CCPP metadata bugfixes in GFS_typedefs.meta, update fv3 files with fms.2021.03, IAU bug fix for restart files

.gitmodules

@@ -8,5 +8,7 @@
 	branch = main
 [submodule "ccpp/physics"]
 	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
-	branch = main
+	#url = https://github.com/NCAR/ccpp-physics
+	#branch = main
+	url = https://github.com/climbfuji/ccpp-physics
+	branch = metadata_bugfixes_following_ccpp_standard_name_updates

atmos_model.F90

@@ -47,12 +47,8 @@ module atmos_model_mod
 use mpp_mod,            only: FATAL, mpp_min, mpp_max, mpp_error, mpp_chksum
 use mpp_domains_mod,    only: domain2d
 use mpp_mod,            only: mpp_get_current_pelist_name
-#ifdef INTERNAL_FILE_NML
 use mpp_mod,            only: input_nml_file
-#else
-use fms_mod,            only: open_namelist_file
-#endif
-use fms_mod,            only: file_exist, error_mesg
+use fms2_io_mod,        only: file_exists
 use fms_mod,            only: close_file, write_version_number, stdlog, stdout
 use fms_mod,            only: clock_flag_default
 use fms_mod,            only: check_nml_error
@@ -551,19 +547,9 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
 !----------------------------------------------------------------------------------------------
 ! initialize atmospheric model - must happen AFTER atmosphere_init so that nests work correctly
 
-   IF ( file_exist('input.nml')) THEN
-#ifdef INTERNAL_FILE_NML
+   IF ( file_exists('input.nml')) THEN
       read(input_nml_file, nml=atmos_model_nml, iostat=io)
       ierr = check_nml_error(io, 'atmos_model_nml')
-#else
-      unit = open_namelist_file ( )
-      ierr=1
-      do while (ierr /= 0)
-         read  (unit, nml=atmos_model_nml, iostat=io, end=10)
-         ierr = check_nml_error(io,'atmos_model_nml')
-      enddo
- 10     call close_file (unit)
-#endif
    endif
 
 !-----------------------------------------------------------------------

ccpp/data/GFS_typedefs.meta

@@ -631,7 +631,7 @@
   standard_name = surface_snow_area_fraction_over_ice
   long_name = surface snow area fraction over ice
   units = frac
-  dimensions = (horizontal_dimension)
+  dimensions = (horizontal_loop_extent)
   type = real
   kind = kind_phys
   active = (control_for_land_surface_scheme == identifier_for_ruc_land_surface_scheme)
@@ -1448,7 +1448,7 @@
   standard_name = temperature_in_surface_snow_at_surface_adjacent_layer_over_land
   long_name = snow temperature at the bottom of the first snow layer over land
   units = K
-  dimensions = (horizontal_dimension)
+  dimensions = (horizontal_loop_extent)
   type = real
   kind = kind_phys
   active = (control_for_land_surface_scheme == identifier_for_ruc_land_surface_scheme)
@@ -10110,7 +10110,7 @@
   standard_name = saturation_vapor_pressure
   long_name = saturation vapor pressure
   units = Pa
-  dimensions = (horizontal_dimension,vertical_layer_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   optional = F
@@ -10119,7 +10119,7 @@
   standard_name = water_vapor_mixing_ratio
   long_name = water vaport mixing ratio
   units = kg/kg
-  dimensions = (horizontal_dimension,vertical_layer_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   optional = F

module_fcst_grid_comp.F90

@@ -24,7 +24,7 @@ module module_fcst_grid_comp
   use esmf
 
   use time_manager_mod,   only: time_type, set_calendar_type, set_time,    &
-                                set_date, days_in_month, month_name,       &
+                                set_date, month_name,                      &
                                 operator(+), operator(-), operator (<),    &
                                 operator (>), operator (/=), operator (/), &
                                 operator (==), operator (*),               &
@@ -43,22 +43,20 @@ module module_fcst_grid_comp
                                 addLsmask2grid
 
   use constants_mod,      only: constants_init
-  use fms_mod,            only: open_namelist_file, file_exist, check_nml_error, &
-                                error_mesg, fms_init, fms_end, close_file,       &
+  use fms_mod,            only: error_mesg, fms_init, fms_end,             &
                                 write_version_number, uppercase
 
   use mpp_mod,            only: mpp_init, mpp_pe, mpp_root_pe,  &
                                 mpp_error, FATAL, WARNING
-  use mpp_mod,            only: mpp_clock_id, mpp_clock_begin, mpp_clock_end
+  use mpp_mod,            only: mpp_clock_id, mpp_clock_begin
 
-  use mpp_io_mod,         only: mpp_open, mpp_close, MPP_NATIVE, MPP_RDONLY, MPP_DELETE
+  use mpp_io_mod,         only: mpp_open, mpp_close, MPP_DELETE
 
   use mpp_domains_mod,    only: mpp_get_compute_domains, domain2D 
-  use memutils_mod,       only: print_memuse_stats
   use sat_vapor_pres_mod, only: sat_vapor_pres_init
 
   use diag_manager_mod,   only: diag_manager_init, diag_manager_end, &
-                                get_base_date, diag_manager_set_time_end
+                                diag_manager_set_time_end
 
   use data_override_mod,  only: data_override_init
   use fv_nggps_diags_mod, only: fv_dyn_bundle_setup
@@ -359,9 +357,7 @@ subroutine fcst_initialize(fcst_comp, importState, exportState, clock, rc)
       if(restart_interval(2)== -1) freq_restart = .true.
     endif
     if(freq_restart) then
-      if(restart_interval(1) == 0) then
-        frestart(1) = total_inttime
-      else if(restart_interval(1) > 0) then
+      if(restart_interval(1) >= 0) then
         tmpvar = restart_interval(1) * 3600
         atm_int_state%Time_step_restart = set_time (tmpvar, 0)
         if(iau_offset > 0 ) then
@@ -371,16 +367,18 @@ subroutine fcst_initialize(fcst_comp, importState, exportState, clock, rc)
           atm_int_state%Time_restart = atm_int_state%Time_init + atm_int_state%Time_step_restart
           frestart(1) = tmpvar
         endif
-        i = 2
-        do while ( atm_int_state%Time_restart < atm_int_state%Time_end )
-          frestart(i) = frestart(i-1) + tmpvar
-          atm_int_state%Time_restart = atm_int_state%Time_restart + atm_int_state%Time_step_restart
-           i = i + 1
-        enddo
+        if(restart_interval(1) > 0) then
+          i = 2
+          do while ( atm_int_state%Time_restart < atm_int_state%Time_end )
+            frestart(i) = frestart(i-1) + tmpvar
+            atm_int_state%Time_restart = atm_int_state%Time_restart + atm_int_state%Time_step_restart
+             i = i + 1
+          enddo
+        endif
       endif
 ! otherwise it is an array with forecast time at which the restart files will be written out
     else if(num_restart_interval >= 1) then
-      if(restart_interval(1) == 0 ) then
+      if(num_restart_interval == 1 .and. restart_interval(1) == 0 ) then
         frestart(1) = total_inttime
       else
         if(iau_offset > 0 ) then
@@ -861,20 +859,18 @@ subroutine fcst_run_phase_2(fcst_comp, importState, exportState,clock,rc)
 !--- intermediate restart
       if (atm_int_state%intrm_rst>0) then
         if (na /= atm_int_state%num_atmos_calls-1) then
-          call get_time(atm_int_state%Time_atmos - atm_int_state%Time_atstart, seconds)
+          call get_time(atm_int_state%Time_atmos - atm_int_state%Time_init, seconds)
           if (ANY(frestart(:) == seconds)) then
-            restart_inctime = set_time(seconds, 0)
-            atm_int_state%Time_restart = atm_int_state%Time_atstart + restart_inctime
-            timestamp = date_to_string (atm_int_state%Time_restart)
+            if (mype == 0) write(0,*)'write out restart at na=',na,' seconds=',seconds,  &
+               'integration lenght=',na*dt_atmos/3600.
+            timestamp = date_to_string (atm_int_state%Time_atmos)
             call atmos_model_restart(atm_int_state%Atm, timestamp)
             call write_stoch_restart_atm('RESTART/'//trim(timestamp)//'.atm_stoch.res.nc')
 
             call wrt_atmres_timestamp(atm_int_state,timestamp)
           endif
         endif
       endif
-!
-      call print_memuse_stats('after full step')
 !
 !-----------------------------------------------------------------------
 !