Merge pull request NOAA-EMC#74 from laurenchilutti/fms2_io_implementa…

…tion

Fms2 io implementation

GFDL_tools/fv_ada_nudge.F90

@@ -38,9 +38,7 @@ module fv_ada_nudge_mod
  use external_sst_mod,  only: i_sst, j_sst, sst_ncep, sst_anom, forecast_mode
  use diag_manager_mod,  only: register_diag_field, send_data
  use constants_mod,     only: pi, grav, rdgas, cp_air, kappa, cnst_radius=>radius, seconds_per_day
- use fms_mod,           only: write_version_number, open_namelist_file, &
-                              check_nml_error, file_exist, close_file
-!use fms_io_mod,        only: field_size
+ use fms_mod,           only: write_version_number, check_nml_error
  use mpp_mod,           only: mpp_error, FATAL, stdlog, get_unit, mpp_pe, input_nml_file
  use mpp_mod,           only: mpp_root_pe, stdout ! snz
  use mpp_mod,           only: mpp_clock_id, mpp_clock_begin, mpp_clock_end
@@ -63,8 +61,10 @@ module fv_ada_nudge_mod
                               get_var3_r4, get_var2_r4, get_var1_real
  use fv_arrays_mod,     only: fv_grid_type, fv_grid_bounds_type, fv_nest_type, R_GRID
 
- use fms_io_mod, only: register_restart_field, restart_file_type, restore_state
- use fms_io_mod, only: save_restart, get_mosaic_tile_file
+ use fms2_io_mod,       only : register_restart_field, open_file, close_file, &
+                               read_restart, register_field, &
+                               register_variable_attribute, file_exists
+ use fv_io_mod,         only : fv_io_register_axis
  use axis_utils_mod, only : frac_index
 
 #ifdef ENABLE_ADA
@@ -235,8 +235,9 @@ module fv_ada_nudge_mod
   integer :: id_u_da, id_v_da, id_t_da, id_q_da, id_ps_da ! snz
   integer :: id_ada
 
-  type(restart_file_type) :: ada_driver_restart ! snz
-  character(len=*), parameter :: restart_file="ada_driver.res.nc" ! snz
+  type(FmsNetcdfFile_t) :: ada_driver_restart ! snz
+  character(len=*), parameter :: restart_file="INPUT/ada_driver.res.nc" ! snz
+  character(len=8), dimension(4) :: dim_names_4d
 
 #ifdef ENABLE_ADA ! snz
   type(model_data_type) :: Atm_var
@@ -1482,7 +1483,6 @@ subroutine fv_ada_nudge_init(time, axes, npz, zvir, ak, bk, ts, phis, gridstruct
 
   integer :: id_restart !< Currently not used for anything other than a return
   !value.
-  character(len=256) :: restart_file_instance
 
   real, pointer, dimension(:,:,:) :: agrid
 
@@ -1522,20 +1522,9 @@ subroutine fv_ada_nudge_init(time, axes, npz, zvir, ak, bk, ts, phis, gridstruct
 
    track_file_name = "No_File_specified"
 
-#ifdef INTERNAL_FILE_NML
-       read(input_nml_file, nml = fv_ada_nudge_nml, iostat = io)
-       ierr = check_nml_error(io,'fv_ada_nudge_nml')
-#else
-    if( file_exist( 'input.nml' ) ) then
-       unit = open_namelist_file ()
-       io = 1
-       do while ( io .ne. 0 )
-          read( unit, nml = fv_ada_nudge_nml, iostat = io, end = 10 )
-          ierr = check_nml_error(io,'fv_ada_nudge_nml')
-       end do
-10     call close_file ( unit )
-    end if
-#endif
+    read(input_nml_file, nml = fv_ada_nudge_nml, iostat = io)
+    ierr = check_nml_error(io,'fv_ada_nudge_nml')
+
     call write_version_number ( 'FV_ADA_NUDGE_MOD', version )
     if ( master ) then
          f_unit=stdlog()
@@ -1793,26 +1782,32 @@ subroutine fv_ada_nudge_init(time, axes, npz, zvir, ak, bk, ts, phis, gridstruct
                'da ps', 'Pa', missing_value=missing_value )
 
 ! snz add the following lines for recording the return values from the previous assim run
-    call get_mosaic_tile_file(restart_file, restart_file_instance,&
-         & .FALSE., domain)
-
-    id_restart = register_restart_field(ada_driver_restart, restart_file_instance, &
-         & "u_adj", Atm_var%u_adj(:,:,:), domain=domain)
-    id_restart = register_restart_field(ada_driver_restart, restart_file_instance, &
-         & "v_adj", Atm_var%v_adj(:,:,:), domain=domain)
-    id_restart = register_restart_field(ada_driver_restart, restart_file_instance, &
-         & "t_adj", Atm_var%t_adj(:,:,:), domain=domain)
-    id_restart = register_restart_field(ada_driver_restart, restart_file_instance, &
-         & "q_adj", Atm_var%q_adj(:,:,:), domain=domain)
-    id_restart = register_restart_field(ada_driver_restart, restart_file_instance, &
-         & "ps_adj", Atm_var%ps_adj(:,:), domain=domain)
-
-    if ( file_exist('INPUT/'//trim(restart_file_instance), domain=domain) ) then
-       if ( mpp_pe() .eq. mpp_root_pe() ) then
-          write (stdout_unit,*) 'Reading ada restart information from ', 'INPUT/'//trim(restart_file_instance)
-       end if
-       call restore_state(ada_driver_restart, DIRECTORY='INPUT')
-    end if
+
+! set dimensions for register restart
+    dim_names_4d(1) = "xaxis_1"
+    dim_names_4d(2) = "yaxis_1"
+    dim_names_4d(3) = "zaxis_1"
+    dim_names_4d(4) = "Time"
+
+    if (open_file(ada_driver_restart, restart_file, "read", domain, is_restart=.true.))
+      call fv_io_register_axis(ada_driver_restart, numx=1, numy=1, numz=1, zsize=(/size(Atm_var%u_adj,3)/))
+      call register_restart_field(ada_driver_restart, &
+           & "u_adj", Atm_var%u_adj(:,:,:), dim_names_4d)
+      call register_restart_field(ada_driver_restart, &
+           & "v_adj", Atm_var%v_adj(:,:,:), dim_names_4d)
+      call register_restart_field(ada_driver_restart, &
+           & "t_adj", Atm_var%t_adj(:,:,:), dim_names_4d)
+      call register_restart_field(ada_driver_restart, &
+           & "q_adj", Atm_var%q_adj(:,:,:), dim_names_4d)
+      call register_restart_field(ada_driver_restart, &
+           & "ps_adj", Atm_var%ps_adj(:,:), dim_names_4d)
+
+      if ( mpp_pe() .eq. mpp_root_pe() ) then
+          write (stdout_unit,*) 'Reading ada restart information from ', 'INPUT/'//trim(restart_file)
+      end if
+      call read_restart(ada_driver_restart)
+      call close_file(ada_driver_restart)
+    endif 
 
 #endif ! snz for ENABLE_ADA
 
@@ -1848,7 +1843,7 @@ subroutine get_ncep_analysis ( ps, u, v, t, q, zvir, ts, nfile, fname, bd, time
                                           !! model run
   integer :: is,  ie,  js,  je
 
-  if( .not. file_exist(fname) ) then
+  if( .not. file_exists(fname) ) then
      call mpp_error(FATAL,'==> Error from get_ncep_analysis: file not found')
   else
      call open_ncfile( fname, ncid )        ! open the file
@@ -2516,7 +2511,21 @@ subroutine fv_ada_nudge_end
 
 #ifdef ENABLE_ADA ! snz
 
-    call save_restart(ada_driver_restart)
+    if (open_file(ada_driver_restart, restart_file, "overwrite", domain, is_restart=.true.)) then
+       call fv_io_register_axis(ada_driver_restart, numx=1, numy=1, numz=1, zsize=(/size(Atm_var%u_adj,3)/))
+       call register_restart_field(ada_driver_restart, &
+            & "u_adj", Atm_var%u_adj(:,:,:), dim_names_4d)
+       call register_restart_field(ada_driver_restart, &
+            & "v_adj", Atm_var%v_adj(:,:,:), dim_names_4d)
+       call register_restart_field(ada_driver_restart, &
+            & "t_adj", Atm_var%t_adj(:,:,:), dim_names_4d)
+       call register_restart_field(ada_driver_restart, &
+            & "q_adj", Atm_var%q_adj(:,:,:), dim_names_4d)
+       call register_restart_field(ada_driver_restart, &
+            & "ps_adj", Atm_var%ps_adj(:,:), dim_names_4d)
+       call write_restart(ada_driver_restart)
+       call close_file(ada_driver_restart)
+    endif
 
     deallocate ( Atm_var%u, Atm_var%v, Atm_var%t, Atm_var%u_adj, Atm_var%v_adj, Atm_var%t_adj)
     deallocate ( Atm_var%q, Atm_var%ps, Atm_var%q_adj, Atm_var%ps_adj)

GFDL_tools/fv_climate_nudge.F90

@@ -20,10 +20,10 @@
 !***********************************************************************
 module fv_climate_nudge_mod
 
-use fms_mod,          only: open_namelist_file, check_nml_error,  &
-                            close_file, stdlog, mpp_pe, mpp_root_pe, &
+use fms_mod,          only: check_nml_error,  &
+                            stdlog, mpp_pe, mpp_root_pe, &
                             write_version_number, string, error_mesg, &
-                            FATAL, WARNING, NOTE, file_exist
+                            FATAL, WARNING, NOTE
 use mpp_mod,          only: input_nml_file
 use diag_manager_mod, only: register_diag_field, send_data,   &
                             register_static_field
@@ -129,20 +129,8 @@ subroutine fv_climate_nudge_init ( Time, axes, flag )
    if (module_is_initialized) return
 
  ! read namelist
-#ifdef INTERNAL_FILE_NML
    read (input_nml_file, nml=fv_climate_nudge_nml, iostat=io)
    ierr = check_nml_error (io, 'fv_climate_nudge_nml')
-#else
-   if (file_exist('input.nml') ) then
-     unit = open_namelist_file()
-     ierr=1
-     do while (ierr /= 0)
-       read (unit, nml=fv_climate_nudge_nml, iostat=io, end=10)
-       ierr = check_nml_error (io, 'fv_climate_nudge_nml')
-     enddo
-10   call close_file (unit)
-   endif
-#endif
 
 !----- write version and namelist to log file -----
 

GFDL_tools/fv_cmip_diag.F90

@@ -21,11 +21,10 @@
 module fv_cmip_diag_mod
 
 use mpp_mod,            only: input_nml_file
-use fms_mod,            only: open_namelist_file, check_nml_error, &
-                              close_file, stdlog, mpp_pe, mpp_root_pe, &
-                              write_version_number, file_exist, &
+use fms_mod,            only: check_nml_error, string, &
+                              stdlog, mpp_pe, mpp_root_pe, &
+                              write_version_number, &
                               error_mesg, FATAL, WARNING, NOTE
-use fms_io_mod,         only: set_domain, nullify_domain, string
 use time_manager_mod,   only: time_type
 use mpp_domains_mod,    only: domain2d
 use diag_manager_mod,   only: register_diag_field, diag_axis_init, &
@@ -120,31 +119,15 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
   endif
 
 !----- read namelist -----
-#ifdef INTERNAL_FILE_NML
   read (input_nml_file, nml=fv_cmip_diag_nml, iostat=io)
   ierr = check_nml_error (io, 'fv_cmip_diag_nml')
-#else
-  if (file_exist('input.nml') ) then
-    iunit = open_namelist_file()
-    ierr=1
-    do while (ierr /= 0)
-      read (iunit, nml=fv_cmip_diag_nml, iostat=io, end=10)
-      ierr = check_nml_error (io, 'fv_cmip_diag_nml')
-    enddo
-10  call close_file (iunit)
-  endif
-#endif
 
 !----- write version and namelist to log file -----
 
   iunit = stdlog()
   call write_version_number ( 'FV_CMIP_DIAG_MOD', version )
   if (mpp_pe() == mpp_root_pe()) write (iunit, nml=fv_cmip_diag_nml)
 
-
-! Set domain so that diag_manager can access tile information
-  call set_domain(Atm(1)%domain)
-
 ! axis identifiers
   area_id = get_diag_field_id ('dynamics', 'area')
   if (area_id .eq. DIAG_FIELD_NOT_FOUND) call error_mesg &
@@ -411,7 +394,6 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
         call diag_field_add_attribute (id_zg1000, 'coordinates', 'p1000')
 
 !--- done ---
-  call nullify_domain()
   module_is_initialized=.true.
 
 !-----------------------------------------------------------------------
@@ -455,8 +437,6 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
   ngc = Atm(n)%ng
   npz = Atm(n)%npz
 
-  call set_domain(Atm(n)%domain)
-
   ! set flags for computing quantities
   compute_rh = .false.
   compute_wa = .false.
@@ -688,10 +668,6 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
     used = send_data (id_zg1000, dat3(:,:,1), Time)
   endif
 
-!----------------------------------------------------------------------
-
-  call nullify_domain()
-
 !----------------------------------------------------------------------
 
 end subroutine fv_cmip_diag

GFDL_tools/fv_diag_column.F90

@@ -8,7 +8,6 @@ module fv_diag_column_mod
   use fms_mod,            only: write_version_number, lowercase
   use mpp_mod,            only: mpp_error, FATAL, stdlog, mpp_pe, mpp_root_pe, mpp_sum, &
                                 mpp_max, NOTE, input_nml_file, get_unit
-  use mpp_io_mod,         only: mpp_flush
   use fv_sg_mod,          only: qsmith
 
   implicit none
@@ -79,20 +78,7 @@ subroutine fv_diag_column_init(Atm, yr_init, mo_init, dy_init, hr_init, do_diag_
     diag_sonde_j(:) = -999
     diag_sonde_tile(:) = -99
 
-#ifdef INTERNAL_FILE_NML
     read(input_nml_file, nml=fv_diag_column_nml,iostat=ios)
-#else
-    inquire (file=trim(Atm%nml_filename), exist=exists)
-    if (.not. exists) then
-      write(errmsg,*) 'fv_diag_column_nml: namelist file ',trim(Atm%nml_filename),' does not exist'
-      call mpp_error(FATAL, errmsg)
-    else
-      open (unit=nlunit, file=Atm%nml_filename, READONLY, status='OLD', iostat=ios)
-    endif
-    rewind(nlunit)
-    read (nlunit, nml=fv_diag_column_nml, iostat=ios)
-    close (nlunit)
-#endif
 
     if (do_diag_debug .or. do_diag_sonde) then
        call read_column_table
@@ -394,10 +380,8 @@ subroutine debug_column(pt, delp, delz, u, v, w, q, npz, ncnst, sphum, nwat, zvi
 
        write(unit, *) '==================================================================='
        write(unit, *)
-
-       call mpp_flush(unit)
-
-
+       flush(unit)
+
     enddo
 
   end subroutine debug_column
@@ -487,8 +471,6 @@ subroutine debug_column_dyn(pt, delp, delz, u, v, w, q, heat_source, cappa, akap
        write(unit, *) '==================================================================='
        write(unit, *)
 
-       call mpp_flush(unit)
-
     enddo
 
   end subroutine debug_column_dyn
@@ -582,8 +564,6 @@ subroutine sounding_column( pt, delp, delz, u, v, q, peln, pkz, thetae, phis, &
              enddo
           endif
 
-          call mpp_flush(unit)
-
     enddo