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Merge branch 'dev/master' into 'master'
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Dev/master

See merge request fms/ocean_BGC!54
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@underwoo
underwoo committed Mar 6, 2020
2 parents 2bc82bc + 231b31c commit 199f2f2
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Showing 3 changed files with 32 additions and 9 deletions.
37 changes: 30 additions & 7 deletions generic_tracers/generic_COBALT.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,7 @@ module generic_COBALT
use time_manager_mod, only: time_type
use fm_util_mod, only: fm_util_start_namelist, fm_util_end_namelist
use constants_mod, only: WTMCO2, WTMO2,WTMN,rdgas,wtmair
use data_override_mod, only: data_override
use fms_mod, only: write_version_number, FATAL, WARNING, stdout, stdlog,mpp_pe,mpp_root_pe
use fms_mod, only: open_namelist_file, check_nml_error, close_file

Expand Down Expand Up @@ -6479,12 +6480,14 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
real :: fe_salt
real :: sal,tt,tkb,ts,ts2,ts3,ts4,ts5

logical :: phos_nh3_override

real, dimension(:,:,:), Allocatable :: pre_totn, net_srcn, post_totn
real, dimension(:,:,:), Allocatable :: pre_totp, post_totp
real, dimension(:,:,:), Allocatable :: pre_totsi, post_totsi
real, dimension(:,:,:), Allocatable :: pre_totfe, net_srcfe, post_totfe
real, dimension(:,:,:), Allocatable :: pre_totc, net_srcc, post_totc
real, dimension(:,:), Allocatable :: pka_nh3
real, dimension(:,:), Allocatable :: pka_nh3,phos_nh3_exchange

real :: tr,ltr

Expand All @@ -6509,6 +6512,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
pka_nh3 = 0.
call g_tracer_get_values(tracer_list,'nh4' ,'field', cobalt%f_nh4 ,isd,jsd,ntau=tau)
end if
allocate(phos_nh3_exchange(isd:ied,jsd:jed))

!---------------------------------------------------------------------
!Calculate co3_ion
Expand Down Expand Up @@ -6585,6 +6589,9 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
call mpp_clock_end(id_clock_carbon_calculations)

if (do_nh3_atm_ocean_exchange) then
!to override pH used for ocean nh3 exchange
call data_override('OCN', 'phos_nh3_exchange', phos_nh3_exchange(isc:iec,jsc:jec), model_time,override=phos_nh3_override)

do j = jsc, jec ; do i = isc, iec
pka_nh3(i,j) = calc_pka_nh3(temp(i,j,1),salt(i,j,1))*grid_tmask(i,j,1)
tr = 298.15/(temp(i,j,1)+273.15)-1.
Expand All @@ -6598,7 +6605,11 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
cobalt%nh3_alpha(i,j) = 5.76e1*exp(13.79*tr-5.39*ltr)*997.
!apply salinity correction
cobalt%nh3_alpha(i,j) = cobalt%nh3_alpha(i,j)/saltout_correction(101325./(1.e-3*rdgas*wtmair*(temp(i,j,1)+273.15)*cobalt%nh3_alpha(i,j)),vb_nh3,salt(i,j,1))* 1./cobalt%Rho_0 !mol/kg/atm
cobalt%nh3_csurf(i,j) = cobalt%f_nh4(i,j,1)/(1.+10**(pka_nh3(i,j)+log10(min(max(cobalt%f_htotal(i,j,1),1e-11),1e-3)))) !in mol/kg
if (phos_nh3_override) then
cobalt%nh3_csurf(i,j) = cobalt%f_nh4(i,j,1)/(1.+10**(pka_nh3(i,j)-max(min(phos_nh3_exchange(i,j),11.),3.))) !in mol/kg
else
cobalt%nh3_csurf(i,j) = cobalt%f_nh4(i,j,1)/(1.+10**(pka_nh3(i,j)+log10(min(max(cobalt%f_htotal(i,j,1),1e-11),1e-3)))) !in mol/kg
end if
cobalt%pnh3_csurf(i,j) = cobalt%nh3_csurf(i,j)/cobalt%nh3_alpha(i,j)*1.e6 !in uatm
enddo; enddo ; !

Expand Down Expand Up @@ -9265,6 +9276,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
end if
if (allocated(pka_nh3)) deallocate(pka_nh3)
deallocate(phos_nh3_exchange)
!
!---------------------------------------------------------------------
!
Expand Down Expand Up @@ -11814,23 +11826,25 @@ end subroutine generic_COBALT_update_from_source
! </SUBROUTINE>

!User must provide the calculations for these boundary values.
subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,tau,dzt)
subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,tau,dzt,model_time)
type(g_tracer_type), pointer :: tracer_list
real, dimension(ilb:,jlb:), intent(in) :: SST, SSS
real, dimension(ilb:,jlb:,:,:), intent(in) :: rho
integer, intent(in) :: ilb,jlb,tau
real, dimension(ilb:,jlb:,:), optional, intent(in) :: dzt

type(time_type), intent(in) :: model_time
integer :: isc,iec, jsc,jec,isd,ied,jsd,jed,nk,ntau , i, j
real :: sal,ST,o2_saturation
real :: tt,tk,ts,ts2,ts3,ts4,ts5
real, dimension(:,:,:) ,pointer :: grid_tmask
real, dimension(:,:,:,:), pointer :: o2_field,dic_field,po4_field,sio4_field,alk_field,di14c_field,nh4_field
real, dimension(:,:,:), ALLOCATABLE :: htotal_field,co3_ion_field
real, dimension(:,:), ALLOCATABLE :: co2_alpha,co2_csurf,co2_sc_no,o2_alpha,o2_csurf,o2_sc_no,nh3_alpha,nh3_csurf,nh3_sc_no
real, dimension(:,:), ALLOCATABLE :: co2_alpha,co2_csurf,co2_sc_no,o2_alpha,o2_csurf,o2_sc_no,nh3_alpha,nh3_csurf,nh3_sc_no,phos_nh3_exchange
real, dimension(:,:), ALLOCATABLE :: c14o2_alpha,c14o2_csurf
real :: pka_nh3,tr,ltr

logical :: phos_nh3_override

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

!
Expand All @@ -11847,6 +11861,8 @@ subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,ta
allocate(nh3_alpha(isd:ied, jsd:jed)); nh3_alpha=0.0
allocate(nh3_csurf(isd:ied, jsd:jed)); nh3_csurf=0.0
allocate(nh3_sc_no(isd:ied, jsd:jed)); nh3_sc_no=0.0
!for nh3 ph emission override
allocate(phos_nh3_exchange(isd:ied, jsd:jed)); phos_nh3_exchange=0.0
allocate(c14o2_alpha(isd:ied, jsd:jed)); c14o2_alpha=0.0
allocate(c14o2_csurf(isd:ied, jsd:jed)); c14o2_csurf=0.0
allocate(o2_alpha(isd:ied, jsd:jed)); o2_alpha=0.0
Expand Down Expand Up @@ -11936,6 +11952,9 @@ subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,ta

if (do_nh3_atm_ocean_exchange) then
! write(*,*) 'min htot ',minval(htotal_field(:,:,1))

call data_override('OCN', 'phos_nh3_exchange', phos_nh3_exchange(isc:iec,jsc:jec), model_time,override=phos_nh3_override)

do j = jsc, jec ; do i = isc, iec !{
!nh3
pka_nh3 = calc_pka_nh3(SST(i,j),SSS(i,j))
Expand All @@ -11945,7 +11964,11 @@ subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,ta
!997/1035 is to convert pure water to salt water
nh3_alpha(i,j) = 5.76e1*exp(13.79*tr-5.39*ltr)*997. !in mol/kg(water)/atm -> mol/m3/atm
nh3_alpha(i,j) = nh3_alpha(i,j)/saltout_correction(101325./(1e-3*rdgas*wtmair*(SST(i,j)+273.15)*nh3_alpha(i,j)),vb_nh3,SSS(i,j)) * 1./cobalt%Rho_0 !mol/kg/atm
nh3_csurf(i,j) = nh4_field(i,j,1,tau)/(1.+10**(pka_nh3+log10(min(max(1e-11,htotal_field(i,j,1)),1e-3))))
if (phos_nh3_override) then
nh3_csurf(i,j) = nh4_field(i,j,1,tau)/(1.+10**(pka_nh3-(max(min(11.,phos_nh3_exchange(i,j)),3.))))
else
nh3_csurf(i,j) = nh4_field(i,j,1,tau)/(1.+10**(pka_nh3+log10(min(max(1e-11,htotal_field(i,j,1)),1e-3))))
end if
cobalt%pnh3_csurf(i,j) = cobalt%nh3_csurf(i,j)/nh3_alpha(i,j)*1.e6 !in uatm
enddo;enddo

Expand Down Expand Up @@ -12127,7 +12150,7 @@ subroutine generic_COBALT_set_boundary_values(tracer_list,SST,SSS,rho,ilb,jlb,ta
co2_sc_no,o2_alpha, &
c14o2_alpha,c14o2_csurf, &
o2_csurf,o2_sc_no, nh3_alpha,nh3_csurf,&
nh3_sc_no)
nh3_sc_no,phos_nh3_exchange)

end subroutine generic_COBALT_set_boundary_values

Expand Down
2 changes: 1 addition & 1 deletion generic_tracers/generic_abiotic.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -489,7 +489,7 @@ subroutine generic_abiotic_register_diag(diag_list)
standard_name="surface_downward_mass_flux_of_carbon_dioxide_abiotic_analogue_expressed_as_carbon")

vardesc_temp = vardesc("fg14co2abio","Surface Downward Abiotic 14CO2 Flux",'h','1','s','kg m-2 s-1','f')
abiotic%id_fgco2abio = register_diag_field(package_name, vardesc_temp%name, axes(1:2), &
abiotic%id_fg14co2abio = register_diag_field(package_name, vardesc_temp%name, axes(1:2), &
init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1, &
standard_name="surface_downward_mass_flux_of_carbon14_dioxide_abiotic_analogue_expressed_as_carbon")

Expand Down
2 changes: 1 addition & 1 deletion generic_tracers/generic_tracer.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -743,7 +743,7 @@ subroutine generic_tracer_coupler_set(IOB_struc, ST,SS,rho,ilb,jlb,tau, dzt, sos
call generic_miniBLING_set_boundary_values(tracer_list,ST,SS,rho,ilb,jlb,tau)

if(do_generic_COBALT) &
call generic_COBALT_set_boundary_values(tracer_list,ST,SS,rho,ilb,jlb,tau,dzt)
call generic_COBALT_set_boundary_values(tracer_list,ST,SS,rho,ilb,jlb,tau,dzt,model_time)

!
!Set coupler fluxes from tracer boundary values (%alpha and %csurf)
Expand Down

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