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Clean up diag indices
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1. renamed lconstructed() -> lallocated()
2. only allocate indices for autotroph / zooplankton diags if base_bio_on is
   true (requires checking base_bio_on before deallocating)
   -- this reverts some of the allocate statements to put them back where they
     are on development (modulo additional whitespace because it is now in a
     new "if (base_bio_on)" block)
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@mnlevy1981
mnlevy1981 committed Oct 13, 2023
1 parent 0ce48a8 commit a064eb9
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Showing 3 changed files with 196 additions and 189 deletions.
2 changes: 1 addition & 1 deletion src/marbl_ciso_diagnostics_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -608,7 +608,7 @@ subroutine marbl_ciso_diagnostics_init( &
end if

! Nonstandard autotroph 2D and 3D fields for each autotroph
if (.not.ind%lconstructed()) then
if (.not.ind%lallocated()) then
allocate(ind%CISO_eps_autotroph(autotroph_cnt))
allocate(ind%CISO_mui_to_co2star(autotroph_cnt))
allocate(ind%CISO_Ca13CO3_form(autotroph_cnt))
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178 changes: 91 additions & 87 deletions src/marbl_diagnostics_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -467,92 +467,6 @@ subroutine marbl_diagnostics_init( &
diags => marbl_interior_tendency_diags &
)

! Allocate memory for PFT diagnostics
if (.not.ind%lconstructed()) then
allocate(ind%N_lim_surf(autotroph_cnt))
allocate(ind%N_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%P_lim_surf(autotroph_cnt))
allocate(ind%P_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%Fe_lim_surf(autotroph_cnt))
allocate(ind%Fe_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%SiO3_lim_surf(autotroph_cnt))
allocate(ind%SiO3_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%C_lim_surf(autotroph_cnt))
allocate(ind%C_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%light_lim_surf(autotroph_cnt))
allocate(ind%light_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%photoC_zint(autotroph_cnt))
allocate(ind%photoC_zint_100m(autotroph_cnt))
allocate(ind%photoC_NO3_zint(autotroph_cnt))
allocate(ind%CaCO3_form_zint(autotroph_cnt))
allocate(ind%CaCO3_form_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_zint(autotroph_cnt))
allocate(ind%auto_graze_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_poc_zint(autotroph_cnt))
allocate(ind%auto_graze_poc_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_doc_zint(autotroph_cnt))
allocate(ind%auto_graze_doc_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_zoo_zint(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_graze_zoo_zint_100m(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_loss_zint(autotroph_cnt))
allocate(ind%auto_loss_zint_100m(autotroph_cnt))
allocate(ind%auto_loss_poc_zint(autotroph_cnt))
allocate(ind%auto_loss_poc_zint_100m(autotroph_cnt))
allocate(ind%auto_loss_doc_zint(autotroph_cnt))
allocate(ind%auto_loss_doc_zint_100m(autotroph_cnt))
allocate(ind%auto_agg_zint(autotroph_cnt))
allocate(ind%auto_agg_zint_100m(autotroph_cnt))
allocate(ind%zoo_loss_zint(zooplankton_cnt))
allocate(ind%zoo_loss_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_zint_150m(zooplankton_cnt))
allocate(ind%zoo_loss_basal_zint(zooplankton_cnt))
allocate(ind%zoo_loss_basal_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_poc_zint(zooplankton_cnt))
allocate(ind%zoo_loss_poc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_doc_zint(zooplankton_cnt))
allocate(ind%zoo_loss_doc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_zint(zooplankton_cnt))
allocate(ind%zoo_graze_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_poc_zint(zooplankton_cnt))
allocate(ind%zoo_graze_poc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_doc_zint(zooplankton_cnt))
allocate(ind%zoo_graze_doc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_zoo_zint(zooplankton_cnt, zooplankton_cnt))
allocate(ind%zoo_graze_zoo_zint_100m(zooplankton_cnt, zooplankton_cnt))
allocate(ind%x_graze_zoo_zint(zooplankton_cnt))
allocate(ind%x_graze_zoo_zint_100m(zooplankton_cnt))
allocate(ind%Qp(autotroph_cnt))
allocate(ind%photoC(autotroph_cnt))
allocate(ind%photoC_NO3(autotroph_cnt))
allocate(ind%photoFe(autotroph_cnt))
allocate(ind%photoNO3(autotroph_cnt))
allocate(ind%photoNH4(autotroph_cnt))
allocate(ind%DOP_uptake(autotroph_cnt))
allocate(ind%PO4_uptake(autotroph_cnt))
allocate(ind%auto_graze(autotroph_cnt))
allocate(ind%auto_graze_poc(autotroph_cnt))
allocate(ind%auto_graze_doc(autotroph_cnt))
allocate(ind%auto_graze_zootot(autotroph_cnt))
allocate(ind%auto_graze_zoo(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_loss(autotroph_cnt))
allocate(ind%auto_loss_poc(autotroph_cnt))
allocate(ind%auto_loss_doc(autotroph_cnt))
allocate(ind%auto_agg(autotroph_cnt))
allocate(ind%bSi_form(autotroph_cnt))
allocate(ind%CaCO3_form(autotroph_cnt))
allocate(ind%Nfix(autotroph_cnt))
allocate(ind%zoo_loss(zooplankton_cnt))
allocate(ind%zoo_loss_basal(zooplankton_cnt))
allocate(ind%zoo_loss_poc(zooplankton_cnt))
allocate(ind%zoo_loss_doc(zooplankton_cnt))
allocate(ind%zoo_graze(zooplankton_cnt))
allocate(ind%zoo_graze_poc(zooplankton_cnt))
allocate(ind%zoo_graze_doc(zooplankton_cnt))
allocate(ind%zoo_graze_zootot(zooplankton_cnt))
allocate(ind%zoo_graze_zoo(zooplankton_cnt, zooplankton_cnt))
allocate(ind%x_graze_zoo(zooplankton_cnt))
end if

if (base_bio_on) then
! General 2D diags
lname = 'Calcite Saturation Depth'
Expand Down Expand Up @@ -929,6 +843,41 @@ subroutine marbl_diagnostics_init( &
end if

! Autotroph 2D diags
if (.not.ind%lallocated()) then
allocate(ind%N_lim_surf(autotroph_cnt))
allocate(ind%N_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%P_lim_surf(autotroph_cnt))
allocate(ind%P_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%Fe_lim_surf(autotroph_cnt))
allocate(ind%Fe_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%SiO3_lim_surf(autotroph_cnt))
allocate(ind%SiO3_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%C_lim_surf(autotroph_cnt))
allocate(ind%C_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%light_lim_surf(autotroph_cnt))
allocate(ind%light_lim_Cweight_avg_100m(autotroph_cnt))
allocate(ind%photoC_zint(autotroph_cnt))
allocate(ind%photoC_zint_100m(autotroph_cnt))
allocate(ind%photoC_NO3_zint(autotroph_cnt))
allocate(ind%CaCO3_form_zint(autotroph_cnt))
allocate(ind%CaCO3_form_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_zint(autotroph_cnt))
allocate(ind%auto_graze_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_poc_zint(autotroph_cnt))
allocate(ind%auto_graze_poc_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_doc_zint(autotroph_cnt))
allocate(ind%auto_graze_doc_zint_100m(autotroph_cnt))
allocate(ind%auto_graze_zoo_zint(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_graze_zoo_zint_100m(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_loss_zint(autotroph_cnt))
allocate(ind%auto_loss_zint_100m(autotroph_cnt))
allocate(ind%auto_loss_poc_zint(autotroph_cnt))
allocate(ind%auto_loss_poc_zint_100m(autotroph_cnt))
allocate(ind%auto_loss_doc_zint(autotroph_cnt))
allocate(ind%auto_loss_doc_zint_100m(autotroph_cnt))
allocate(ind%auto_agg_zint(autotroph_cnt))
allocate(ind%auto_agg_zint_100m(autotroph_cnt))
end if
do n=1,autotroph_cnt
lname = trim(autotroph_settings(n)%lname) // ' N Limitation, Surface'
sname = trim(autotroph_settings(n)%sname) // '_N_lim_surf'
Expand Down Expand Up @@ -1373,6 +1322,27 @@ subroutine marbl_diagnostics_init( &
end if

! Zooplankton 2D diags
if (.not.ind%lallocated()) then
allocate(ind%zoo_loss_zint(zooplankton_cnt))
allocate(ind%zoo_loss_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_zint_150m(zooplankton_cnt))
allocate(ind%zoo_loss_basal_zint(zooplankton_cnt))
allocate(ind%zoo_loss_basal_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_poc_zint(zooplankton_cnt))
allocate(ind%zoo_loss_poc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_loss_doc_zint(zooplankton_cnt))
allocate(ind%zoo_loss_doc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_zint(zooplankton_cnt))
allocate(ind%zoo_graze_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_poc_zint(zooplankton_cnt))
allocate(ind%zoo_graze_poc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_doc_zint(zooplankton_cnt))
allocate(ind%zoo_graze_doc_zint_100m(zooplankton_cnt))
allocate(ind%zoo_graze_zoo_zint(zooplankton_cnt, zooplankton_cnt))
allocate(ind%zoo_graze_zoo_zint_100m(zooplankton_cnt, zooplankton_cnt))
allocate(ind%x_graze_zoo_zint(zooplankton_cnt))
allocate(ind%x_graze_zoo_zint_100m(zooplankton_cnt))
end if
do n = 1,zooplankton_cnt
lname = trim(zooplankton_settings(n)%lname) // ' Loss Vertical Integral'
sname = trim(zooplankton_settings(n)%sname) // '_loss_zint'
Expand Down Expand Up @@ -2604,6 +2574,28 @@ subroutine marbl_diagnostics_init( &
end if

! Autotroph 3D diags
if (.not.ind%lallocated()) then
allocate(ind%Qp(autotroph_cnt))
allocate(ind%photoC(autotroph_cnt))
allocate(ind%photoC_NO3(autotroph_cnt))
allocate(ind%photoFe(autotroph_cnt))
allocate(ind%photoNO3(autotroph_cnt))
allocate(ind%photoNH4(autotroph_cnt))
allocate(ind%DOP_uptake(autotroph_cnt))
allocate(ind%PO4_uptake(autotroph_cnt))
allocate(ind%auto_graze(autotroph_cnt))
allocate(ind%auto_graze_poc(autotroph_cnt))
allocate(ind%auto_graze_doc(autotroph_cnt))
allocate(ind%auto_graze_zootot(autotroph_cnt))
allocate(ind%auto_graze_zoo(autotroph_cnt, zooplankton_cnt))
allocate(ind%auto_loss(autotroph_cnt))
allocate(ind%auto_loss_poc(autotroph_cnt))
allocate(ind%auto_loss_doc(autotroph_cnt))
allocate(ind%auto_agg(autotroph_cnt))
allocate(ind%bSi_form(autotroph_cnt))
allocate(ind%CaCO3_form(autotroph_cnt))
allocate(ind%Nfix(autotroph_cnt))
end if
do n=1,autotroph_cnt
if (lvariable_PtoC) then
lname = trim(autotroph_settings(n)%lname) // ' P:C ratio'
Expand Down Expand Up @@ -2902,6 +2894,18 @@ subroutine marbl_diagnostics_init( &
end if

! Zooplankton 3D diags
if (.not.ind%lallocated()) then
allocate(ind%zoo_loss(zooplankton_cnt))
allocate(ind%zoo_loss_basal(zooplankton_cnt))
allocate(ind%zoo_loss_poc(zooplankton_cnt))
allocate(ind%zoo_loss_doc(zooplankton_cnt))
allocate(ind%zoo_graze(zooplankton_cnt))
allocate(ind%zoo_graze_poc(zooplankton_cnt))
allocate(ind%zoo_graze_doc(zooplankton_cnt))
allocate(ind%zoo_graze_zootot(zooplankton_cnt))
allocate(ind%zoo_graze_zoo(zooplankton_cnt, zooplankton_cnt))
allocate(ind%x_graze_zoo(zooplankton_cnt))
end if
do n = 1,zooplankton_cnt
lname = trim(zooplankton_settings(n)%lname) // ' Loss'
sname = trim(zooplankton_settings(n)%sname) // '_loss'
Expand Down Expand Up @@ -3058,7 +3062,7 @@ subroutine marbl_diagnostics_init( &
! FIXME #60: this approach is not thread-safe
! i.e. if this is called from 2 threads simulatneously, a race condition
! on the allocation status check and allocation is introduced
if (.not.ind%lconstructed()) then
if (.not. ind%lallocated()) then
allocate(ind%restore_tend(marbl_tracer_indices%total_cnt))
end if

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