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Merge pull request #122 from jiandewang/feature/update-NCAR-GMAO-2023…
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update MOM6 to its main repo 20231025 (NCAR candidate) and 20231031(GMAO FMS_cap) updating
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jiandewang authored Nov 14, 2023
2 parents 02d4dc4 + 80a93f6 commit a36cb73
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4 changes: 0 additions & 4 deletions .github/workflows/coupled-api.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,3 @@ jobs:
- name: Compile MOM6 for the NUOPC driver
shell: bash
run: make check_mom6_api_nuopc -j

- name: Compile MOM6 for the MCT driver
shell: bash
run: make check_mom6_api_mct -j
11 changes: 9 additions & 2 deletions .readthedocs.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,14 @@
# Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

build:
os: ubuntu-22.04
tools:
python: "3.11"

# Extra formats
# PDF generation is failing for now; disabled on 2020-12-02
#formats:
Expand All @@ -10,7 +19,5 @@ sphinx:
configuration: docs/conf.py

python:
# make sure we're using Python 3
version: 3
install:
- requirements: docs/requirements.txt
7 changes: 0 additions & 7 deletions .testing/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,6 @@ build/opt/Makefile: MOM_ENV=$(PATH_FMS) $(OPT_FCFLAGS) $(MOM_LDFLAGS)
build/opt_target/Makefile: MOM_ENV=$(PATH_FMS) $(OPT_FCFLAGS) $(MOM_LDFLAGS)
build/coupled/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
build/nuopc/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
build/mct/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
build/cov/Makefile: MOM_ENV=$(PATH_FMS) $(COV_FCFLAGS) $(COV_LDFLAGS)
build/unit/Makefile: MOM_ENV=$(PATH_FMS) $(COV_FCFLAGS) $(COV_LDFLAGS)

Expand All @@ -269,7 +268,6 @@ build/opt/Makefile: MOM_ACFLAGS=
build/opt_target/Makefile: MOM_ACFLAGS=
build/coupled/Makefile: MOM_ACFLAGS=--with-driver=FMS_cap
build/nuopc/Makefile: MOM_ACFLAGS=--with-driver=nuopc_cap
build/mct/Makefile: MOM_ACFLAGS=--with-driver=mct_cap
build/cov/Makefile: MOM_ACFLAGS=
build/unit/Makefile: MOM_ACFLAGS=--with-driver=unit_tests

Expand Down Expand Up @@ -370,11 +368,6 @@ build/coupled/ocean_model_MOM.o: build/coupled/Makefile
cd $(@D) && make $(@F)
check_mom6_api_coupled: build/coupled/ocean_model_MOM.o

# MCT driver
build/mct/mom_ocean_model_mct.o: build/mct/Makefile
cd $(@D) && make $(@F)
check_mom6_api_mct: build/mct/mom_ocean_model_mct.o


#---
# Testing
Expand Down
8 changes: 8 additions & 0 deletions config_src/drivers/FMS_cap/ocean_model_MOM.F90
Original file line number Diff line number Diff line change
Expand Up @@ -1201,6 +1201,14 @@ subroutine ocean_model_get_UV_surf(OS, Ocean, name, array2D, isc, jsc)
array2D(i,j) = G%mask2dBu(I+i0,J+j0) * &
0.5*(sfc_state%v(i+i0,J+j0)+sfc_state%v(i+i0+1,J+j0))
enddo ; enddo
case('uc')
do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
array2D(i,j) = G%mask2dCu(I+i0,J+j0) * sfc_state%u(I+i0,j+j0)
enddo ; enddo
case('vc')
do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
array2D(i,j) = G%mask2dCv(I+i0,J+j0) * sfc_state%v(i+i0,J+j0)
enddo ; enddo
case default
call MOM_error(FATAL,'ocean_model_get_UV_surf: unknown argument name='//name)
end select
Expand Down
File renamed without changes.
65 changes: 46 additions & 19 deletions config_src/drivers/nuopc_cap/mom_cap.F90
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,11 @@ module MOM_cap_mod
use MOM_cap_methods, only: mom_import, mom_export, mom_set_geomtype, mod2med_areacor
use MOM_cap_methods, only: med2mod_areacor, state_diagnose
use MOM_cap_methods, only: ChkErr
use MOM_ensemble_manager, only: ensemble_manager_init

#ifdef CESMCOUPLED
use shr_log_mod, only: shr_log_setLogUnit
use nuopc_shr_methods, only: get_component_instance
#endif
use time_utils_mod, only: esmf2fms_time

Expand Down Expand Up @@ -147,7 +149,8 @@ module MOM_cap_mod
logical :: cesm_coupled = .false.
type(ESMF_GeomType_Flag) :: geomtype
#endif
character(len=8) :: restart_mode = 'alarms'
character(len=8) :: restart_mode = 'alarms'
character(len=16) :: inst_suffix = ''
real(8) :: timere

contains
Expand Down Expand Up @@ -434,6 +437,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
! (same as restartfile if single restart file)
character(len=*), parameter :: subname='(MOM_cap:InitializeAdvertise)'
character(len=32) :: calendar
character(len=:), allocatable :: rpointer_filename
integer :: inst_index
real(8) :: MPI_Wtime, timeiads
!--------------------------------

Expand Down Expand Up @@ -465,6 +470,13 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
CALL ESMF_TimeIntervalGet(TINT, S=DT_OCEAN, RC=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return

#ifdef CESMCOUPLED
call get_component_instance(gcomp, inst_suffix, inst_index, rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return
call ensemble_manager_init(inst_suffix)
rpointer_filename = 'rpointer.ocn'//trim(inst_suffix)
#endif

! reset shr logging to my log file
if (localPet==0) then
call NUOPC_CompAttributeGet(gcomp, name="diro", &
Expand All @@ -474,11 +486,20 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
isPresent=isPresentLogfile, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return
if (isPresentDiro .and. isPresentLogfile) then
call NUOPC_CompAttributeGet(gcomp, name="diro", value=diro, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return
call NUOPC_CompAttributeGet(gcomp, name="logfile", value=logfile, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return
open(newunit=stdout,file=trim(diro)//"/"//trim(logfile))
call NUOPC_CompAttributeGet(gcomp, name="diro", value=diro, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return
call NUOPC_CompAttributeGet(gcomp, name="logfile", value=logfile, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return

if (cesm_coupled) then
! Multiinstance logfile name needs a correction
if(len_trim(inst_suffix) > 0) then
n = index(logfile, '.')
logfile = logfile(1:n-1)//trim(inst_suffix)//logfile(n:)
endif
endif

open(newunit=stdout,file=trim(diro)//"/"//trim(logfile))
else
stdout = output_unit
endif
Expand Down Expand Up @@ -535,12 +556,6 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)

time0 = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND)


! rsd need to figure out how to get this without share code
!call shr_nuopc_get_component_instance(gcomp, inst_suffix, inst_index)
!inst_name = "OCN"//trim(inst_suffix)


if (is_root_pe()) then
write(stdout,*) subname//'start time: y,m,d-',year,month,day,'h,m,s=',hour,minute,second
endif
Expand Down Expand Up @@ -595,9 +610,9 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)

if (localPet == 0) then
! this hard coded for rpointer.ocn right now
open(newunit=readunit, file='rpointer.ocn', form='formatted', status='old', iostat=iostat)
open(newunit=readunit, file=rpointer_filename, form='formatted', status='old', iostat=iostat)
if (iostat /= 0) then
call ESMF_LogSetError(ESMF_RC_FILE_OPEN, msg=subname//' ERROR opening rpointer.ocn', &
call ESMF_LogSetError(ESMF_RC_FILE_OPEN, msg=subname//' ERROR opening '//rpointer_filename, &
line=__LINE__, file=u_FILE_u, rcToReturn=rc)
return
endif
Expand All @@ -607,7 +622,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
if (len(trim(restartfiles))>1 .and. iostat<0) then
exit ! done reading restart files list.
else
call ESMF_LogSetError(ESMF_RC_FILE_READ, msg=subname//' ERROR reading rpointer.ocn', &
call ESMF_LogSetError(ESMF_RC_FILE_READ, msg=subname//' ERROR reading '//rpointer_filename, &
line=__LINE__, file=u_FILE_u, rcToReturn=rc)
return
endif
Expand All @@ -630,7 +645,12 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
endif

ocean_public%is_ocean_pe = .true.
call ocean_model_init(ocean_public, ocean_state, time0, time_start, input_restart_file=trim(adjustl(restartfiles)))
if (cesm_coupled .and. len_trim(inst_suffix)>0) then
call ocean_model_init(ocean_public, ocean_state, time0, time_start, &
input_restart_file=trim(adjustl(restartfiles)), inst_index=inst_index)
else
call ocean_model_init(ocean_public, ocean_state, time0, time_start, input_restart_file=trim(adjustl(restartfiles)))
endif

! GMM, this call is not needed in CESM. Check with EMC if it can be deleted.
call ocean_model_flux_init(ocean_state)
Expand Down Expand Up @@ -1511,6 +1531,7 @@ subroutine ModelAdvance(gcomp, rc)
character(len=128) :: fldname
character(len=*),parameter :: subname='(MOM_cap:ModelAdvance)'
character(len=8) :: suffix
character(len=:), allocatable :: rpointer_filename
integer :: num_rest_files
real(8) :: MPI_Wtime, timers

Expand Down Expand Up @@ -1685,20 +1706,26 @@ subroutine ModelAdvance(gcomp, rc)
call ESMF_VMGet(vm, localPet=localPet, rc=rc)
if (ChkErr(rc,__LINE__,u_FILE_u)) return

rpointer_filename = 'rpointer.ocn'//trim(inst_suffix)

write(restartname,'(A,".mom6.r.",I4.4,"-",I2.2,"-",I2.2,"-",I5.5)') &
trim(casename), year, month, day, seconds
call ESMF_LogWrite("MOM_cap: Writing restart : "//trim(restartname), ESMF_LOGMSG_INFO)
! write restart file(s)
call ocean_model_restart(ocean_state, restartname=restartname, num_rest_files=num_rest_files)
if (localPet == 0) then
! Write name of restart file in the rpointer file - this is currently hard-coded for the ocean
open(newunit=writeunit, file='rpointer.ocn', form='formatted', status='unknown', iostat=iostat)
open(newunit=writeunit, file=rpointer_filename, form='formatted', status='unknown', iostat=iostat)
if (iostat /= 0) then
call ESMF_LogSetError(ESMF_RC_FILE_OPEN, &
msg=subname//' ERROR opening rpointer.ocn', line=__LINE__, file=u_FILE_u, rcToReturn=rc)
msg=subname//' ERROR opening '//rpointer_filename, line=__LINE__, file=u_FILE_u, rcToReturn=rc)
return
endif
write(writeunit,'(a)') trim(restartname)//'.nc'
if (len_trim(inst_suffix) == 0) then
write(writeunit,'(a)') trim(restartname)//'.nc'
else
write(writeunit,'(a)') trim(restartname)//'.'//trim(inst_suffix)//'.nc'
endif

if (num_rest_files > 1) then
! append i.th restart file name to rpointer
Expand Down
20 changes: 13 additions & 7 deletions config_src/drivers/nuopc_cap/mom_ocean_model_nuopc.F90
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ module MOM_ocean_model_nuopc
use MOM_time_manager, only : operator(/=), operator(<=), operator(>=)
use MOM_time_manager, only : operator(<), real_to_time_type, time_type_to_real
use MOM_interpolate, only : time_interp_external_init
use MOM_tracer_flow_control, only : call_tracer_flux_init
use MOM_tracer_flow_control, only : tracer_flow_control_CS, call_tracer_flux_init, call_tracer_set_forcing
use MOM_unit_scaling, only : unit_scale_type
use MOM_variables, only : surface
use MOM_verticalGrid, only : verticalGrid_type
Expand Down Expand Up @@ -210,6 +210,8 @@ module MOM_ocean_model_nuopc
type(marine_ice_CS), pointer :: &
marine_ice_CSp => NULL() !< A pointer to the control structure for the
!! marine ice effects module.
type(tracer_flow_control_CS), pointer :: &
tracer_flow_CSp => NULL() !< A pointer to the tracer flow control structure
type(wave_parameters_CS), pointer, public :: &
Waves => NULL() !< A pointer to the surface wave control structure
type(surface_forcing_CS), pointer :: &
Expand All @@ -229,7 +231,7 @@ module MOM_ocean_model_nuopc
!! This subroutine initializes both the ocean state and the ocean surface type.
!! Because of the way that indicies and domains are handled, Ocean_sfc must have
!! been used in a previous call to initialize_ocean_type.
subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, input_restart_file)
subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, input_restart_file, inst_index)
type(ocean_public_type), target, &
intent(inout) :: Ocean_sfc !< A structure containing various publicly
!! visible ocean surface properties after initialization,
Expand All @@ -246,6 +248,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
!! tracer fluxes, and can be used to spawn related
!! internal variables in the ice model.
character(len=*), optional, intent(in) :: input_restart_file !< If present, name of restart file to read
integer, optional :: inst_index !< Ensemble index provided by the cap (instead of FMS ensemble manager)

! Local variables
real :: Rho0 ! The Boussinesq ocean density, in kg m-3.
Expand All @@ -255,7 +258,6 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
!! min(HFrz, OBLD), where OBLD is the boundary layer depth.
!! If HFrz <= 0 (default), melt potential will not be computed.
logical :: use_melt_pot !< If true, allocate melt_potential array
logical :: use_CFC !< If true, allocated arrays for surface CFCs.


! This include declares and sets the variable "version".
Expand Down Expand Up @@ -283,7 +285,8 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
call initialize_MOM(OS%Time, Time_init, param_file, OS%dirs, OS%MOM_CSp, &
OS%restart_CSp, Time_in, offline_tracer_mode=OS%offline_tracer_mode, &
input_restart_file=input_restart_file, &
diag_ptr=OS%diag, count_calls=.true., waves_CSp=OS%Waves)
diag_ptr=OS%diag, count_calls=.true., tracer_flow_CSp=OS%tracer_flow_CSp, &
waves_CSp=OS%Waves, ensemble_num=inst_index)
call get_MOM_state_elements(OS%MOM_CSp, G=OS%grid, GV=OS%GV, US=OS%US, C_p=OS%C_p, &
C_p_scaled=OS%fluxes%C_p, use_temp=use_temperature)

Expand Down Expand Up @@ -376,16 +379,14 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
use_melt_pot=.false.
endif

call get_param(param_file, mdl, "USE_CFC_CAP", use_CFC, &
default=.false., do_not_log=.true.)
call get_param(param_file, mdl, "USE_WAVES", OS%Use_Waves, &
"If true, enables surface wave modules.", default=.false.)

! Consider using a run-time flag to determine whether to do the diagnostic
! vertical integrals, since the related 3-d sums are not negligible in cost.
call allocate_surface_state(OS%sfc_state, OS%grid, use_temperature, &
do_integrals=.true., gas_fields_ocn=gas_fields_ocn, &
use_meltpot=use_melt_pot, use_cfcs=use_CFC)
use_meltpot=use_melt_pot)

call surface_forcing_init(Time_in, OS%grid, OS%US, param_file, OS%diag, &
OS%forcing_CSp, OS%restore_salinity, OS%restore_temp, OS%use_waves)
Expand Down Expand Up @@ -611,6 +612,11 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
call finish_MOM_initialization(OS%Time, OS%dirs, OS%MOM_CSp, OS%restart_CSp)
endif

if (do_thermo) &
call call_tracer_set_forcing(OS%sfc_state, OS%fluxes, OS%Time, &
real_to_time_type(dt_coupling), OS%grid, OS%US, OS%GV%Rho0, &
OS%tracer_flow_CSp)

call disable_averaging(OS%diag)
Master_time = OS%Time ; Time1 = OS%Time

Expand Down
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