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Fixes marbl column fields initialization #4

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Fixes marbl column fields initialization #4

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c95235f
MARBL parameter change to improve alkalinity
njeffery Oct 22, 2025
63f3455
Initialize fields to correct floating invalid errors
njeffery Dec 2, 2025
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112 changes: 99 additions & 13 deletions src/marbl_interior_tendency_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -294,7 +294,7 @@ subroutine marbl_interior_tendency_compute( &
tracer_local(:,:), zooplankton_local, totalChl_local)

call set_surface_particulate_terms(surface_flux_forcing_indices, POC, POP, P_CaCO3, &
P_CaCO3_ALT_CO2, P_SiO2, dust, P_iron, QA_dust_def(:), dust_flux_in)
P_CaCO3_ALT_CO2, P_SiO2, dust, P_iron, QA_dust_def(:), dust_flux_in, PON_remin, PON_sed_loss)

call marbl_timers%start(marbl_timer_indices%carbonate_chem_id, &
marbl_status_log)
Expand Down Expand Up @@ -343,9 +343,17 @@ subroutine marbl_interior_tendency_compute( &
PAR, zooplankton_derived_terms, autotroph_derived_terms, &
delta_z1, tracer_local(:, :), dissolved_organic_matter)

do k = 1, km
!Initialize
Fe_scavenge_rate(:) = c0
Fe_scavenge(:) = c0
Lig_scavenge(:) = c0
sed_denitrif(:) = c0
other_remin(:) = c0
FeFree(:) = c0

call compute_scavenging(k, km, marbl_tracer_indices, tracer_local(:,:), &
do k = 1, kmt

call compute_scavenging(k, kmt, marbl_tracer_indices, tracer_local(:,:), &
POC, P_CaCO3, P_SiO2, dust, Fefree(:), Fe_scavenge_rate(:), &
Fe_scavenge(:), Lig_scavenge(:), marbl_status_log)

Expand Down Expand Up @@ -375,7 +383,7 @@ subroutine marbl_interior_tendency_compute( &
return
end if

if (k < km) then
if (k < kmt) then
call update_particulate_terms_from_prior_level(k+1, POC, POP, P_CaCO3, &
P_CaCO3_ALT_CO2, P_SiO2, dust, P_iron, QA_dust_def(:))
endif
Expand Down Expand Up @@ -788,7 +796,7 @@ end subroutine setup_local_tracers
!***********************************************************************

subroutine set_surface_particulate_terms(surface_flux_forcing_indices, POC, POP, P_CaCO3, &
P_CaCO3_ALT_CO2, P_SiO2, dust, P_iron, QA_dust_def, NET_DUST_IN)
P_CaCO3_ALT_CO2, P_SiO2, dust, P_iron, QA_dust_def, NET_DUST_IN, PON_remin, PON_sed_loss)

! Set incoming fluxes (put into outgoing flux for first level usage).
! Set dissolution length, production fraction and mass terms.
Expand Down Expand Up @@ -817,6 +825,8 @@ subroutine set_surface_particulate_terms(surface_flux_forcing_indices, POC, POP,
type(column_sinking_particle_type) , intent(inout) :: dust ! base units = g
type(column_sinking_particle_type) , intent(inout) :: P_iron ! base units = nmol Fe
real (r8) , intent(inout) :: QA_dust_def(:) ! incoming deficit in the QA(dust) POC flux (km)
real (r8), dimension(:) , intent(inout) :: PON_remin ! remin of PON
real (r8), dimension(:) , intent(inout) :: PON_sed_loss ! loss of PON to sediments

!-----------------------------------------------------------------------
! local variables
Expand Down Expand Up @@ -869,6 +879,80 @@ subroutine set_surface_particulate_terms(surface_flux_forcing_indices, POC, POP,
! Set incoming fluxes
!-----------------------------------------------------------------------

! Initialize
POC%sflux_in(:) = c0
POC%hflux_in(:) = c0

POP%sflux_in(:) = c0
POP%hflux_in(:) = c0

P_CaCO3%sflux_in(:) = c0
P_CaCO3%hflux_in(:) = c0

P_CaCO3_ALT_CO2%sflux_in(:) = c0
P_CaCO3_ALT_CO2%hflux_in(:) = c0

P_SiO2%sflux_in(:) = c0
P_SiO2%hflux_in(:) = c0

dust%sflux_in(:) = c0
dust%hflux_in(:) = c0

P_iron%sflux_in(:) = c0
P_iron%hflux_in(:) = c0

POC%sflux_out(:) = c0
POC%hflux_out(:) = c0

POP%sflux_out(:) = c0
POP%hflux_out(:) = c0

P_CaCO3%sflux_out(:) = c0
P_CaCO3%hflux_out(:) = c0

P_CaCO3_ALT_CO2%sflux_out(:) = c0
P_CaCO3_ALT_CO2%hflux_out(:) = c0

P_SiO2%sflux_out(:) = c0
P_SiO2%hflux_out(:) = c0

dust%sflux_out(:) = c0
dust%hflux_out(:) = c0

P_iron%sflux_out(:) = c0
P_iron%hflux_out(:) = c0

QA_dust_def(:) = c0

! initialize additional fields

POC%sed_loss(:) = c0
POP%sed_loss(:) = c0
P_SiO2%sed_loss(:) = c0
P_CaCO3%sed_loss(:) = c0
P_CaCO3_ALT_CO2%sed_loss(:) = c0
P_iron%sed_loss(:) = c0
dust%sed_loss(:) = c0

POC%remin(:) = c0
POP%remin(:) = c0
P_CaCO3%remin(:) = c0
P_CaCO3_ALT_CO2%remin(:) = c0
P_SiO2%remin(:) = c0
dust%remin(:) = c0
P_iron%remin(:) = c0

POC%prod(:) = c0
POP%prod(:) = c0
P_CaCO3%prod(:) = c0
P_CaCO3_ALT_CO2%prod(:) = c0
P_SiO2%prod(:) = c0
dust%prod(:) = c0
P_iron%prod(:) = c0

PON_remin(:) = c0
PON_sed_loss(:) = c0

ksurf = 1

P_CaCO3%sflux_in(ksurf) = c0
Expand Down Expand Up @@ -2079,12 +2163,14 @@ subroutine compute_dissolved_organic_matter (km, marbl_tracer_indices, &
DONr_remin => dissolved_organic_matter%DONr_remin(:), & ! output remineralization of DONr
DOP_prod => dissolved_organic_matter%DOP_prod(:), & ! output production of DOP
DOP_remin => dissolved_organic_matter%DOP_remin(:), & ! output remineralization of DOP
DOPr_remin => dissolved_organic_matter%DOPr_remin(:) & ! output remineralization of DOPr
DOPr_remin => dissolved_organic_matter%DOPr_remin(:), & ! output remineralization of DOPr
DOP_loss_P_bal => dissolved_organic_matter%DOP_loss_P_bal(:) & ! DOP loss, due to P budget balancing
)

!-----------------------------------------------------------------------
! compute terms for DOM
!-----------------------------------------------------------------------
DOP_loss_P_bal(:) = c0

DOC_prod(:) = sum(zoo_loss_doc(:,:), dim=1) + sum(auto_loss_doc(:,:), dim=1) &
+ sum(auto_graze_doc(:,:), dim=1) + sum(zoo_graze_doc(:,:), dim=1)
Expand Down Expand Up @@ -2169,7 +2255,7 @@ subroutine compute_scavenging(k, km, marbl_tracer_indices, &
type(column_sinking_particle_type), intent(in) :: P_CaCO3
type(column_sinking_particle_type), intent(in) :: P_SiO2
type(column_sinking_particle_type), intent(in) :: dust
real(r8), intent(out) :: Fefree(km)
real(r8), intent(inout) :: Fefree(km)
real(r8), intent(out) :: Fe_scavenge_rate(km)
real(r8), intent(out) :: Fe_scavenge(km)
real(r8), intent(out) :: Lig_scavenge(km)
Expand Down Expand Up @@ -2340,7 +2426,7 @@ subroutine compute_scavenging(k, km, marbl_tracer_indices, &
! scavening of FeLig2 is not implemented
!-----------------------------------------------------------------------

sinking_mass = (POC%sflux_in(k) + POC%hflux_in(k) ) * (3.0_r8 * 12.01_r8) &
sinking_mass = (POC%sflux_in(k) + POC%hflux_in(k) ) * (3.0_r8 * POC%mass) &
+ (P_CaCO3%sflux_in(k) + P_CaCO3%hflux_in(k)) * P_CaCO3%mass &
+ (P_SiO2%sflux_in(k) + P_SiO2%hflux_in(k) ) * P_SiO2%mass &
+ (dust%sflux_in(k) + dust%hflux_in(k) ) * dust_Fe_scavenge_scale
Expand Down Expand Up @@ -2386,7 +2472,7 @@ subroutine compute_large_detritus_prod(k, domain, marbl_tracer_indices, &
type(column_sinking_particle_type), intent(inout) :: P_SiO2
type(column_sinking_particle_type), intent(inout) :: dust
type(column_sinking_particle_type), intent(inout) :: P_iron
real(r8), intent(out) :: DOP_loss_P_bal
real(r8), intent(inout) :: DOP_loss_P_bal
type(marbl_log_type), intent(inout) :: marbl_status_log

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -2575,8 +2661,8 @@ subroutine compute_particulate_terms(k, domain, &
real (r8), dimension(:) , intent(in) :: tracer_local ! local copies of model tracer concentrations
type(carbonate_type) , intent(in) :: carbonate
real(r8) , intent(in) :: fesedflux ! sedimentary Fe input
real(r8) , intent(out) :: PON_remin ! remin of PON
real(r8) , intent(out) :: PON_sed_loss ! loss of PON to sediments
real(r8) , intent(inout) :: PON_remin ! remin of PON
real(r8) , intent(inout) :: PON_sed_loss ! loss of PON to sediments
type(column_sinking_particle_type), intent(inout) :: POC ! base units = nmol C
type(column_sinking_particle_type), intent(inout) :: POP ! base units = nmol P
type(column_sinking_particle_type), intent(inout) :: P_CaCO3 ! base units = nmol CaCO3
Expand All @@ -2585,8 +2671,8 @@ subroutine compute_particulate_terms(k, domain, &
type(column_sinking_particle_type), intent(inout) :: dust ! base units = g
type(column_sinking_particle_type), intent(inout) :: P_iron ! base units = nmol Fe
real (r8) , intent(inout) :: QA_dust_def ! incoming deficit in the QA(dust) POC flux
real (r8) , intent(out) :: sed_denitrif ! sedimentary denitrification (umolN/cm^2/s)
real (r8) , intent(out) :: other_remin ! sedimentary remin not due to oxic or denitrification
real (r8) , intent(inout) :: sed_denitrif ! sedimentary denitrification (umolN/cm^2/s)
real (r8) , intent(inout) :: other_remin ! sedimentary remin not due to oxic or denitrification
type(marbl_particulate_share_type), intent(inout) :: marbl_particulate_share
type(marbl_tracer_index_type) , intent(in) :: marbl_tracer_indices
real (r8) , intent(inout) :: glo_avg_fields_interior_tendency(:)
Expand Down
2 changes: 1 addition & 1 deletion src/marbl_settings_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,7 @@ subroutine marbl_settings_set_defaults_general_parms()
parm_FeLig_scavenge_rate0 = 1.2_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_Lig_degrade_rate0 = 0.000094_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_Fe_desorption_rate0 = 1.0e-6_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_f_prod_sp_CaCO3 = 0.070_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_f_prod_sp_CaCO3 = 0.049_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_POC_diss = 100.0e2_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_SiO2_diss = 650.0e2_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
parm_SiO2_gamma = 0.00_r8 ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
Expand Down