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Merge gfdl updates #2

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Nov 17, 2021
Merged

Merge gfdl updates #2

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1324656
Add weighted d[uv]_dt_str diagnostics (#1539)
NoraLoose Nov 5, 2021
f2e9983
+Argument cleanup in vertical diffusivity code
Hallberg-NOAA Oct 22, 2021
2e7624b
+Move rotate_dyn_horgrid to MOM_dyn_horgrid module
Hallberg-NOAA Oct 27, 2021
5a2bb8d
+Reduce use of dyn_horgrid in initialize_MOM
Hallberg-NOAA Oct 27, 2021
688bff9
(*)Fix compile-time issues with MOM_sum_driver.F90
Hallberg-NOAA Oct 27, 2021
73d5a62
Merge branch 'porous_topo2' into porous_updated
sditkovsky Nov 17, 2021
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39 changes: 24 additions & 15 deletions config_src/drivers/unit_drivers/MOM_sum_driver.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,14 @@ program MOM_main
use MOM_coms, only : EFP_type, operator(+), operator(-), assignment(=), EFP_to_real, real_to_EFP
use MOM_cpu_clock, only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
use MOM_cpu_clock, only : CLOCK_COMPONENT
use MOM_domains, only : MOM_domains_init, MOM_infra_init, MOM_infra_end
use MOM_domains, only : MOM_domain_type, MOM_domains_init, MOM_infra_init, MOM_infra_end
use MOM_dyn_horgrid, only : dyn_horgrid_type, create_dyn_horgrid, destroy_dyn_horgrid
use MOM_error_handler, only : MOM_error, MOM_mesg, WARNING, FATAL, is_root_pe
use MOM_error_handler, only : MOM_set_verbosity
use MOM_file_parser, only : read_param, get_param, log_param, log_version, param_file_type
use MOM_file_parser, only : open_param_file, close_param_file
use MOM_grid, only : MOM_grid_init, ocean_grid_type
use MOM_grid_initialize, only : set_grid_metrics
use MOM_hor_index, only : hor_index_type, hor_index_init
use MOM_io, only : MOM_io_init, file_exists, open_file, close_file
use MOM_io, only : check_nml_error, io_infra_init, io_infra_end
use MOM_io, only : APPEND_FILE, ASCII_FILE, READONLY_FILE, SINGLE_FILE
Expand All @@ -33,9 +34,10 @@ program MOM_main

#include <MOM_memory.h>

type(ocean_grid_type) :: grid ! A structure containing metrics and grid info.

type(param_file_type) :: param_file ! The structure indicating the file(s)
type(MOM_domain_type), pointer :: Domain => NULL() !< Ocean model domain
type(dyn_horgrid_type), pointer :: grid => NULL() ! A structure containing metrics and grid info
type(hor_index_type) :: HI ! A hor_index_type for array extents
type(param_file_type) :: param_file ! The structure indicating the file(s)
! containing all run-time parameters.
real :: max_depth ! The maximum ocean depth [m]
integer :: verbosity
Expand Down Expand Up @@ -76,14 +78,16 @@ program MOM_main
verbosity = 2 ; call read_param(param_file, "VERBOSITY", verbosity)
call MOM_set_verbosity(verbosity)

call MOM_domains_init(grid%domain, param_file)
call MOM_domains_init(Domain, param_file)

call MOM_io_init(param_file)
! call diag_mediator_init(param_file)
call MOM_grid_init(grid, param_file)
call hor_index_init(Domain, HI, param_file)
call create_dyn_horgrid(grid, HI)
grid%Domain => Domain

is = grid%isc ; ie = grid%iec ; js = grid%jsc ; je = grid%jec
isd = grid%isd ; ied = grid%ied ; jsd = grid%jsd ; jed = grid%jed
is = HI%isc ; ie = HI%iec ; js = HI%jsc ; je = HI%jec
isd = HI%isd ; ied = HI%ied ; jsd = HI%jsd ; jed = HI%jed

! Read all relevant parameters and write them to the model log.
call log_version(param_file, "MOM", version, "")
Expand All @@ -99,7 +103,7 @@ program MOM_main
allocate(depth_tot_std(num_sums)) ; depth_tot_std(:) = 0.0
allocate(depth_tot_fastR(num_sums)) ; depth_tot_fastR(:) = 0.0

! Set up the parameters of the physical domain (i.e. the grid), G
! Set up the parameters of the physical grid
call set_grid_metrics(grid, param_file)

! Set up the bottom depth, grid%bathyT either analytically or from file
Expand Down Expand Up @@ -157,21 +161,24 @@ program MOM_main
endif
enddo

call destroy_dyn_horgrid(grid)
call io_infra_end ; call MOM_infra_end

contains

!> This subroutine sets up the benchmark test case topography for debugging
subroutine benchmark_init_topog_local(D, G, param_file, max_depth)
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure
real, dimension(SZI_(G),SZJ_(G)), intent(out) :: D !< The ocean bottom depth in m
type(dyn_horgrid_type), intent(in) :: G !< The dynamic horizontal grid type
real, dimension(G%isd:G%ied,G%jsd:G%jed), &
intent(out) :: D !< Ocean bottom depth in m or [Z ~> m] if US is present
type(param_file_type), intent(in) :: param_file !< A structure to parse for run-time parameters
real, intent(in) :: max_depth !< The maximum ocean depth [m]

real :: min_depth ! The minimum ocean depth in m.
real :: PI ! 3.1415926... calculated as 4*atan(1)
real :: D0 ! A constant to make the maximum !
! basin depth MAXIMUM_DEPTH. !
real :: m_to_Z ! A dimensional rescaling factor.
real :: x, y
! This include declares and sets the variable "version".
# include "version_variable.h"
Expand All @@ -180,12 +187,14 @@ subroutine benchmark_init_topog_local(D, G, param_file, max_depth)
is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec
isd = G%isd ; ied = G%ied ; jsd = G%jsd ; jed = G%jed

call log_version(param_file, mdl, version)
m_to_Z = 1.0 ! ; if (present(US)) m_to_Z = US%m_to_Z

call log_version(param_file, mdl, version, "")
call get_param(param_file, mdl, "MINIMUM_DEPTH", min_depth, &
"The minimum depth of the ocean.", units="m", default=0.0)
"The minimum depth of the ocean.", units="m", default=0.0, scale=m_to_Z)

PI = 4.0*atan(1.0)
D0 = max_depth / 0.5;
D0 = max_depth / 0.5

! Calculate the depth of the bottom.
do i=is,ie ; do j=js,je
Expand Down
94 changes: 44 additions & 50 deletions src/core/MOM.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,7 @@ module MOM
use MOM_dynamics_unsplit_RK2, only : initialize_dyn_unsplit_RK2, end_dyn_unsplit_RK2
use MOM_dynamics_unsplit_RK2, only : MOM_dyn_unsplit_RK2_CS
use MOM_dyn_horgrid, only : dyn_horgrid_type, create_dyn_horgrid, destroy_dyn_horgrid
use MOM_dyn_horgrid, only : rotate_dyn_horgrid
use MOM_EOS, only : EOS_init, calculate_density, calculate_TFreeze, EOS_domain
use MOM_fixed_initialization, only : MOM_initialize_fixed
use MOM_forcing_type, only : allocate_forcing_type, allocate_mech_forcing
Expand Down Expand Up @@ -123,7 +124,6 @@ module MOM
use MOM_tracer_flow_control, only : tracer_flow_control_init, call_tracer_surface_state
use MOM_tracer_flow_control, only : tracer_flow_control_end
use MOM_transcribe_grid, only : copy_dyngrid_to_MOM_grid, copy_MOM_grid_to_dyngrid
use MOM_transcribe_grid, only : rotate_dyngrid
use MOM_unit_scaling, only : unit_scale_type, unit_scaling_init
use MOM_unit_scaling, only : unit_scaling_end, fix_restart_unit_scaling
use MOM_variables, only : surface, allocate_surface_state, deallocate_surface_state
Expand Down Expand Up @@ -1714,7 +1714,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
type(hor_index_type), pointer :: HI => NULL() ! A hor_index_type for array extents
type(hor_index_type), target :: HI_in ! HI on the input grid
type(verticalGrid_type), pointer :: GV => NULL()
type(dyn_horgrid_type), pointer :: dG => NULL()
type(dyn_horgrid_type), pointer :: dG => NULL(), test_dG => NULL()
type(dyn_horgrid_type), pointer :: dG_in => NULL()
type(diag_ctrl), pointer :: diag => NULL()
type(unit_scale_type), pointer :: US => NULL()
Expand Down Expand Up @@ -2174,8 +2174,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
! Swap axes for quarter and 3-quarter turns
if (CS%rotate_index) then
allocate(CS%G)
call clone_MOM_domain(G_in%Domain, CS%G%Domain, turns=turns, &
domain_name="MOM_rot")
call clone_MOM_domain(G_in%Domain, CS%G%Domain, turns=turns, domain_name="MOM_rot")
first_direction = modulo(first_direction + turns, 2)
else
CS%G => G_in
Expand All @@ -2200,38 +2199,50 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
local_indexing=.not.global_indexing)
call create_dyn_horgrid(dG_in, HI_in, bathymetry_at_vel=bathy_at_vel)
call clone_MOM_domain(G_in%Domain, dG_in%Domain)
! Also allocate the input ocean_grid_type type at this point based on the same information.
call MOM_grid_init(G_in, param_file, US, HI_in, bathymetry_at_vel=bathy_at_vel)

! Allocate initialize time-invariant MOM variables.
call MOM_initialize_fixed(dG_in, US, OBC_in, param_file, .false., dirs%output_directory)

! Copy the grid metrics and bathymetry to the ocean_grid_type
call copy_dyngrid_to_MOM_grid(dG_in, G_in, US)

call callTree_waypoint("returned from MOM_initialize_fixed() (initialize_MOM)")

! Determine HI and dG for the model index map.
call verticalGridInit( param_file, CS%GV, US )
GV => CS%GV

! Shift from using the temporary dynamic grid type to using the final (potentially static)
! and properly rotated ocean-specific grid type and horizontal index type.
if (CS%rotate_index) then
allocate(HI)
call rotate_hor_index(HI_in, turns, HI)
! NOTE: If indices are rotated, then G and G_in must both be initialized separately, and
! the dynamic grid must be created to handle the grid rotation. G%domain has already been
! initialzed above.
call MOM_grid_init(G, param_file, US, HI, bathymetry_at_vel=bathy_at_vel)
call create_dyn_horgrid(dG, HI, bathymetry_at_vel=bathy_at_vel)
call clone_MOM_domain(G%Domain, dG%Domain)
call rotate_dyngrid(dG_in, dG, US, turns)
call rotate_dyn_horgrid(dG_in, dG, US, turns)
call copy_dyngrid_to_MOM_grid(dG, G, US)

if (associated(OBC_in)) then
! TODO: General OBC index rotations is not yet supported.
if (modulo(turns, 4) /= 1) &
call MOM_error(FATAL, "OBC index rotation of 180 and 270 degrees is not yet supported.")
allocate(CS%OBC)
call rotate_OBC_config(OBC_in, dG_in, CS%OBC, dG, turns)
endif

call destroy_dyn_horgrid(dG)
else
! If not rotated, then G_in and G are the same grid.
HI => HI_in
dG => dG_in
G => G_in
CS%OBC => OBC_in
endif

call verticalGridInit( param_file, CS%GV, US )
GV => CS%GV

! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
if (CS%debug .or. dG%symmetric) &
call clone_MOM_domain(dG%Domain, dG%Domain_aux, symmetric=.false.)
! dG_in is retained for now so that it can be used with write_ocean_geometry_file() below.

call callTree_waypoint("grids initialized (initialize_MOM)")

Expand All @@ -2240,9 +2251,9 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
call tracer_registry_init(param_file, CS%tracer_Reg)

! Allocate and initialize space for the primary time-varying MOM variables.
is = dG%isc ; ie = dG%iec ; js = dG%jsc ; je = dG%jec ; nz = GV%ke
isd = dG%isd ; ied = dG%ied ; jsd = dG%jsd ; jed = dG%jed
IsdB = dG%IsdB ; IedB = dG%IedB ; JsdB = dG%JsdB ; JedB = dG%JedB
is = HI%isc ; ie = HI%iec ; js = HI%jsc ; je = HI%jec ; nz = GV%ke
isd = HI%isd ; ied = HI%ied ; jsd = HI%jsd ; jed = HI%jed
IsdB = HI%IsdB ; IedB = HI%IedB ; JsdB = HI%JsdB ; JedB = HI%JedB
ALLOC_(CS%u(IsdB:IedB,jsd:jed,nz)) ; CS%u(:,:,:) = 0.0
ALLOC_(CS%v(isd:ied,JsdB:JedB,nz)) ; CS%v(:,:,:) = 0.0
ALLOC_(CS%h(isd:ied,jsd:jed,nz)) ; CS%h(:,:,:) = GV%Angstrom_H
Expand Down Expand Up @@ -2279,12 +2290,12 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
else
conv2salt = GV%H_to_kg_m2
endif
call register_tracer(CS%tv%T, CS%tracer_Reg, param_file, dG%HI, GV, &
call register_tracer(CS%tv%T, CS%tracer_Reg, param_file, HI, GV, &
tr_desc=vd_T, registry_diags=.true., flux_nameroot='T', &
flux_units='W', flux_longname='Heat', &
flux_scale=conv2watt, convergence_units='W m-2', &
convergence_scale=conv2watt, CMOR_tendprefix="opottemp", diag_form=2)
call register_tracer(CS%tv%S, CS%tracer_Reg, param_file, dG%HI, GV, &
call register_tracer(CS%tv%S, CS%tracer_Reg, param_file, HI, GV, &
tr_desc=vd_S, registry_diags=.true., flux_nameroot='S', &
flux_units=S_flux_units, flux_longname='Salt', &
flux_scale=conv2salt, convergence_units='kg m-2 s-1', &
Expand Down Expand Up @@ -2364,24 +2375,24 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
call restart_init(param_file, restart_CSp)
call set_restart_fields(GV, US, param_file, CS, restart_CSp)
if (CS%split) then
call register_restarts_dyn_split_RK2(dG%HI, GV, param_file, &
call register_restarts_dyn_split_RK2(HI, GV, param_file, &
CS%dyn_split_RK2_CSp, restart_CSp, CS%uh, CS%vh)
elseif (CS%use_RK2) then
call register_restarts_dyn_unsplit_RK2(dG%HI, GV, param_file, &
call register_restarts_dyn_unsplit_RK2(HI, GV, param_file, &
CS%dyn_unsplit_RK2_CSp, restart_CSp)
else
call register_restarts_dyn_unsplit(dG%HI, GV, param_file, &
call register_restarts_dyn_unsplit(HI, GV, param_file, &
CS%dyn_unsplit_CSp, restart_CSp)
endif

! This subroutine calls user-specified tracer registration routines.
! Additional calls can be added to MOM_tracer_flow_control.F90.
call call_tracer_register(dG%HI, GV, US, param_file, CS%tracer_flow_CSp, &
call call_tracer_register(HI, GV, US, param_file, CS%tracer_flow_CSp, &
CS%tracer_Reg, restart_CSp)

call MEKE_alloc_register_restart(dG%HI, param_file, CS%MEKE, restart_CSp)
call set_visc_register_restarts(dG%HI, GV, param_file, CS%visc, restart_CSp)
call mixedlayer_restrat_register_restarts(dG%HI, param_file, &
call MEKE_alloc_register_restart(HI, param_file, CS%MEKE, restart_CSp)
call set_visc_register_restarts(HI, GV, param_file, CS%visc, restart_CSp)
call mixedlayer_restrat_register_restarts(HI, param_file, &
CS%mixedlayer_restrat_CSp, restart_CSp)

if (CS%rotate_index .and. associated(OBC_in) .and. use_temperature) then
Expand Down Expand Up @@ -2410,33 +2421,16 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &

! This needs the number of tracers and to have called any code that sets whether
! reservoirs are used.
call open_boundary_register_restarts(dg%HI, GV, CS%OBC, CS%tracer_Reg, &
call open_boundary_register_restarts(HI, GV, CS%OBC, CS%tracer_Reg, &
param_file, restart_CSp, use_temperature)
endif

call callTree_waypoint("restart registration complete (initialize_MOM)")
call restart_registry_lock(restart_CSp)

! Shift from using the temporary dynamic grid type to using the final
! (potentially static) ocean-specific grid type.
! The next line would be needed if G%Domain had not already been init'd above:
! call clone_MOM_domain(dG%Domain, G%Domain)

! NOTE: If indices are rotated, then G and G_in must both be initialized.
! If not rotated, then G_in and G are the same grid.
if (CS%rotate_index) then
call MOM_grid_init(G, param_file, US, HI, bathymetry_at_vel=bathy_at_vel)
call copy_dyngrid_to_MOM_grid(dG, G, US)
call destroy_dyn_horgrid(dG)
endif
call MOM_grid_init(G_in, param_file, US, HI_in, bathymetry_at_vel=bathy_at_vel)
call copy_dyngrid_to_MOM_grid(dG_in, G_in, US)
if (.not. CS%rotate_index) G => G_in

! Write out all of the grid data used by this run.
new_sim = determine_is_new_run(dirs%input_filename, dirs%restart_input_dir, G_in, restart_CSp)
write_geom_files = ((write_geom==2) .or. ((write_geom==1) .and. new_sim))

! Write out all of the grid data used by this run.
if (write_geom_files) call write_ocean_geometry_file(dG_in, param_file, dirs%output_directory, US=US)

call destroy_dyn_horgrid(dG_in)
Expand Down Expand Up @@ -2562,16 +2556,16 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &

if (test_grid_copy) then
! Copy the data from the temporary grid to the dyn_hor_grid to CS%G.
call create_dyn_horgrid(dG, G%HI)
call clone_MOM_domain(G%Domain, dG%Domain)
call create_dyn_horgrid(test_dG, G%HI)
call clone_MOM_domain(G%Domain, test_dG%Domain)

call clone_MOM_domain(G%Domain, CS%G%Domain)
call MOM_grid_init(CS%G, param_file, US)

call copy_MOM_grid_to_dyngrid(G, dg, US)
call copy_dyngrid_to_MOM_grid(dg, CS%G, US)
call copy_MOM_grid_to_dyngrid(G, test_dG, US)
call copy_dyngrid_to_MOM_grid(test_dG, CS%G, US)

call destroy_dyn_horgrid(dG)
call destroy_dyn_horgrid(test_dG)
call MOM_grid_end(G) ; deallocate(G)

G => CS%G
Expand Down
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