Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update icepack standalone for new bgc #36

Closed
wants to merge 2 commits into from
Closed

Update icepack standalone for new bgc #36

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c1099ac
Update icepack for new bgc
apcraig Apr 18, 2024
d747f23
Move bgc tracer index initialization to driver, implemented with temp…
apcraig Apr 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 16 additions & 12 deletions columnphysics/icepack_algae.F90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ subroutine zbio (dt, nblyr, &
!change to inout when updating ocean fields
ocean_bio ! ocean concentrations (mmol/m^3)

real (kind=dbl_kind), dimension (nbtrcr), intent(out) :: &
real (kind=dbl_kind), optional, dimension (:), intent(out) :: &
!change to inout when updating ocean fields
ocean_bio_dh ! ocean concentrations * hbrine * phi (mmol/m^2)

Expand All @@ -208,13 +208,15 @@ subroutine zbio (dt, nblyr, &
PP_net , & ! net PP (mg C/m^2/d) times aice
grow_net , & ! net specific growth (m/d) times vice
upNO , & ! tot nitrate uptake rate (mmol/m^2/d) times aice
upNH , & ! tot ammonium uptake rate (mmol/m^2/d) times aice
upNH ! tot ammonium uptake rate (mmol/m^2/d) times aice

real (kind=dbl_kind), optional, intent(inout):: &
totalChla ! total chla (mg chla/m^2)

real (kind=dbl_kind), dimension (nblyr+1), intent(inout):: & ! diagnostics
bioPorosityIceCell , & ! porosity on vertical interface points
bioSalinityIceCell , & ! salinity on vertical interface points (ppt)
bioTemperatureIceCell ! temperature on vertical interface points (oC)
real (kind=dbl_kind), optional, dimension (nblyr+1), intent(inout):: & ! diagnostics
bioPorosityIceCell , & ! porosity on vertical interface points
bioSalinityIceCell , & ! salinity on vertical interface points (ppt)
bioTemperatureIceCell ! temperature on vertical interface points (oC)

logical (kind=log_kind), intent(in) :: &
first_ice ! initialized values should be used
Expand Down Expand Up @@ -265,6 +267,7 @@ subroutine zbio (dt, nblyr, &
write_flux_diag = .false.

call bgc_carbon_sum(nblyr, hbri_old, trcrn(:), carbonInitial,n_doc,n_dic,n_algae,n_don)
if (icepack_warnings_aborted(subname)) return

if (aice_old > puny) then
hsnow_i = vsno_old/aice_old
Expand Down Expand Up @@ -324,7 +327,9 @@ subroutine zbio (dt, nblyr, &
enddo

call bgc_carbon_sum(nblyr, hbri, trcrn(:), carbonFinal,n_doc,n_dic,n_algae,n_don)
if (icepack_warnings_aborted(subname)) return
call bgc_carbon_flux(flux_bio_atm,flux_bion,n_doc,n_dic,n_algae,n_don,carbonFlux)
if (icepack_warnings_aborted(subname)) return

carbonError = carbonInitial-carbonFlux*dt-carbonFinal

Expand Down Expand Up @@ -379,7 +384,6 @@ subroutine zbio (dt, nblyr, &
!call icepack_warnings_setabort(.true.,__FILE__,__LINE__)
call icepack_warnings_add(subname//" zbio: Carbon conservation failure after z_biogeochemistry")
endif

if (icepack_warnings_aborted(subname)) return

if (write_flux_diag) then
Expand Down Expand Up @@ -408,7 +412,6 @@ subroutine zbio (dt, nblyr, &
enddo
endif
endif

if (icepack_warnings_aborted(subname)) return

call merge_bgc_fluxes (dt, nblyr, &
Expand Down Expand Up @@ -450,6 +453,7 @@ subroutine zbio (dt, nblyr, &
enddo
endif
endif
if (icepack_warnings_aborted(subname)) return

end subroutine zbio

Expand Down Expand Up @@ -645,6 +649,7 @@ subroutine skl_biogeochemistry (dt, &
rphi_sk = c1/phi_sk
PVt = c0
iTin = Tf
ice_growth = (congel-meltb)/dt

do nn = 1, nbtrcr
cinit (nn) = c0
Expand All @@ -666,7 +671,6 @@ subroutine skl_biogeochemistry (dt, &
cling (nn) = c1
endif

ice_growth = (congel-meltb)/dt
cinit (nn) = trcrn(bio_index(nn)) * sk_l * rphi_sk
cinit_v(nn) = cinit(nn)/sk_l
if (cinit(nn) < c0) then
Expand Down Expand Up @@ -908,7 +912,7 @@ subroutine z_biogeochemistry (n_cat, dt, &
ocean_bio , & ! ocean concentrations (mmol/m^3)
bphin ! Porosity on the bgrid

real (kind=dbl_kind), dimension (:), intent(out) :: &
real (kind=dbl_kind), optional, dimension (:), intent(out) :: &
ocean_bio_dh ! ocean concentrations * hbrine * phi (mmol/m^2)

real (kind=dbl_kind), intent(in) :: &
Expand Down Expand Up @@ -1053,7 +1057,7 @@ subroutine z_biogeochemistry (n_cat, dt, &
darcyV = c0
C_top(:) = c0
C_bot(:) = c0
ocean_bio_dh(:) = c0
if (present(ocean_bio_dh)) ocean_bio_dh(:) = c0
mobile(:) = c0
conserve_C(:) = .true.
nitrification(:) = c0
Expand Down Expand Up @@ -1177,7 +1181,7 @@ subroutine z_biogeochemistry (n_cat, dt, &
endif

C_bot(m) = ocean_bio(m)*hbri_old*iphin_N(nblyr+1)
ocean_bio_dh(m) = C_bot(m)
if (present(ocean_bio_dh)) ocean_bio_dh(m) = C_bot(m)

enddo ! m

Expand Down
4 changes: 3 additions & 1 deletion columnphysics/icepack_parameters.F90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -572,7 +572,7 @@ subroutine icepack_init_parameters( &
bgc_flux_type_in, z_tracers_in, scale_bgc_in, solve_zbgc_in, &
modal_aero_in, use_macromolecules_in, restartbgc_in, skl_bgc_in, &
solve_zsal_in, grid_o_in, l_sk_in, &
grid_oS_in, l_skS_in, dEdd_algae_in, &
initbio_frac_in, grid_oS_in, l_skS_in, dEdd_algae_in, &
phi_snow_in, T_max_in, fsal_in, &
fr_resp_in, algal_vel_in, R_dFe2dust_in, dustFe_sol_in, &
op_dep_min_in, fr_graze_s_in, fr_graze_e_in, fr_mort2min_in, &
Expand Down Expand Up @@ -882,6 +882,7 @@ subroutine icepack_init_parameters( &
grid_o_in , & ! for bottom flux
l_sk_in , & ! characteristic diffusive scale (zsalinity) (m)
grid_o_t_in , & ! top grid point length scale
initbio_frac_in, & ! fraction of ocean tracer concentration used to initialize tracer
phi_snow_in ! snow porosity at the ice/snow interface

real (kind=dbl_kind), intent(in), optional :: &
Expand Down Expand Up @@ -1359,6 +1360,7 @@ subroutine icepack_init_parameters( &
if (present(l_sk_in) ) l_sk = l_sk_in
if (present(grid_o_t_in) ) grid_o_t = grid_o_t_in
if (present(frazil_scav_in) ) frazil_scav = frazil_scav_in
if (present(initbio_frac_in) ) initbio_frac = initbio_frac_in
if (present(grid_oS_in) ) grid_oS = grid_oS_in
if (present(l_skS_in) ) l_skS = l_skS_in
if (present(phi_snow_in) ) phi_snow = phi_snow_in
Expand Down
Loading
Loading