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Simplify changes to the generic tracer interface for cobalt-p4: ocean_BGC side #8

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merged 7 commits into from
Jan 26, 2024
Merged

Simplify changes to the generic tracer interface for cobalt-p4: ocean_BGC side #8

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07458ae
mod g_tracer_interface
yichengt900 Jan 22, 2024
2a1c210
mod tracer interface
yichengt900 Jan 23, 2024
a81621e
Simplify g_tracer interface changes
yichengt900 Jan 23, 2024
3017ad7
remove unused descriptions
yichengt900 Jan 23, 2024
3010068
tmp changes in cobalt_ci.yml to pass ci test
yichengt900 Jan 23, 2024
fe01728
add optional for geolat and eqn_of_state
yichengt900 Jan 26, 2024
5797074
Change branch back to dev/cefi
yichengt900 Jan 26, 2024
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5 changes: 4 additions & 1 deletion .github/workflows/cobalt_ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ on:
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

env:
BRANCH_NAME: dev/cefi

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "build"
Expand Down Expand Up @@ -46,7 +49,7 @@ jobs:
- name: git clone MOM6_OBGC_examples and build mom6sis2-cobalt
run: |
cd ..
git clone https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6_OBGC_examples.git --recursive
git clone -b $BRANCH_NAME https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6_OBGC_examples.git --recursive
rm -rf MOM6_OBGC_examples/src/ocean_BGC
cp -r ocean_BGC MOM6_OBGC_examples/src
cd MOM6_OBGC_examples/builds
Expand Down
35 changes: 17 additions & 18 deletions generic_tracers/generic_COBALT.F90
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Expand Up @@ -144,8 +144,7 @@ module generic_COBALT
#ifndef INTERNAL_FILE_NML
use fms_mod, only: open_namelist_file, close_file
#endif
use MOM_EOS, only: calculate_density
use MOM_variables, only: thermo_var_ptrs
use MOM_EOS, only: calculate_density, EOS_type

use g_tracer_utils, only : g_tracer_type,g_tracer_start_param_list,g_tracer_end_param_list
use g_tracer_utils, only : g_tracer_add,g_tracer_add_param, g_tracer_set_files
Expand Down Expand Up @@ -7853,13 +7852,12 @@ end subroutine generic_COBALT_update_from_bottom
!subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
! ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
! If you'd like to pass the thermodynamic variables for a mld calculation
subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dzt,hblt_depth,&
ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff,geolat,eqn_of_state)
!subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
! ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)

type(g_tracer_type), pointer :: tracer_list
type(thermo_var_ptrs), intent(in) :: tv
real, dimension(ilb:,jlb:,:), intent(in) :: Temp,Salt,rho_dzt,dzt
real, dimension(ilb:,jlb:), intent(in) :: hblt_depth
integer, intent(in) :: ilb,jlb,tau
Expand All @@ -7873,11 +7871,12 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
real, dimension(:,ilb:,jlb:,:), intent(in) :: opacity_band
real, dimension(ilb:,jlb:), intent(in) :: internal_heat
real, dimension(ilb:,jlb:), intent(in) :: frunoff
real, dimension(ilb:,jlb:), optional, intent(in) :: geolat
type(EOS_type), optional, intent(in) :: eqn_of_state !< Equation of state structure

character(len=fm_string_len), parameter :: sub_name = 'generic_COBALT_update_from_source'
integer :: isc,iec, jsc,jec,isd,ied,jsd,jed,nk,ntau, i, j, k , m, n, k_100, k_200, kbot
real, dimension(:,:,:) ,pointer :: grid_tmask
real, dimension(:,:), pointer :: geolon,geolat
integer, dimension(:,:),pointer :: mask_coast,grid_kmt
!
!------------------------------------------------------------------------
Expand Down Expand Up @@ -7952,8 +7951,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
r_dt = 1.0 / dt

call g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
grid_tmask=grid_tmask,grid_mask_coast=mask_coast,grid_kmt=grid_kmt,&
geolon=geolon,geolat=geolat)
grid_tmask=grid_tmask,grid_mask_coast=mask_coast,grid_kmt=grid_kmt)

call mpp_clock_begin(id_clock_carbon_calculations)
!Get necessary fields
Expand Down Expand Up @@ -8317,7 +8315,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz


! calculate the mld for the photoacclimation calculations
call calculate_density(Temp(i,j,kmld_ref),Salt(i,j,kmld_ref),101325.0,rho_mld_ref,tv%eqn_of_state)
call calculate_density(Temp(i,j,kmld_ref),Salt(i,j,kmld_ref),101325.0,rho_mld_ref,eqn_of_state)
!if ((i.eq.isc).and.(j.eq.jsc)) then
! write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
!endif
Expand All @@ -8332,7 +8330,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
deltaRhoAtKm1 = deltaRhoAtK
dKm1 = dK
dK = cobalt%mld_aclm(i,j) + 0.5*dzt(i,j,k)
call calculate_density(Temp(i,j,k),Salt(i,j,k),101325.0,rho_k,tv%eqn_of_state)
call calculate_density(Temp(i,j,k),Salt(i,j,k),101325.0,rho_k,eqn_of_state)
cobalt%rho_test(i,j,k) = rho_k
deltaRhoAtK = rho_k - rho_mld_ref
if (deltaRhoAtK.lt.cobalt%densdiff_mld) then
Expand All @@ -8341,14 +8339,15 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
afac = (cobalt%densdiff_mld - deltaRhoAtKm1)/(deltaRhoAtK - deltaRhoAtKm1)
cobalt%mld_aclm(i,j) = afac*dK + (1.0-afac)*dKm1
deltaRhoFlag = 1.0
!if ((i.eq.isc).and.(j.eq.jsc)) then
! write(outunit,*) 'lat,lon=',geolat,geolon
! write(outunit,*) 'kmld_ref, k = ',kmld_ref, k
! write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
! write(outunit,*) 'rho_k = ',rho_k
! write(outunit,*) 'deltaRhoAtK = ',deltaRhoAtK
! write(outunit,*) 'mld_aclm = ',cobalt%mld_aclm(i,j)
!endif
! if ((i.eq.isc).and.(j.eq.jsc)) then
! write(outunit,*) 'i,j=',i,j
! write(outunit,*) 'lat,lon=',geolat(i,j)
! write(outunit,*) 'kmld_ref, k = ',kmld_ref, k
! write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
! write(outunit,*) 'rho_k = ',rho_k
! write(outunit,*) 'deltaRhoAtK = ',deltaRhoAtK
! write(outunit,*) 'mld_aclm = ',cobalt%mld_aclm(i,j)
! endif
endif
enddo !} k

Expand Down
32 changes: 20 additions & 12 deletions generic_tracers/generic_tracer.F90
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Expand Up @@ -103,9 +103,9 @@ module generic_tracer
use generic_COBALT, only : generic_COBALT_init, generic_COBALT_update_from_source,generic_COBALT_register_diag
use generic_COBALT, only : generic_COBALT_update_from_bottom,generic_COBALT_update_from_coupler
use generic_COBALT, only : generic_COBALT_set_boundary_values, generic_COBALT_end, do_generic_COBALT
use generic_COBALT, only : as_param_cobalt
use generic_COBALT, only : as_param_cobalt

use MOM_variables, only : thermo_var_ptrs
use MOM_EOS, only: EOS_type

implicit none ; private

Expand Down Expand Up @@ -248,17 +248,16 @@ end subroutine generic_tracer_register
! Grid mask
! </IN>
! </SUBROUTINE>
subroutine generic_tracer_init(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
subroutine generic_tracer_init(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
integer, intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3)
type(time_type), intent(in) :: init_time
real, dimension(:,:,:),target, intent(in) :: grid_tmask
integer, dimension(:,:) , intent(in) :: grid_kmt
real, dimension(:,:),target, intent(in) :: geolon,geolat
type(g_tracer_type), pointer :: g_tracer,g_tracer_next

character(len=fm_string_len), parameter :: sub_name = 'generic_tracer_init'

call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)

!Allocate and initialize all registered generic tracers
!JGJ 2013/05/31 merged COBALT into siena_201303
Expand Down Expand Up @@ -505,11 +504,10 @@ end subroutine generic_tracer_diag
! </IN>
! </SUBROUTINE>

subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dtts,&
subroutine generic_tracer_source(Temp,Salt,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dtts,&
grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,&
frunoff,grid_ht, current_wave_stress, sosga)
frunoff,grid_ht, current_wave_stress, sosga, geolat, eqn_of_state)
real, dimension(ilb:,jlb:,:), intent(in) :: Temp,Salt,rho_dzt,dzt
type(thermo_var_ptrs), intent(in) :: tv
real, dimension(ilb:,jlb:), intent(in) :: hblt_depth
integer, intent(in) :: ilb,jlb,tau
real, intent(in) :: dtts
Expand All @@ -524,7 +522,8 @@ subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau
real, dimension(ilb:,jlb:),optional, intent(in) :: grid_ht
real, dimension(ilb:,jlb:),optional , intent(in) :: current_wave_stress
real, optional , intent(in) :: sosga ! global avg. sea surface salinity

real, dimension(ilb:,jlb:),optional, intent(in) :: geolat
type(EOS_type), optional, intent(in) :: eqn_of_state


character(len=fm_string_len), parameter :: sub_name = 'generic_tracer_update_from_source'
Expand Down Expand Up @@ -554,9 +553,18 @@ subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau
hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
nbands,max_wavelength_band,sw_pen_band,opacity_band, grid_ht)

if(do_generic_COBALT) call generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dzt,&
hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
if (do_generic_COBALT) then
if (present(geolat) .and. present(eqn_of_state)) then
call generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,&
hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff,&
geolat,eqn_of_state)
else
call generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,&
hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
endif
endif

if(do_generic_SF6) call generic_SF6_update_from_source(tracer_list,rho_dzt,dzt,hblt_depth,&
ilb,jlb,tau,dtts,grid_dat,model_time)
Expand Down
20 changes: 3 additions & 17 deletions generic_tracers/generic_tracer_utils.F90
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Expand Up @@ -330,9 +330,6 @@ module g_tracer_utils
!coast mask
integer, _ALLOCATABLE, dimension(:,:):: grid_mask_coast _NULL

real, _ALLOCATABLE, dimension(:,:) :: geolon _NULL
real, _ALLOCATABLE, dimension(:,:) :: geolat _NULL

! IN and OUT (restart) files
character(len=fm_string_len) :: ice_restart_file, ocean_restart_file
end type g_tracer_common
Expand Down Expand Up @@ -1600,19 +1597,18 @@ end subroutine g_tracer_set_csdiag
! grid_mask array and initial time.
! </DESCRIPTION>
! <TEMPLATE>
! call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
! call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
! </TEMPLATE>
! <IN NAME="" TYPE="">
!
! </IN>
! </SUBROUTINE>

subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
integer, intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3)
real, dimension(isd:,jsd:,:),intent(in) :: grid_tmask
integer,dimension(isd:,jsd:),intent(in) :: grid_kmt
type(time_type), intent(in) :: init_time
real, dimension(isd:,jsd:), intent(in) :: geolon,geolat

character(len=fm_string_len), parameter :: sub_name = 'g_tracer_set_common'
integer :: i,j
Expand Down Expand Up @@ -1641,12 +1637,6 @@ subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid

if(.NOT. _ALLOCATED(g_tracer_com%grid_mask_coast)) allocate(g_tracer_com%grid_mask_coast(isd:ied,jsd:jed))

if(.NOT. _ALLOCATED(g_tracer_com%geolon)) allocate(g_tracer_com%geolon(isd:ied,jsd:jed))
g_tracer_com%geolon = geolon

if(.NOT. _ALLOCATED(g_tracer_com%geolat)) allocate(g_tracer_com%geolat(isd:ied,jsd:jed))
g_tracer_com%geolat = geolat

!Determine the coast line.
!In order to that grid_tmask must have the proper value on the data domain boundaries isd,ied,jsd,jed
!so that we can decide if the coast line coinsides with a point on the compute domain boundary
Expand Down Expand Up @@ -1681,16 +1671,14 @@ end subroutine g_tracer_set_common
! </SUBROUTINE>

subroutine g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
axes,grid_tmask,grid_mask_coast,grid_kmt,init_time,diag_CS,geolon,geolat)
axes,grid_tmask,grid_mask_coast,grid_kmt,init_time,diag_CS)

integer, intent(out) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau
integer,optional, intent(out) :: axes(3)
type(time_type), optional, intent(out) :: init_time
real, optional, dimension(:,:,:),pointer :: grid_tmask
integer, optional, dimension(:,:), pointer :: grid_mask_coast
integer, optional, dimension(:,:), pointer :: grid_kmt
real, optional, dimension(:,:), pointer :: geolon
real, optional, dimension(:,:), pointer :: geolat
type(g_diag_ctrl), optional, pointer :: diag_CS

character(len=fm_string_len), parameter :: sub_name = 'g_tracer_get_common'
Expand All @@ -1713,8 +1701,6 @@ subroutine g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
if(present(grid_mask_coast)) grid_mask_coast=> g_tracer_com%grid_mask_coast
if(present(grid_kmt)) grid_kmt => g_tracer_com%grid_kmt
if(present(diag_CS)) diag_CS => g_tracer_com%diag_CS
if(present(geolon)) geolon => g_tracer_com%geolon
if(present(geolat)) geolat => g_tracer_com%geolat
! if(present(ice_restart_file)) ice_restart_file = g_tracer_com%ice_restart_file
! if(present(ocean_restart_file)) ocean_restart_file = g_tracer_com%ocean_restart_file

Expand Down
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