driver: icedrv_restart: Added option for restart files to be read/wri…

…tten in NetCDF format (#427)

* Trial fix for netCDF start time problem

* driver: icedrv_history: fix start time for NetCDF history output

The start time for netCDF output was hardcoded to be at 00:00:00
and there was a bug in icedrv_calendar such that idate0 was fixed
at Jan. 1. Both bugs are fixed. NOTE: if dt and istep0 are set
such that the start time contains fractional seconds, they will
be rounded down in the NetCDF output to the nearest integer.

* driver: icedrv_history: fix start time for NetCDF History output

Start of netCDF time axis is fixed at Jan. 01 00:00:00 of
init_year and time value calculation is now fixed.

* Added restart_format variable to icedrv_restart_shared and to namelist.

No functionality implemented yet, just checking it's added correctly.

* need to also add new namelist to icepack_in

* Added error handling for incorrect restart format, should probably update final_restart at some point

* NetCDF restart file created, next need to populate fields

* NetCDF Restart output is now populated

* if block error handling in restartfile

* driver: icedrv_restart: enabled restart/ice_ic files to be written/read as NetCDF

Added the option for restart (aka initial condition) files to be in NetCDF
instead of binary for ease of setting custom inital conditions

* modified set_nml.ionetcdf to default to netcdf restart files if we set ionetcdf

* Fixed error in which some tracers were not being writting. NetCDF restart files are now identical

* fixed istep1 = istep0 but and added test_suite for netcdf

* removed bgc from the netcdf restart test suite

* put netcdf functions into conditional compilation blocks

* Removed unused variables (sec0, h0, m0, s0) from icedrv_history

* Removing unused variables in icedrv_history (after merging in from consortium-main)

* Changed history_cdf namelist to history_format and updated documentation

* Fixed warning message if restart_format is incorrect

* halfway done reorganizing restartfile

* finished reorganization in restartfile, need to do dumpfile next

* Halfway done editing dumpfile

* finished editing dumpfile

* updated namelist settings and documentation. all tests pass

* removed the netcdf_nobgc test suite

* Fix minor issues found during testing
  - icedrv_init write format for history_format
  - dims allocation in icedrv_restart
  - cleaned up some intent lines (old)
  - add return at end of io_suite.ts
  - update namelist documentation of history_format, restart_format
Update to current main trunk

* Update history_format default

Check history_format and restart_format input values

---------

Co-authored-by: apcraig <anthony.p.craig@gmail.com>

.gitignore

@@ -11,3 +11,9 @@ doc/build
 # Ignore testsuite file/directories
 testsuite*
 caselist*
+
+# Ignore compiled .mod files
+*.mod
+
+# Ignore test case directories (no consistent name so we'll just ignore conda)
+conda_*

configuration/driver/icedrv_RunMod.F90

@@ -35,7 +35,7 @@ subroutine icedrv_run
       use icedrv_forcing, only: get_forcing, get_wave_spec
       use icedrv_forcing_bgc, only: faero_default, fiso_default, get_forcing_bgc
       use icedrv_flux, only: init_flux_atm_ocn
-      use icedrv_history, only: history_cdf, history_close
+      use icedrv_history, only: history_format, history_close
 
       logical (kind=log_kind) :: skl_bgc, z_tracers, tr_aero, tr_zaero, &
                                  wave_spec, tr_fsd, tr_iso
@@ -63,7 +63,7 @@ subroutine icedrv_run
          call calendar(time)    ! at the end of the timestep
 
          if (stop_now >= 1) then
-            if (history_cdf) call history_close()
+            if (history_format == 'nc') call history_close()
             exit timeLoop
          endif
 
@@ -101,7 +101,7 @@ subroutine ice_step
       use icedrv_diagnostics_bgc, only: hbrine_diags, zsal_diags, bgc_diags
       use icedrv_flux, only: init_history_therm, init_history_bgc, &
           daidtt, daidtd, dvidtt, dvidtd, dagedtt, dagedtd, init_history_dyn
-      use icedrv_history, only: history_cdf, history_write
+      use icedrv_history, only: history_format, history_write
       use icedrv_restart, only: dumpfile, final_restart
       use icedrv_restart_bgc, only: write_restart_bgc
       use icedrv_step, only: prep_radiation, step_therm1, step_therm2, &
@@ -225,7 +225,7 @@ subroutine ice_step
          if (tr_brine)                call hbrine_diags
       endif
 
-      if (history_cdf) then
+      if (history_format == 'nc') then
          call history_write()
       endif
 

configuration/driver/icedrv_history.F90

@@ -22,7 +22,8 @@ module icedrv_history
 
       ! history output file info
 
-      logical (kind=log_kind), public :: history_cdf      ! flag to turn on cdf history files
+      character (len=char_len), public :: &
+         history_format                           ! format of history files, only supported type is 'nc'
 
       character (len=char_len_long) :: hist_file  ! hist file name
 
@@ -68,11 +69,7 @@ subroutine history_write()
          count1(1), count2(2), count3(3), count4(4), & ! cdf start/count arrays
          varid, &                        ! cdf varid
          status, &                       ! cdf status flag
-         iflag, &                        ! history file attributes
-         sec0, &                         ! number of seconds into the day at istep0
-         h0, &                           ! start hour
-         m0, &                           ! start minute
-         s0                              ! start second
+         iflag                           ! history file attributes
 
       character (len=8) :: &
          cdate                           ! date string

configuration/driver/icedrv_init.F90

@@ -62,8 +62,8 @@ subroutine input_data
       use icedrv_calendar, only: year_init, istep0
       use icedrv_calendar, only: dumpfreq, diagfreq, dump_last
       use icedrv_calendar, only: npt, dt, ndtd, days_per_year, use_leap_years
-      use icedrv_history, only: history_cdf
-      use icedrv_restart_shared, only: restart, restart_dir, restart_file
+      use icedrv_history, only: history_format
+      use icedrv_restart_shared, only: restart, restart_dir, restart_file, restart_format
       use icedrv_flux, only: update_ocn_f, l_mpond_fresh, cpl_bgc
       use icedrv_flux, only: default_season
       use icedrv_forcing, only: precip_units,    fyear_init,      ycycle
@@ -133,8 +133,9 @@ subroutine input_data
         days_per_year,  use_leap_years, year_init,       istep0,        &
         dt,             npt,            ndtd,            dump_last,     &
         ice_ic,         restart,        restart_dir,     restart_file,  &
+        restart_format, &
         dumpfreq,       diagfreq,       diag_file,       cpl_bgc,       &
-        conserv_check,  history_cdf
+        conserv_check,  history_format
 
       namelist /grid_nml/ &
         kcatbound
@@ -254,9 +255,10 @@ subroutine input_data
       restart = .false.      ! if true, read restart files for initialization
       restart_dir  = './'    ! write to executable dir for default
       restart_file = 'iced'  ! restart file name prefix
-      history_cdf = .false.  ! history netcdf file flag
-      ice_ic       = 'default'      ! initial conditions are specified in the code
-                                    ! otherwise, the filename for reading restarts
+      restart_format = 'bin' ! default restart format is binary, other option 'nc'
+      history_format = 'none'     ! if 'nc', write history files. Otherwise do nothing
+      ice_ic       = 'default'    ! initial conditions are specified in the code
+                                  ! otherwise, the filename for reading restarts
       ndtd = 1               ! dynamic time steps per thermodynamic time step
       l_mpond_fresh = .false.     ! logical switch for including meltpond freshwater
                                   ! flux feedback to ocean model
@@ -544,6 +546,16 @@ subroutine input_data
          call icedrv_system_abort(file=__FILE__,line=__LINE__)
       endif
 
+      if (restart_format /= 'bin' .and. restart_format /= 'nc') then
+         write (nu_diag,*) 'WARNING: restart_format value unknown '//trim(restart_format)
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+
+      if (history_format /= 'none' .and. history_format /= 'nc') then
+         write (nu_diag,*) 'WARNING: history_format value unknown '//trim(history_format)
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+
       if (tr_aero .and. trim(shortwave) /= 'dEdd') then
          write (nu_diag,*) 'WARNING: aerosols activated but dEdd'
          write (nu_diag,*) 'WARNING: shortwave is not.'
@@ -645,7 +657,9 @@ subroutine input_data
                                trim(restart_dir)
          write(nu_diag,*)    ' restart_file              = ', &
                                trim(restart_file)
-         write(nu_diag,1010) ' history_cdf               = ', history_cdf
+         write(nu_diag,1030) ' restart_format            = ', &
+                               trim(restart_format)
+         write(nu_diag,1030) ' history_format            = ', trim(history_format)
          write(nu_diag,*)    ' ice_ic                    = ', &
                                trim(ice_ic)
          write(nu_diag,1010) ' conserv_check             = ', conserv_check