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Add new burial diagnostics #486

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aebc46b
Add d_bury_d_bury_coeff to sinking particle type
mnlevy1981 Nov 6, 2025
39b0e1f
Create new diagnostics for burial deriviatives
mnlevy1981 Nov 6, 2025
aca092e
Add new bury diagnostics to YAML file
mnlevy1981 Nov 6, 2025
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27 changes: 27 additions & 0 deletions defaults/diagnostics_latest.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -849,6 +849,33 @@ pfeToSed :
frequency : medium
operator : average
diag_mode : minimal
d_POC_bury_d_bury_coeff :
dependencies :
base_bio_on : .true.
longname : d[POC burial]/d[POC burial coefficient]
units : nmol/cm^2/s
vertical_grid : none
frequency : never
operator : average
diag_mode : full
d_POP_bury_d_bury_coeff :
dependencies :
base_bio_on : .true.
longname : d[POP burial]/d[POP burial coefficient]
units : nmol/cm^2/s
vertical_grid : none
frequency : never
operator : average
diag_mode : full
d_bSi_bury_d_bury_coeff :
dependencies :
base_bio_on : .true.
longname : d[bSi burial]/d[bSi burial coefficient]
units : nmol/cm^2/s
vertical_grid : none
frequency : never
operator : average
diag_mode : full
CaCO3_form_zint :
dependencies :
base_bio_on : .true.
Expand Down
33 changes: 33 additions & 0 deletions defaults/json/diagnostics_latest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2649,6 +2649,28 @@
"units": "mmol/m^3",
"vertical_grid": "layer_avg"
},
"d_POC_bury_d_bury_coeff": {
"dependencies": {
"base_bio_on": ".true."
},
"diag_mode": "full",
"frequency": "never",
"longname": "d[POC burial]/d[POC burial coefficient]",
"operator": "average",
"units": "nmol/cm^2/s",
"vertical_grid": "none"
},
"d_POP_bury_d_bury_coeff": {
"dependencies": {
"base_bio_on": ".true."
},
"diag_mode": "full",
"frequency": "never",
"longname": "d[POP burial]/d[POP burial coefficient]",
"operator": "average",
"units": "nmol/cm^2/s",
"vertical_grid": "none"
},
"d_SF_ABIO_DI14C_d_ABIO_DI14C": {
"dependencies": {
"abio_dic_on": ".true.",
Expand Down Expand Up @@ -2688,6 +2710,17 @@
"units": "cm/s",
"vertical_grid": "none"
},
"d_bSi_bury_d_bury_coeff": {
"dependencies": {
"base_bio_on": ".true."
},
"diag_mode": "full",
"frequency": "never",
"longname": "d[bSi burial]/d[bSi burial coefficient]",
"operator": "average",
"units": "nmol/cm^2/s",
"vertical_grid": "none"
},
"dustToSed": {
"dependencies": {
"base_bio_on": ".true."
Expand Down
40 changes: 40 additions & 0 deletions src/marbl_diagnostics_mod.F90
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Expand Up @@ -848,6 +848,42 @@ subroutine marbl_diagnostics_init( &
return
end if

lname = 'd[POC burial]/d[POC burial coefficient]'
sname = 'd_POC_bury_d_bury_coeff'
units = unit_system%conc_flux_units
vgrid = 'none'
truncate = .false.
call diags%add_diagnostic(lname, sname, units, vgrid, truncate, &
ind%d_POC_bury_d_bury_coeff, marbl_status_log)
if (marbl_status_log%labort_marbl) then
call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
return
end if

lname = 'd[POP burial]/d[POP burial coefficient]'
sname = 'd_POP_bury_d_bury_coeff'
units = unit_system%conc_flux_units
vgrid = 'none'
truncate = .false.
call diags%add_diagnostic(lname, sname, units, vgrid, truncate, &
ind%d_POP_bury_d_bury_coeff, marbl_status_log)
if (marbl_status_log%labort_marbl) then
call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
return
end if

lname = 'd[bSi burial]/d[bSi burial coefficient]'
sname = 'd_bSi_bury_d_bury_coeff'
units = unit_system%conc_flux_units
vgrid = 'none'
truncate = .false.
call diags%add_diagnostic(lname, sname, units, vgrid, truncate, &
ind%d_bSi_bury_d_bury_coeff, marbl_status_log)
if (marbl_status_log%labort_marbl) then
call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
return
end if

! Autotroph 2D diags
if (.not.ind%lallocated()) then
allocate(ind%N_lim_surf(autotroph_cnt))
Expand Down Expand Up @@ -3919,6 +3955,10 @@ subroutine store_diagnostics_particulates(marbl_domain, &
diags(ind%dustToSed)%field_2d(1) = sum(dust%sed_loss)
diags(ind%pfeToSed)%field_2d(1) = sum(P_iron%sed_loss)

diags(ind%d_POC_bury_d_bury_coeff)%field_2d(1) = POC%d_bury_d_bury_coeff
diags(ind%d_POP_bury_d_bury_coeff)%field_2d(1) = POP%d_bury_d_bury_coeff
diags(ind%d_bSi_bury_d_bury_coeff)%field_2d(1) = P_SiO2%d_bury_d_bury_coeff

end associate

end subroutine store_diagnostics_particulates
Expand Down
4 changes: 4 additions & 0 deletions src/marbl_interface_private_types.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -163,6 +163,7 @@ module marbl_interface_private_types
real(r8) :: rho ! QA mass ratio of POC to this particle class
real(r8) :: to_floor ! flux hitting sea floor (base units/L^2/sec)
real(r8) :: flux_at_ref_depth ! flux at particulate_flux_ref_depth (base units/L^2/sec)
real(r8) :: d_bury_d_bury_coeff ! Derivative of burial with respect to bury coeff (base units/L^2/sec)
real(r8), allocatable :: sflux_in (:) ! incoming flux of soft subclass (base units/L^2/sec)
real(r8), allocatable :: hflux_in (:) ! incoming flux of hard subclass (base units/L^2/sec)
real(r8), allocatable :: prod (:) ! production term (base units/L^3/sec)
Expand Down Expand Up @@ -547,6 +548,9 @@ module marbl_interface_private_types
integer(int_kind) :: bsiToSed
integer(int_kind) :: dustToSed
integer(int_kind) :: pfeToSed
integer(int_kind) :: d_POC_bury_d_bury_coeff
integer(int_kind) :: d_POP_bury_d_bury_coeff
integer(int_kind) :: d_bSi_bury_d_bury_coeff

! Autotroph 2D diags
integer(int_kind), allocatable :: N_lim_surf(:)
Expand Down
36 changes: 18 additions & 18 deletions src/marbl_interior_tendency_mod.F90
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Expand Up @@ -3179,6 +3179,16 @@ subroutine compute_particulate_terms(k, domain, bot_flux_to_tend, p_remin_scalef

! first compute burial efficiency, then compute loss to sediments
bury_frac = 0.013_r8 + 0.53_r8 * flux_alt*flux_alt / (7.0_r8 + flux_alt)**2
if (POC_bury_coeff * bury_frac < POM_bury_frac_max) then
POC%d_bury_d_bury_coeff = POC%to_floor * bury_frac
else
POC%d_bury_d_bury_coeff = c0
end if
if (POP_bury_coeff * bury_frac < POM_bury_frac_max) then
POP%d_bury_d_bury_coeff = POP%to_floor * bury_frac
else
POP%d_bury_d_bury_coeff = c0
end if
if (p_remin_scalef /= c1) bury_frac = c1 - p_remin_scalef * (c1 - bury_frac)
POC%sed_loss(k) = POC%to_floor * min(POM_bury_frac_max, POC_bury_coeff * bury_frac)

Expand All @@ -3189,20 +3199,12 @@ subroutine compute_particulate_terms(k, domain, bot_flux_to_tend, p_remin_scalef

if (ladjust_bury_coeff) then
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_POC_bury) = POC%sed_loss(k)
if (POC_bury_coeff * bury_frac < POM_bury_frac_max) then
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POC_bury_d_bury_coeff) = &
POC%to_floor * bury_frac
else
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POC_bury_d_bury_coeff) = c0
endif
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POC_bury_d_bury_coeff) = &
POC%d_bury_d_bury_coeff

glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_POP_bury) = POP%sed_loss(k)
if (POP_bury_coeff * bury_frac < POM_bury_frac_max) then
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POP_bury_d_bury_coeff) = &
POP%to_floor * bury_frac
else
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POP_bury_d_bury_coeff) = c0
endif
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_POP_bury_d_bury_coeff) = &
POP%d_bury_d_bury_coeff
endif

sed_denitrif(1:k) = bot_flux_to_tend(1:k) * parm_sed_denitrif_coeff * POC%to_floor &
Expand Down Expand Up @@ -3248,18 +3250,16 @@ subroutine compute_particulate_terms(k, domain, bot_flux_to_tend, p_remin_scalef
if (p_remin_scalef /= c1) bury_frac = c1 - p_remin_scalef * (c1 - bury_frac)
if (bSi_bury_coeff * bury_frac < bSi_bury_frac_max) then
P_SiO2%sed_loss(k) = P_SiO2%to_floor * bSi_bury_coeff * bury_frac
P_SiO2%d_bury_d_bury_coeff = P_SiO2%to_floor * bury_frac
else
P_SiO2%sed_loss(k) = P_SiO2%to_floor * bSi_bury_frac_max
P_SiO2%d_bury_d_bury_coeff = c0
endif

if (ladjust_bury_coeff) then
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_bSi_bury) = P_SiO2%sed_loss(k)
if (bSi_bury_coeff * bury_frac < bSi_bury_frac_max) then
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_bSi_bury_d_bury_coeff) = &
P_SiO2%to_floor * bury_frac
else
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_bSi_bury_d_bury_coeff) = c0
endif
glo_avg_fields_interior_tendency(glo_avg_field_ind_interior_tendency_d_bSi_bury_d_bury_coeff) = &
P_SiO2%d_bury_d_bury_coeff
endif

P_CaCO3%to_floor = P_CaCO3%sflux_out(k) + P_CaCO3%hflux_out(k)
Expand Down
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