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+Add explicit API documentation to MOM6 framework #1297

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merged 8 commits into from
Jan 26, 2021
Merged

+Add explicit API documentation to MOM6 framework #1297

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3126f05
+Made get_domain_extent work with domain2D types
Hallberg-NOAA Jan 24, 2021
74f2290
+Added MOM_coupler_types.F90
Hallberg-NOAA Jan 24, 2021
9ad5dcb
Use new MOM_coupler_types interfaces with tracers
Hallberg-NOAA Jan 24, 2021
73304eb
Eliminated mpp calls from coupled_driver
Hallberg-NOAA Jan 24, 2021
a54f47a
+Eliminated fms calls from solo_driver
Hallberg-NOAA Jan 24, 2021
6712015
+Added 7 thin wrapper routines to MOM_io_infra.F90
Hallberg-NOAA Jan 25, 2021
f483b29
Merge branch 'dev/gfdl' into framework_APIs
Hallberg-NOAA Jan 25, 2021
7ce0ce3
Merge branch 'dev/gfdl' into framework_APIs
Hallberg-NOAA Jan 26, 2021
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14 changes: 6 additions & 8 deletions config_src/coupled_driver/MOM_surface_forcing_gfdl.F90
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Expand Up @@ -7,6 +7,9 @@ module MOM_surface_forcing_gfdl
!#CTRL# use MOM_controlled_forcing, only : ctrl_forcing_CS
use MOM_coms, only : reproducing_sum, field_chksum
use MOM_constants, only : hlv, hlf
use MOM_coupler_types, only : coupler_2d_bc_type, coupler_type_write_chksums
use MOM_coupler_types, only : coupler_type_initialized, coupler_type_spawn
use MOM_coupler_types, only : coupler_type_copy_data
use MOM_cpu_clock, only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
use MOM_cpu_clock, only : CLOCK_SUBCOMPONENT
use MOM_diag_mediator, only : diag_ctrl, safe_alloc_ptr, time_type
Expand All @@ -23,7 +26,7 @@ module MOM_surface_forcing_gfdl
use MOM_grid, only : ocean_grid_type
use MOM_interpolate, only : init_external_field, time_interp_external
use MOM_interpolate, only : time_interp_external_init
use MOM_io, only : slasher, write_version_number, MOM_read_data
use MOM_io, only : slasher, write_version_number, MOM_read_data, stdout
use MOM_restart, only : register_restart_field, restart_init, MOM_restart_CS
use MOM_restart, only : restart_init_end, save_restart, restore_state
use MOM_string_functions, only : uppercase
Expand All @@ -33,11 +36,7 @@ module MOM_surface_forcing_gfdl
use user_revise_forcing, only : user_alter_forcing, user_revise_forcing_init
use user_revise_forcing, only : user_revise_forcing_CS

use coupler_types_mod, only : coupler_2d_bc_type, coupler_type_write_chksums
use coupler_types_mod, only : coupler_type_initialized, coupler_type_spawn
use coupler_types_mod, only : coupler_type_copy_data
use data_override_mod, only : data_override_init, data_override
use fms_mod, only : stdout

implicit none ; private

Expand Down Expand Up @@ -318,8 +317,7 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,

if ((.not.coupler_type_initialized(fluxes%tr_fluxes)) .and. &
coupler_type_initialized(IOB%fluxes)) &
call coupler_type_spawn(IOB%fluxes, fluxes%tr_fluxes, &
(/is,is,ie,ie/), (/js,js,je,je/))
call coupler_type_spawn(IOB%fluxes, fluxes%tr_fluxes, (/is,is,ie,ie/), (/js,js,je,je/))
! It might prove valuable to use the same array extents as the rest of the
! ocean model, rather than using haloless arrays, in which case the last line
! would be: ( (/isd,is,ie,ied/), (/jsd,js,je,jed/))
Expand Down Expand Up @@ -1628,7 +1626,7 @@ subroutine ice_ocn_bnd_type_chksum(id, timestep, iobt)
!! ocean in a coupled model whose checksums are reported
integer :: n,m, outunit

outunit = stdout()
outunit = stdout

write(outunit,*) "BEGIN CHECKSUM(ice_ocean_boundary_type):: ", id, timestep
write(outunit,100) 'iobt%u_flux ', field_chksum( iobt%u_flux )
Expand Down
79 changes: 27 additions & 52 deletions config_src/coupled_driver/ocean_model_MOM.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -17,10 +17,14 @@ module ocean_model_mod
use MOM, only : get_ocean_stocks, step_offline
use MOM_coms, only : field_chksum
use MOM_constants, only : CELSIUS_KELVIN_OFFSET, hlf
use MOM_coupler_types, only : coupler_1d_bc_type, coupler_2d_bc_type
use MOM_coupler_types, only : coupler_type_spawn, coupler_type_write_chksums
use MOM_coupler_types, only : coupler_type_initialized, coupler_type_copy_data
use MOM_coupler_types, only : coupler_type_set_diags, coupler_type_send_data
use MOM_diag_mediator, only : diag_ctrl, enable_averaging, disable_averaging
use MOM_diag_mediator, only : diag_mediator_close_registration, diag_mediator_end
use MOM_domains, only : pass_var, pass_vector, AGRID, BGRID_NE, CGRID_NE
use MOM_domains, only : TO_ALL, Omit_Corners
use MOM_domains, only : MOM_domain_type, domain2d, clone_MOM_domain, get_domain_extent
use MOM_domains, only : pass_var, pass_vector, AGRID, BGRID_NE, CGRID_NE, TO_ALL, Omit_Corners
use MOM_error_handler, only : MOM_error, MOM_mesg, FATAL, WARNING, is_root_pe
use MOM_error_handler, only : callTree_enter, callTree_leave
use MOM_EOS, only : gsw_sp_from_sr, gsw_pt_from_ct
Expand All @@ -31,7 +35,7 @@ module ocean_model_mod
use MOM_forcing_type, only : forcing_diagnostics, mech_forcing_diags
use MOM_get_input, only : Get_MOM_Input, directories
use MOM_grid, only : ocean_grid_type
use MOM_io, only : close_file, file_exists, read_data, write_version_number
use MOM_io, only : close_file, file_exists, read_data, write_version_number, stdout
use MOM_marine_ice, only : iceberg_forces, iceberg_fluxes, marine_ice_init, marine_ice_CS
use MOM_restart, only : MOM_restart_CS, save_restart
use MOM_string_functions, only : uppercase
Expand All @@ -52,14 +56,6 @@ module ocean_model_mod
use MOM_ice_shelf, only : add_shelf_forces, ice_shelf_end, ice_shelf_save_restart
use MOM_wave_interface, only: wave_parameters_CS, MOM_wave_interface_init
use MOM_wave_interface, only: MOM_wave_interface_init_lite, Update_Surface_Waves
use coupler_types_mod, only : coupler_1d_bc_type, coupler_2d_bc_type
use coupler_types_mod, only : coupler_type_spawn, coupler_type_write_chksums
use coupler_types_mod, only : coupler_type_initialized, coupler_type_copy_data
use coupler_types_mod, only : coupler_type_set_diags, coupler_type_send_data
use mpp_domains_mod, only : domain2d, mpp_get_layout, mpp_get_global_domain
use mpp_domains_mod, only : mpp_define_domains, mpp_get_compute_domain, mpp_get_data_domain
use atmos_ocean_fluxes_mod, only : aof_set_coupler_flux
use fms_mod, only : stdout

#include <MOM_memory.h>

Expand Down Expand Up @@ -107,7 +103,7 @@ module ocean_model_mod
!! points of the two velocity components. Valid entries
!! include AGRID, BGRID_NE, CGRID_NE, BGRID_SW, and CGRID_SW,
!! corresponding to the community-standard Arakawa notation.
!! (These are named integers taken from mpp_parameter_mod.)
!! (These are named integers taken from the MOM_domains module.)
!! Following MOM5, stagger is BGRID_NE by default when the
!! ocean is initialized, but here it is set to -999 so that
!! a global max across ocean and non-ocean processors can be
Expand Down Expand Up @@ -391,14 +387,8 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
call MOM_wave_interface_init_lite(param_file)
endif

if (associated(OS%grid%Domain%maskmap)) then
call initialize_ocean_public_type(OS%grid%Domain%mpp_domain, Ocean_sfc, &
OS%diag, maskmap=OS%grid%Domain%maskmap, &
gas_fields_ocn=gas_fields_ocn)
else
call initialize_ocean_public_type(OS%grid%Domain%mpp_domain, Ocean_sfc, &
OS%diag, gas_fields_ocn=gas_fields_ocn)
endif
call initialize_ocean_public_type(OS%grid%Domain, Ocean_sfc, OS%diag, &
gas_fields_ocn=gas_fields_ocn)

! This call can only occur here if the coupler_bc_type variables have been
! initialized already using the information from gas_fields_ocn.
Expand Down Expand Up @@ -513,8 +503,7 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, time_start_upda
(/is,is,ie,ie/), (/js,js,je,je/), as_needed=.true.)

! Translate Ice_ocean_boundary into fluxes and forces.
call mpp_get_compute_domain(Ocean_sfc%Domain, index_bnds(1), index_bnds(2), &
index_bnds(3), index_bnds(4))
call get_domain_extent(Ocean_sfc%Domain, index_bnds(1), index_bnds(2), index_bnds(3), index_bnds(4))

if (do_dyn) then
call convert_IOB_to_forces(Ice_ocean_boundary, OS%forces, index_bnds, OS%Time_dyn, OS%grid, OS%US, &
Expand Down Expand Up @@ -733,7 +722,7 @@ end subroutine ocean_model_end
subroutine ocean_model_save_restart(OS, Time, directory, filename_suffix)
type(ocean_state_type), pointer :: OS !< A pointer to the structure containing the
!! internal ocean state (in).
type(time_type), intent(in) :: Time !< The model time at this call, needed for mpp_write calls.
type(time_type), intent(in) :: Time !< The model time at this call, needed for writing files.
character(len=*), optional, intent(in) :: directory !< An optional directory into which to
!! write these restart files.
character(len=*), optional, intent(in) :: filename_suffix !< An optional suffix (e.g., a time-stamp)
Expand Down Expand Up @@ -765,16 +754,12 @@ subroutine ocean_model_save_restart(OS, Time, directory, filename_suffix)
end subroutine ocean_model_save_restart

!> Initialize the public ocean type
subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap, &
gas_fields_ocn)
type(domain2D), intent(in) :: input_domain !< The ocean model domain description
subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, gas_fields_ocn)
type(MOM_domain_type), intent(in) :: input_domain !< The ocean model domain description
type(ocean_public_type), intent(inout) :: Ocean_sfc !< A structure containing various publicly
!! visible ocean surface properties after initialization, whose
!! elements are allocated here.
type(diag_ctrl), intent(in) :: diag !< A structure that regulates diagnsotic output
logical, dimension(:,:), &
optional, intent(in) :: maskmap !< A mask indicating which virtual processors
!! are actually in use. If missing, all are used.
!! visible ocean surface properties after
!! initialization, whose elements are allocated here.
type(diag_ctrl), intent(in) :: diag !< A structure that regulates diagnostic output
type(coupler_1d_bc_type), &
optional, intent(in) :: gas_fields_ocn !< If present, this type describes the
!! ocean and surface-ice fields that will participate
Expand All @@ -786,14 +771,9 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,
! and have no halos.
integer :: isc, iec, jsc, jec

call mpp_get_layout(input_domain,layout)
call mpp_get_global_domain(input_domain, xsize=xsz, ysize=ysz)
if (PRESENT(maskmap)) then
call mpp_define_domains((/1,xsz,1,ysz/),layout,Ocean_sfc%Domain, maskmap=maskmap)
else
call mpp_define_domains((/1,xsz,1,ysz/),layout,Ocean_sfc%Domain)
endif
call mpp_get_compute_domain(Ocean_sfc%Domain, isc, iec, jsc, jec)
call clone_MOM_domain(input_domain, Ocean_sfc%Domain, halo_size=0, symmetric=.false.)

call get_domain_extent(Ocean_sfc%Domain, isc, iec, jsc, jec)

allocate ( Ocean_sfc%t_surf (isc:iec,jsc:jec), &
Ocean_sfc%s_surf (isc:iec,jsc:jec), &
Expand Down Expand Up @@ -849,8 +829,7 @@ subroutine convert_state_to_ocean_type(sfc_state, Ocean_sfc, G, US, patm, press_
is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec
call pass_vector(sfc_state%u, sfc_state%v, G%Domain)

call mpp_get_compute_domain(Ocean_sfc%Domain, isc_bnd, iec_bnd, &
jsc_bnd, jec_bnd)
call get_domain_extent(Ocean_sfc%Domain, isc_bnd, iec_bnd, jsc_bnd, jec_bnd)
if (present(patm)) then
! Check that the inidicies in patm are (isc_bnd:iec_bnd,jsc_bnd:jec_bnd).
if (.not.present(press_to_z)) call MOM_error(FATAL, &
Expand Down Expand Up @@ -1044,20 +1023,17 @@ subroutine ocean_model_data2D_get(OS, Ocean, name, array2D, isc, jsc)
integer , intent(in) :: isc !< The starting i-index of array2D
integer , intent(in) :: jsc !< The starting j-index of array2D

integer :: g_isc, g_iec, g_jsc, g_jec,g_isd, g_ied, g_jsd, g_jed, i, j
integer :: g_isc, g_iec, g_jsc, g_jec, g_isd, g_ied, g_jsd, g_jed, i, j

if (.not.associated(OS)) return
if (.not.OS%is_ocean_pe) return

! The problem is %areaT is on MOM domain but Ice_Ocean_Boundary%... is on mpp domain.
! We want to return the MOM data on the mpp (compute) domain
! Get MOM domain extents
call mpp_get_compute_domain(OS%grid%Domain%mpp_domain, g_isc, g_iec, g_jsc, g_jec)
call mpp_get_data_domain (OS%grid%Domain%mpp_domain, g_isd, g_ied, g_jsd, g_jed)
! The problem is that %areaT is on MOM domain but Ice_Ocean_Boundary%... is on a haloless domain.
! We want to return the MOM data on the haloless (compute) domain
call get_domain_extent(OS%grid%Domain, g_isc, g_iec, g_jsc, g_jec, g_isd, g_ied, g_jsd, g_jed)

g_isc = g_isc-g_isd+1 ; g_iec = g_iec-g_isd+1 ; g_jsc = g_jsc-g_jsd+1 ; g_jec = g_jec-g_jsd+1


select case(name)
case('area')
array2D(isc:,jsc:) = OS%US%L_to_m**2*OS%grid%areaT(g_isc:g_iec,g_jsc:g_jec)
Expand Down Expand Up @@ -1127,7 +1103,7 @@ subroutine ocean_public_type_chksum(id, timestep, ocn)
!! visible ocean surface fields.
integer :: n, m, outunit

outunit = stdout()
outunit = stdout

write(outunit,*) "BEGIN CHECKSUM(ocean_type):: ", id, timestep
write(outunit,100) 'ocean%t_surf ', field_chksum(ocn%t_surf )
Expand Down Expand Up @@ -1180,8 +1156,7 @@ subroutine ocean_model_get_UV_surf(OS, Ocean, name, array2D, isc, jsc)
G => OS%grid
is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec

call mpp_get_compute_domain(Ocean%Domain, isc_bnd, iec_bnd, &
jsc_bnd, jec_bnd)
call get_domain_extent(Ocean%Domain, isc_bnd, iec_bnd, jsc_bnd, jec_bnd)

i0 = is - isc_bnd ; j0 = js - jsc_bnd

Expand Down
39 changes: 14 additions & 25 deletions config_src/solo_driver/MOM_driver.F90
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Expand Up @@ -33,15 +33,20 @@ program MOM_main
use MOM, only : get_MOM_state_elements, MOM_state_is_synchronized
use MOM, only : step_offline
use MOM_coms, only : Set_PElist
use MOM_domains, only : MOM_infra_init, MOM_infra_end
use MOM_domains, only : MOM_infra_init, MOM_infra_end, set_MOM_thread_affinity
use MOM_ensemble_manager, only : ensemble_manager_init, get_ensemble_size
use MOM_ensemble_manager, only : ensemble_pelist_setup
use MOM_error_handler, only : MOM_error, MOM_mesg, WARNING, FATAL, is_root_pe
use MOM_error_handler, only : callTree_enter, callTree_leave, callTree_waypoint
use MOM_file_parser, only : read_param, get_param, log_param, log_version, param_file_type
use MOM_file_parser, only : close_param_file
use MOM_forcing_type, only : forcing, mech_forcing, forcing_diagnostics
use MOM_forcing_type, only : mech_forcing_diags, MOM_forcing_chksum, MOM_mech_forcing_chksum
use MOM_get_input, only : directories
use MOM_get_input, only : get_MOM_input, directories
use MOM_grid, only : ocean_grid_type
use MOM_ice_shelf, only : initialize_ice_shelf, ice_shelf_end, ice_shelf_CS
use MOM_ice_shelf, only : shelf_calc_flux, add_shelf_forces, ice_shelf_save_restart
use MOM_ice_shelf, only : initialize_ice_shelf_fluxes, initialize_ice_shelf_forces
use MOM_interpolate, only : time_interp_external_init
use MOM_io, only : file_exists, open_file, close_file
use MOM_io, only : check_nml_error, io_infra_init, io_infra_end
Expand All @@ -50,30 +55,19 @@ program MOM_main
use MOM_string_functions,only : uppercase
use MOM_surface_forcing, only : set_forcing, forcing_save_restart
use MOM_surface_forcing, only : surface_forcing_init, surface_forcing_CS
use MOM_time_manager, only : time_type, set_date, get_date
use MOM_time_manager, only : real_to_time, time_type_to_real
use MOM_time_manager, only : time_type, set_date, get_date, real_to_time, time_type_to_real
use MOM_time_manager, only : operator(+), operator(-), operator(*), operator(/)
use MOM_time_manager, only : operator(>), operator(<), operator(>=)
use MOM_time_manager, only : increment_date, set_calendar_type, month_name
use MOM_time_manager, only : JULIAN, GREGORIAN, NOLEAP, THIRTY_DAY_MONTHS
use MOM_time_manager, only : NO_CALENDAR
use MOM_time_manager, only : JULIAN, GREGORIAN, NOLEAP, THIRTY_DAY_MONTHS, NO_CALENDAR
use MOM_tracer_flow_control, only : tracer_flow_control_CS
use MOM_unit_scaling, only : unit_scale_type
use MOM_variables, only : surface
use MOM_verticalGrid, only : verticalGrid_type
use MOM_wave_interface, only : wave_parameters_CS, MOM_wave_interface_init
use MOM_wave_interface, only : MOM_wave_interface_init_lite, Update_Surface_Waves
use MOM_write_cputime, only : write_cputime, MOM_write_cputime_init
use MOM_write_cputime, only : write_cputime_start_clock, write_cputime_CS
use MOM_get_input, only : get_MOM_input
use ensemble_manager_mod, only : ensemble_manager_init, get_ensemble_size
use ensemble_manager_mod, only : ensemble_pelist_setup
use fms_affinity_mod, only : fms_affinity_init, fms_affinity_set,fms_affinity_get

use MOM_ice_shelf, only : initialize_ice_shelf, ice_shelf_end, ice_shelf_CS
use MOM_ice_shelf, only : shelf_calc_flux, add_shelf_forces, ice_shelf_save_restart
use MOM_ice_shelf, only : initialize_ice_shelf_fluxes, initialize_ice_shelf_forces

use MOM_wave_interface, only: wave_parameters_CS, MOM_wave_interface_init
use MOM_wave_interface, only: MOM_wave_interface_init_lite, Update_Surface_Waves

implicit none

Expand Down Expand Up @@ -253,13 +247,8 @@ program MOM_main
endif
endif

!$ call fms_affinity_init
!$ call fms_affinity_set('OCEAN', use_hyper_thread, ocean_nthreads)
!$ call omp_set_num_threads(ocean_nthreads)
!$OMP PARALLEL
!$ write(6,*) "ocean_solo OMPthreading ", fms_affinity_get(), omp_get_thread_num(), omp_get_num_threads()
!$ flush(6)
!$OMP END PARALLEL
! This call sets the number and affinity of threads with openMP.
!$ call set_MOM_thread_affinity(ocean_nthreads, use_hyper_thread)

! Read ocean_solo restart, which can override settings from the namelist.
if (file_exists(trim(dirs%restart_input_dir)//'ocean_solo.res')) then
Expand Down Expand Up @@ -337,7 +326,7 @@ program MOM_main
call callTree_waypoint("done surface_forcing_init")


call get_param(param_file,mod_name,"USE_WAVES",Use_Waves,&
call get_param(param_file,mod_name, "USE_WAVES", Use_Waves, &
"If true, enables surface wave modules.",default=.false.)
if (use_waves) then
call MOM_wave_interface_init(Time, grid, GV, US, param_file, Waves_CSp, diag)
Expand Down
1 change: 0 additions & 1 deletion src/core/MOM.F90
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Expand Up @@ -47,7 +47,6 @@ module MOM
use MOM_time_manager, only : operator(-), operator(>), operator(*), operator(/)
use MOM_time_manager, only : operator(>=), operator(==), increment_date
use MOM_unit_tests, only : unit_tests
use coupler_types_mod, only : coupler_type_send_data, coupler_1d_bc_type, coupler_type_spawn

! MOM core modules
use MOM_ALE, only : ALE_init, ALE_end, ALE_main, ALE_CS, adjustGridForIntegrity
Expand Down
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