       use ice_restart_shared, only: restart, runid, runtype
       use ice_init, only: input_data, init_state
-      use ice_init_column, only: init_thermo_vertical, init_shortwave, init_zbgc
+      use ice_init_column, only: init_thermo_vertical, init_shortwave, init_zbgc, input_zbgc, count_tracers
       use ice_kinds_mod
       use ice_restoring, only: ice_HaloRestore_init
       use ice_timers, only: timer_total, init_ice_timers, ice_timer_start
       use ice_transport_driver, only: init_transport
+      use lib_mpp, only:   mpi_comm_opa      ! NEMO MPI communicator
 
       logical(kind=log_kind) :: tr_aero, tr_zaero, skl_bgc, z_tracers, &
          tr_fsd, wave_spec
       character(len=*),parameter :: subname = '(cice_init)'
 
-      call init_communicate     ! initial setup for message passing
+      call init_communicate(mpi_comm_opa) ! initial setup for message passing
       call init_fileunits       ! unit numbers
 
       call icepack_configure()  ! initialize icepack
@@ -102,8 +103,8 @@ subroutine cice_init
           file=__FILE__,line= __LINE__)
 
       call input_data           ! namelist variables
-
-      if (trim(runid) == 'bering') call check_finished_file
+      call input_zbgc           ! vertical biogeochemistry namelist
+      call count_tracers        ! count tracers
 
       call init_domain_blocks   ! set up block decomposition
       call init_grid1           ! domain distribution
@@ -150,11 +151,9 @@ subroutine cice_init
          write_diags=(my_task == master_task))  ! write diag on master only
 
       call icepack_warnings_flush(nu_diag)
-      if (icepack_warnings_aborted()) call abort_ice(error_message="subname", &
+      if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
          file=__FILE__, line=__LINE__)
 
-      call calendar(time)       ! determine the initial date
-
 #ifndef CICE_IN_NEMO
       call init_forcing_ocn(dt) ! initialize sss and sst from data
 #endif
@@ -170,6 +169,7 @@ subroutine cice_init
       call init_diags           ! initialize diagnostic output points
       call init_history_therm   ! initialize thermo history variables
       call init_history_dyn     ! initialize dynamic history variables
+      call calc_timesteps       ! update timestep counter if not using npt_unit="1"
 
       call icepack_query_tracer_flags(tr_aero_out=tr_aero, tr_zaero_out=tr_zaero)
       call icepack_warnings_flush(nu_diag)
@@ -185,10 +185,8 @@ subroutine cice_init
       if (trim(runtype) == 'continue' .or. restart) &
          call init_shortwave    ! initialize radiative transfer
 
-      istep  = istep  + 1    ! update time step counters
-      istep1 = istep1 + 1
-      time = time + dt       ! determine the time and date
-      call calendar(time)    ! at the end of the first timestep
+      ! determine the time and date at the end of the first timestep
+      call advance_timestep()
 
    !--------------------------------------------------------------------
    ! coupler communication or forcing data initialization
@@ -227,7 +225,7 @@ subroutine init_restart
 
       use ice_arrays_column, only: dhsn
       use ice_blocks, only: nx_block, ny_block
-      use ice_calendar, only: time, calendar
+      use ice_calendar, only: calendar
       use ice_constants, only: c0
       use ice_domain, only: nblocks
       use ice_domain_size, only: ncat, n_aero, nfsd
@@ -265,6 +263,8 @@ subroutine init_restart
           nt_alvl, nt_vlvl, nt_apnd, nt_hpnd, nt_ipnd, &
           nt_iage, nt_FY, nt_aero, nt_fsd
 
+      character(len=*),parameter :: subname = '(init_restart)'
+
       call icepack_query_tracer_sizes(ntrcr_out=ntrcr)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
@@ -280,13 +280,13 @@ subroutine init_restart
            nt_apnd_out=nt_apnd, nt_hpnd_out=nt_hpnd, nt_ipnd_out=nt_ipnd, &
            nt_iage_out=nt_iage, nt_FY_out=nt_FY, nt_aero_out=nt_aero, nt_fsd_out=nt_fsd)
       call icepack_warnings_flush(nu_diag)
-      if (icepack_warnings_aborted()) call abort_ice(error_message="subname", &
+      if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
          file=__FILE__, line=__LINE__)
 
       if (trim(runtype) == 'continue') then 
          ! start from core restart file
          call restartfile()           ! given by pointer in ice_in
-         call calendar(time)          ! update time parameters
+         call calendar()              ! update time parameters
          if (kdyn == 2) call read_restart_eap ! EAP
       else if (restart) then          ! ice_ic = core restart file
          call restartfile (ice_ic)    !  or 'default' or 'none'
@@ -327,7 +327,7 @@ subroutine init_restart
             call read_restart_lvl
          else
             do iblk = 1, nblocks 
-               call init_lvl(trcrn(:,:,nt_alvl,:,iblk), &
+               call init_lvl(iblk,trcrn(:,:,nt_alvl,:,iblk), &
                              trcrn(:,:,nt_vlvl,:,iblk))
             enddo ! iblk
          endif
@@ -452,39 +452,11 @@ subroutine init_restart
       !$OMP END PARALLEL DO
 
       call icepack_warnings_flush(nu_diag)
-      if (icepack_warnings_aborted()) call abort_ice(error_message="subname", &
+      if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
          file=__FILE__, line=__LINE__)
 
       end subroutine init_restart
 
-!=======================================================================
-!
-! Check whether a file indicating that the previous run finished cleanly
-! If so, then do not continue the current restart.  This is needed only 
-! for runs on machine 'bering' (set using runid = 'bering').
-!
-!  author: Adrian Turner, LANL
-
-      subroutine check_finished_file()
-
-      use ice_communicate, only: my_task, master_task
-      use ice_restart_shared, only: restart_dir
-
-      character(len=char_len_long) :: filename
-      logical :: lexist = .false.
-
-      if (my_task == master_task) then
-
-         filename = trim(restart_dir)//"finished"
-         inquire(file=filename, exist=lexist)
-         if (lexist) then
-            call abort_ice("subname"//"ERROR: Found already finished file - quitting")
-         end if
-
-      endif
-
-      end subroutine check_finished_file
-
 !=======================================================================
 
       end module CICE_InitMod