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Apply restoring to all tracers #214

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merged 4 commits into from
Jan 16, 2018
Merged

Apply restoring to all tracers #214

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f1aef7a
Apply restoring to all tracers
mnlevy1981 Jan 8, 2018
37dc086
By default, CESM will also restore ALK_ALT_CO2
mnlevy1981 Jan 8, 2018
6b59dca
Previous fix to restore tracers ignored CISO
mnlevy1981 Jan 12, 2018
ea6dbff
Reverting change to spacing
mnlevy1981 Jan 12, 2018
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9 changes: 6 additions & 3 deletions autogenerated_src/default_settings.json
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Original file line number Diff line number Diff line change
Expand Up @@ -923,19 +923,22 @@
"PO4",
"NO3",
"SiO3",
"ALK"
"ALK",
"ALK_ALT_CO2"
],
"GRID = CESM_x1": [
"PO4",
"NO3",
"SiO3",
"ALK"
"ALK",
"ALK_ALT_CO2"
],
"GRID = CESM_x3": [
"PO4",
"NO3",
"SiO3",
"ALK"
"ALK",
"ALK_ALT_CO2"
],
"default": ""
},
Expand Down
1 change: 1 addition & 0 deletions src/default_settings.yaml
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Expand Up @@ -840,5 +840,6 @@ tracer_dependent :
- 'NO3'
- 'SiO3'
- 'ALK'
- 'ALK_ALT_CO2'
GRID = CESM_x3 : *CESM_TRACER_RESTORE
GRID = CESM_x1 : *CESM_TRACER_RESTORE
59 changes: 10 additions & 49 deletions src/marbl_diagnostics_mod.F90
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Expand Up @@ -3275,7 +3275,7 @@ subroutine marbl_diagnostics_set_interior_forcing ( &
sed_denitrif, other_remin, marbl_interior_forcing_diags)

call store_diagnostics_carbon_fluxes(domain, POC, P_CaCO3, dtracers, &
interior_restore, marbl_tracer_indices, marbl_interior_forcing_diags)
marbl_tracer_indices, marbl_interior_forcing_diags)

call store_diagnostics_nitrification(&
nitrif, denitrif, marbl_interior_forcing_diags)
Expand All @@ -3297,18 +3297,18 @@ subroutine marbl_diagnostics_set_interior_forcing ( &

call store_diagnostics_nitrogen_fluxes(domain, &
PON_sed_loss, denitrif, sed_denitrif, autotroph_secondary_species, dtracers, &
interior_restore, marbl_tracer_indices, marbl_interior_forcing_diags)
marbl_tracer_indices, marbl_interior_forcing_diags)

call store_diagnostics_phosphorus_fluxes(domain, POP, &
autotroph_secondary_species, dtracers, interior_restore, &
autotroph_secondary_species, dtracers, &
marbl_tracer_indices, marbl_interior_forcing_diags)

call store_diagnostics_silicon_fluxes(domain, P_SiO2, dtracers, &
interior_restore, marbl_tracer_indices, marbl_interior_forcing_diags)
marbl_tracer_indices, marbl_interior_forcing_diags)

call store_diagnostics_iron_fluxes(domain, P_iron, dust, &
interior_forcings(interior_forcing_ind%fesedflux_id)%field_1d(1,:), &
dtracers, interior_restore, marbl_tracer_indices, marbl_interior_forcing_diags)
dtracers, marbl_tracer_indices, marbl_interior_forcing_diags)

call store_diagnostics_interior_restore(interior_restore, &
marbl_interior_forcing_diags)
Expand Down Expand Up @@ -4035,13 +4035,12 @@ end subroutine store_diagnostics_iron_cycle
!***********************************************************************

subroutine store_diagnostics_carbon_fluxes(marbl_domain, POC, P_CaCO3, dtracers, &
interior_restore, marbl_tracer_indices, marbl_diags)
marbl_tracer_indices, marbl_diags)

type(marbl_domain_type) , intent(in) :: marbl_domain
type(column_sinking_particle_type) , intent(in) :: POC
type(column_sinking_particle_type) , intent(in) :: P_CaCO3
real(r8) , intent(in) :: dtracers(:,:) ! tracer_cnt, km
real(r8) , intent(in) :: interior_restore(:,:) ! tracer_cnt, km
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
type(marbl_diagnostics_type) , intent(inout) :: marbl_diags

Expand Down Expand Up @@ -4069,17 +4068,10 @@ subroutine store_diagnostics_carbon_fluxes(marbl_domain, POC, P_CaCO3, dtracers,
sum(dtracers(marbl_tracer_indices%zoo_inds(:)%C_ind,:), dim=1) + &
sum(dtracers(marbl_tracer_indices%auto_inds(:)%C_ind,:),dim=1)

! subtract tracer restoring terms
work = work - (interior_restore(dic_ind,:) + interior_restore(doc_ind,:) + &
interior_restore(docr_ind,:) + &
sum(interior_restore(marbl_tracer_indices%zoo_inds(:)%C_ind,:), dim=1) + &
sum(interior_restore(marbl_tracer_indices%auto_inds(:)%C_ind,:),dim=1))

do auto_ind = 1, autotroph_cnt
n = marbl_tracer_indices%auto_inds(auto_ind)%CaCO3_ind
if (n .gt. 0) then
work = work + dtracers(n,:)
work = work - interior_restore(n,:)
end if
end do

Expand All @@ -4096,7 +4088,7 @@ end subroutine store_diagnostics_carbon_fluxes

subroutine store_diagnostics_nitrogen_fluxes(marbl_domain, &
PON_sed_loss, denitrif, sed_denitrif, autotroph_secondary_species, dtracers, &
interior_restore, marbl_tracer_indices, marbl_diags)
marbl_tracer_indices, marbl_diags)

use marbl_settings_mod, only : Q

Expand All @@ -4106,7 +4098,6 @@ subroutine store_diagnostics_nitrogen_fluxes(marbl_domain, &
real(r8) , intent(in) :: sed_denitrif(:) ! km
type(autotroph_secondary_species_type) , intent(in) :: autotroph_secondary_species(:,:)
real(r8) , intent(in) :: dtracers(:,:) ! tracer_cnt, km
real(r8) , intent(in) :: interior_restore(:,:) ! tracer_cnt, km
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
type(marbl_diagnostics_type) , intent(inout) :: marbl_diags

Expand Down Expand Up @@ -4136,12 +4127,6 @@ subroutine store_diagnostics_nitrogen_fluxes(marbl_domain, &
Q * sum(dtracers(marbl_tracer_indices%auto_inds(:)%C_ind,:), dim=1) + &
denitrif(:) + sed_denitrif(:)

! subtract tracer restoring terms
work = work - (interior_restore(no3_ind,:) + interior_restore(nh4_ind,:) + &
interior_restore(don_ind,:) + interior_restore(donr_ind,:) + &
Q * sum(interior_restore(marbl_tracer_indices%zoo_inds(:)%C_ind,:), dim=1) + &
Q * sum(interior_restore(marbl_tracer_indices%auto_inds(:)%C_ind,:), dim=1))

! subtract out N fixation
do n = 1, autotroph_cnt
if (autotrophs(n)%Nfixer) then
Expand All @@ -4161,7 +4146,7 @@ end subroutine store_diagnostics_nitrogen_fluxes
!***********************************************************************

subroutine store_diagnostics_phosphorus_fluxes(marbl_domain, POP, &
autotroph_secondary_species, dtracers, interior_restore, &
autotroph_secondary_species, dtracers, &
marbl_tracer_indices, marbl_diags)

use marbl_pft_mod, only : Qp_zoo
Expand All @@ -4171,7 +4156,6 @@ subroutine store_diagnostics_phosphorus_fluxes(marbl_domain, POP, &
type(column_sinking_particle_type) , intent(in) :: POP
type(autotroph_secondary_species_type) , intent(in) :: autotroph_secondary_species(:,:)
real(r8) , intent(in) :: dtracers(:,:) ! tracer_cnt, km
real(r8) , intent(in) :: interior_restore(:,:) ! tracer_cnt, km
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
type(marbl_diagnostics_type) , intent(inout) :: marbl_diags

Expand Down Expand Up @@ -4204,18 +4188,6 @@ subroutine store_diagnostics_phosphorus_fluxes(marbl_domain, POP, &
end do
endif

! subtract restoring terms
work = work - (interior_restore(po4_ind,:) + interior_restore(dop_ind,:) + interior_restore(dopr_ind,:) + &
Qp_zoo * sum(interior_restore(marbl_tracer_indices%zoo_inds(:)%C_ind,:), dim=1))

if (lvariable_PtoC) then
work = work - sum(interior_restore(marbl_tracer_indices%auto_inds(:)%P_ind,:),dim=1)
else
do n = 1, autotroph_cnt
work = work - autotroph_secondary_species(n,:)%Qp * interior_restore(marbl_tracer_indices%auto_inds(n)%C_ind,:)
end do
endif

call compute_vertical_integrals(work, delta_z, kmt, &
full_depth_integral=diags(ind%Jint_Ptot)%field_2d(1), &
near_surface_integral=diags(ind%Jint_100m_Ptot)%field_2d(1), &
Expand All @@ -4228,12 +4200,11 @@ end subroutine store_diagnostics_phosphorus_fluxes
!***********************************************************************

subroutine store_diagnostics_silicon_fluxes(marbl_domain, P_SiO2, dtracers, &
interior_restore, marbl_tracer_indices, marbl_diags)
marbl_tracer_indices, marbl_diags)

type(marbl_domain_type) , intent(in) :: marbl_domain
type(column_sinking_particle_type) , intent(in) :: P_SiO2
real(r8) , intent(in) :: dtracers(:,:) ! tracer_cnt, km
real(r8) , intent(in) :: interior_restore(:,:) ! tracer_cnt, km
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
type(marbl_diagnostics_type) , intent(inout) :: marbl_diags

Expand All @@ -4255,13 +4226,9 @@ subroutine store_diagnostics_silicon_fluxes(marbl_domain, P_SiO2, dtracers, &
! vertical integrals
work = dtracers(marbl_tracer_indices%sio3_ind,:)

! subtract tracer restoring terms
work = work - interior_restore(marbl_tracer_indices%sio3_ind,:)

do n = 1, autotroph_cnt
if (marbl_tracer_indices%auto_inds(n)%Si_ind > 0) then
work = work + dtracers(marbl_tracer_indices%auto_inds(n)%Si_ind,:)
work = work - interior_restore(marbl_tracer_indices%auto_inds(n)%Si_ind,:)
end if
end do

Expand All @@ -4277,7 +4244,7 @@ end subroutine store_diagnostics_silicon_fluxes
!***********************************************************************

subroutine store_diagnostics_iron_fluxes(marbl_domain, P_iron, dust, &
fesedflux, dtracers, interior_restore, marbl_tracer_indices, marbl_diags)
fesedflux, dtracers, marbl_tracer_indices, marbl_diags)

use marbl_settings_mod, only : Qfe_zoo
use marbl_settings_mod, only : dust_to_Fe
Expand All @@ -4287,7 +4254,6 @@ subroutine store_diagnostics_iron_fluxes(marbl_domain, P_iron, dust, &
type(column_sinking_particle_type) , intent(in) :: dust
real(r8) , intent(in) :: fesedflux(:) ! km
real(r8) , intent(in) :: dtracers(:,:) ! tracer_cnt, km
real(r8) , intent(in) :: interior_restore(:,:) ! tracer_cnt, km
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
type(marbl_diagnostics_type) , intent(inout) :: marbl_diags

Expand All @@ -4312,11 +4278,6 @@ subroutine store_diagnostics_iron_fluxes(marbl_domain, P_iron, dust, &
Qfe_zoo * sum(dtracers(marbl_tracer_indices%zoo_inds(:)%C_ind, :),dim=1) - &
dust%remin(:) * dust_to_Fe

! subtract tracer restoring terms
work = work - (interior_restore(fe_ind, :) + &
sum(interior_restore(marbl_tracer_indices%auto_inds(:)%Fe_ind, :),dim=1) + &
Qfe_zoo * sum(interior_restore(marbl_tracer_indices%zoo_inds(:)%C_ind, :),dim=1))

call compute_vertical_integrals(work, delta_z, kmt, &
full_depth_integral=diags(ind%Jint_Fetot)%field_2d(1), &
near_surface_integral=diags(ind%Jint_100m_Fetot)%field_2d(1), &
Expand Down
9 changes: 6 additions & 3 deletions src/marbl_mod.F90
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Expand Up @@ -834,6 +834,9 @@ subroutine marbl_set_interior_forcing( &

end associate

! ADD RESTORING
dtracers = dtracers + interior_restore

end subroutine marbl_set_interior_forcing

!***********************************************************************
Expand Down Expand Up @@ -4317,7 +4320,7 @@ subroutine marbl_compute_dtracer_local (auto_cnt, zoo_cnt, autotrophs, &
! nitrate & ammonium
!-----------------------------------------------------------------------

dtracers(no3_ind) = interior_restore(no3_ind) + nitrif - denitrif - sed_denitrif - sum(NO3_V(:))
dtracers(no3_ind) = nitrif - denitrif - sed_denitrif - sum(NO3_V(:))

dtracers(nh4_ind) = -sum(NH4_V(:)) - nitrif + DON_remin + DONr_remin &
+ Q * (sum(zoo_loss_dic(:)) + sum(zoo_graze_dic(:)) + sum(auto_loss_dic(:)) + sum(auto_graze_dic(:)) &
Expand Down Expand Up @@ -4354,7 +4357,7 @@ subroutine marbl_compute_dtracer_local (auto_cnt, zoo_cnt, autotrophs, &
! dissolved SiO3
!-----------------------------------------------------------------------

dtracers(sio3_ind) = interior_restore(sio3_ind) + P_SiO2_remin
dtracers(sio3_ind) = P_SiO2_remin

do auto_ind = 1, auto_cnt
if (marbl_tracer_indices%auto_inds(auto_ind)%Si_ind > 0) then
Expand All @@ -4368,7 +4371,7 @@ subroutine marbl_compute_dtracer_local (auto_cnt, zoo_cnt, autotrophs, &
! phosphate
!-----------------------------------------------------------------------

dtracers(po4_ind) = interior_restore(po4_ind) + DOP_remin + DOPr_remin - sum(PO4_V(:)) &
dtracers(po4_ind) = DOP_remin + DOPr_remin - sum(PO4_V(:)) &
+ (c1 - POPremin_refract) * POP_remin + sum(remaining_P_dip(:)) &
+ Qp_zoo * ( sum(zoo_loss_dic(:)) + sum(zoo_graze_dic(:)) )

Expand Down