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Merged
laurenchilutti merged 8 commits into from
May 10, 2021
Merged

Fms2 io implementation #74

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ca1066f
Removing use of mpp_io_mod and fms_io_mod from the dycore code. Repl…
laurenchilutti Mar 5, 2021
c4d0928
Adding a call to set_filename_appendix so that nest is added to file…
laurenchilutti Mar 10, 2021
fe683c8
Updating dimension string arrays to address GNU compilation errors.
laurenchilutti Apr 21, 2021
fb96053
Merge branch 'master' into fms2_io_implementation
laurenchilutti Apr 21, 2021
04a6d6e
prepending INPUT/ to hrr_ctrl.nc and gfs_ctrl.nc in external_ic
laurenchilutti Apr 29, 2021
22fa998
Merge branch 'master' into fms2_io_implementation
laurenchilutti May 3, 2021
9746100
Adding pelist argument to some open_file calls, correcting some typos…
laurenchilutti May 4, 2021
35ee073
correcting minor typo and using fv_io_register_axis rather than regis…
laurenchilutti May 7, 2021
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97 changes: 53 additions & 44 deletions GFDL_tools/fv_ada_nudge.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)/))
Comment thread
laurenchilutti marked this conversation as resolved.
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)
Expand Down
18 changes: 3 additions & 15 deletions GFDL_tools/fv_climate_nudge.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 -----

Expand Down
30 changes: 3 additions & 27 deletions GFDL_tools/fv_cmip_diag.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -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, &
Expand Down Expand Up @@ -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 &
Expand Down Expand Up @@ -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.

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down
24 changes: 2 additions & 22 deletions GFDL_tools/fv_diag_column.F90
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)

Comment thread
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enddo

end subroutine debug_column
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -582,8 +564,6 @@ subroutine sounding_column( pt, delp, delz, u, v, q, peln, pkz, thetae, phis, &
enddo
endif

call mpp_flush(unit)

enddo


Expand Down
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