cleanup phytoplankton uptake section (#58)

* cleanup phytoplankton uptake section * complete removal of net_phyto_resp by removing registration and sending * fix typo --------- Co-authored-by: Yi-Cheng Teng - NOAA GFDL <143743249+yichengt900@users.noreply.github.com>
NOAA-CEFI-Regional-Ocean-Modeling · May 17, 2024 · e62cd4c · e62cd4c
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diff --git a/generic_tracers/cobalt_reg_diag.F90 b/generic_tracers/cobalt_reg_diag.F90
@@ -612,10 +612,6 @@ subroutine cobalt_reg_diagnostics(diag_list,axes,init_time,phyto,zoo,bact,cobalt
     phyto(LARGE)%id_jprod_n = register_diag_field(package_name, vardesc_temp%name, axes(1:3),&
          init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
 
-    vardesc_temp = vardesc("net_phyto_resp","Net phytoplankton respiration layer integral",'h','L','s','mol m-2 s-1','f')
-    cobalt%id_net_phyto_resp = register_diag_field(package_name, vardesc_temp%name, axes(1:3),&
-         init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
-
     !
     ! Register zooplankton diagnostics, starting with losses of zooplankton to ingestion by zooplankton
     !
@@ -1916,7 +1912,7 @@ subroutine cobalt_reg_diagnostics(diag_list,axes,init_time,phyto,zoo,bact,cobalt
     cobalt%id_btm_omega_calc = register_diag_field(package_name, vardesc_temp%name, axes(1:2),&
          init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
 
-    vardesc_temp = vardesc("cased_2d","calcium carbonite in sediment",'h','1','s','mol m-3','f')
+    vardesc_temp = vardesc("cased_2d","calcium carbonate in sediment",'h','1','s','mol m-3','f')
     cobalt%id_cased_2d = register_diag_field(package_name, vardesc_temp%name, axes(1:2),&
          init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
 
@@ -2401,10 +2397,6 @@ subroutine cobalt_reg_diagnostics(diag_list,axes,init_time,phyto,zoo,bact,cobalt
     cobalt%id_wc_vert_int_chemoautopp = register_diag_field(package_name, vardesc_temp%name, axes(1:2),&
          init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
 
-    vardesc_temp = vardesc("wc_vert_int_net_phyto_resp","Water column net phyto respiration vertical integral",'h','1','s','mol N m-2 s-1','f')
-    cobalt%id_wc_vert_int_net_phyto_resp = register_diag_field(package_name, vardesc_temp%name, axes(1:2),&
-         init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
-
     vardesc_temp = vardesc("wc_vert_int_npp","Water column net primary production vertical integral",'h','1','s','mol N m-2 s-1','f')
     cobalt%id_wc_vert_int_npp = register_diag_field(package_name, vardesc_temp%name, axes(1:2),&
          init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)

diff --git a/generic_tracers/cobalt_send_diag.F90 b/generic_tracers/cobalt_send_diag.F90
@@ -328,9 +328,6 @@ subroutine cobalt_send_diagnostics(model_time,grid_tmask,Temp,rho_dzt,dzt,&
        used = g_send_data(cobalt%id_jprod_po4, cobalt%jprod_po4*rho_dzt,           &
        model_time, rmask = grid_tmask,&
        is_in=isc, js_in=jsc, ks_in=1,ie_in=iec, je_in=jec, ke_in=nk)
-       used = g_send_data(cobalt%id_net_phyto_resp, cobalt%net_phyto_resp*rho_dzt,           &
-       model_time, rmask = grid_tmask,&
-       is_in=isc, js_in=jsc, ks_in=1,ie_in=iec, je_in=jec, ke_in=nk)
        used = g_send_data(cobalt%id_jprod_fed, cobalt%jprod_fed*rho_dzt,           &
        model_time, rmask = grid_tmask,&
        is_in=isc, js_in=jsc, ks_in=1,ie_in=iec, je_in=jec, ke_in=nk)
@@ -1172,9 +1169,6 @@ subroutine cobalt_send_diagnostics(model_time,grid_tmask,Temp,rho_dzt,dzt,&
        used = g_send_data(cobalt%id_wc_vert_int_chemoautopp, cobalt%wc_vert_int_chemoautopp, &
        model_time, rmask = grid_tmask(:,:,1),&
        is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
-       used = g_send_data(cobalt%id_wc_vert_int_net_phyto_resp, cobalt%wc_vert_int_net_phyto_resp, &
-       model_time, rmask = grid_tmask(:,:,1),&
-       is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
        used = g_send_data(cobalt%id_wc_vert_int_npp,    cobalt%wc_vert_int_npp,         &
        model_time, rmask = grid_tmask(:,:,1),&
        is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)

diff --git a/generic_tracers/cobalt_types.F90 b/generic_tracers/cobalt_types.F90
@@ -688,7 +688,6 @@ module cobalt_types
           jprod_nh4,&
           jprod_nh4_plus_btm,&
           jprod_po4,&
-          net_phyto_resp,&
           det_jzloss_n,&
           det_jzloss_p,&
           det_jzloss_fe,&
@@ -885,7 +884,6 @@ module cobalt_types
           wc_vert_int_o2,&
           wc_vert_int_alk,&
           wc_vert_int_chemoautopp,&
-          wc_vert_int_net_phyto_resp,&
           wc_vert_int_npp, &
           wc_vert_int_jdiss_sidet,&
           wc_vert_int_jdiss_cadet,&
@@ -1017,7 +1015,6 @@ module cobalt_types
           id_jprod_po4     = -1,       &
           id_jprod_nh4     = -1,       &
           id_jprod_nh4_plus_btm = -1,  &
-          id_net_phyto_resp = -1,      &
           id_det_jzloss_n  = -1,       &
           id_det_jhploss_n = -1,       &
           id_jdiss_sidet   = -1,       &
@@ -1187,7 +1184,6 @@ module cobalt_types
           id_wc_vert_int_alk = -1,     &
           id_wc_vert_int_chemoautopp = -1, &
           id_wc_vert_int_npp = -1, &
-          id_wc_vert_int_net_phyto_resp = -1, &
           id_wc_vert_int_jdiss_sidet = -1, &
           id_wc_vert_int_jdiss_cadet = -1, &
           id_wc_vert_int_jo2resp = -1,     &

diff --git a/generic_tracers/generic_COBALT.F90 b/generic_tracers/generic_COBALT.F90
@@ -2465,7 +2465,6 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
        cobalt%jno3denit_wc(i,j,k) = 0.0
        cobalt%jremin_ndet(i,j,k) = 0.0
        cobalt%jo2resp_wc(i,j,k) = 0.0
-       cobalt%net_phyto_resp(i,j,k) = 0.0
     enddo;  enddo ;  enddo !} i,j,k
 !
 !-----------------------------------------------------------------------------------
@@ -2876,22 +2875,20 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
           phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
        phyto(n)%juptake_nh4(i,j,k) = max(0.0,phyto(n)%nh4lim(i,j,k)* phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
        phyto(n)%juptake_no3(i,j,k) = max(0.0,phyto(n)%no3lim(i,j,k)* phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
-       ! uncomment for "no mass change" test (next 2 lines)
-       ! phyto(n)%juptake_nh4(i,j,k) = phyto(n)%juptake_nh4(i,j,k) + phyto(n)%juptake_n2(i,j,k)
-       ! phyto(n)%juptake_n2(i,j,k) = 0.0
 
        ! If growth is negative, results in net respiration and production of nh4, aerobic loss in all cases
+       ! jo2resp_wc is a cumulative variable that tracks the total oxygen consumption in the water column
        cobalt%jprod_nh4(i,j,k) = cobalt%jprod_nh4(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
        cobalt%jo2resp_wc(i,j,k) = cobalt%jo2resp_wc(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))*cobalt%o2_2_nh4
-       cobalt%net_phyto_resp(i,j,k) = cobalt%net_phyto_resp(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
        do n = 2, NUM_PHYTO !{
+          ! Nitrate versus ammonia uptake proportional to their relative limitations
           phyto(n)%juptake_no3(i,j,k) = max( 0.0, phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k)*   &
              phyto(n)%no3lim(i,j,k)/(phyto(n)%no3lim(i,j,k)+phyto(n)%nh4lim(i,j,k)+epsln) )
           phyto(n)%juptake_nh4(i,j,k) = max( 0.0, phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k)*   &
              phyto(n)%nh4lim(i,j,k)/(phyto(n)%no3lim(i,j,k)+phyto(n)%nh4lim(i,j,k)+epsln) )
+          ! If growth is negative, results in net respiration and production of nh4, aerobic loss in all cases
           cobalt%jprod_nh4(i,j,k) = cobalt%jprod_nh4(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
           cobalt%jo2resp_wc(i,j,k) = cobalt%jo2resp_wc(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))*cobalt%o2_2_nh4
-          cobalt%net_phyto_resp(i,j,k) = cobalt%net_phyto_resp(i,j,k) - min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_n(i,j,k))
        enddo !} n
     enddo;  enddo ; enddo !} i,j,k
     !
@@ -2901,11 +2898,13 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
        n=DIAZO
        phyto(n)%juptake_po4(i,j,k) = (phyto(n)%juptake_n2(i,j,k)+phyto(n)%juptake_nh4(i,j,k) + &
           phyto(n)%juptake_no3(i,j,k))*phyto(n)%uptake_p_2_n(i,j,k)
+       ! If growth is negative, results in net release of po4
        cobalt%jprod_po4(i,j,k) = cobalt%jprod_po4(i,j,k) - &
           min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_p(i,j,k))
        do n = 2, NUM_PHYTO
           phyto(n)%juptake_po4(i,j,k) = (phyto(n)%juptake_nh4(i,j,k)+phyto(n)%juptake_no3(i,j,k))* &
             phyto(n)%uptake_p_2_n(i,j,k)
+          ! If growth is negative, results in net release of po4
           cobalt%jprod_po4(i,j,k) = cobalt%jprod_po4(i,j,k) - &
             min(0.0,phyto(n)%mu(i,j,k)*phyto(n)%f_p(i,j,k))
        enddo !} n
@@ -2916,12 +2915,14 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
     do k = 1, nk ; do j = jsc, jec ; do i = isc, iec   !{
        do n = 1, NUM_PHYTO  !{
           if (phyto(n)%q_fe_2_n(i,j,k).lt.phyto(n)%fe_2_n_max) then
+             ! Scaling fe uptake with the maximum iron-limited photosynthesis allows for luxury iron uptake
+             ! when other nutrients are limiting but iron is not
              phyto(n)%juptake_fe(i,j,k) = phyto(n)%P_C_max(i,j,k)*cobalt%expkT(i,j,k)*phyto(n)%f_n(i,j,k)* &
                 phyto(n)%felim(i,j,k)*cobalt%fe_2_n_upt_fac
              phyto(n)%jexuloss_fe(i,j,k) = 0.0
           else
+             ! if you've exceeded the maximum quota, stop uptake and exude extra
              phyto(n)%juptake_fe(i,j,k) = 0.0
-             !phyto(n)%jexuloss_fe(i,j,k) = (phyto(n)%q_fe_2_n(i,j,k)-phyto(n)%fe_2_n_max)*phyto(n)%f_n(i,j,k)/dt
              phyto(n)%jexuloss_fe(i,j,k) = cobalt%expkT(i,j,k)*phyto(n)%bresp(i,j,k)*phyto(n)%f_fe(i,j,k)
           endif
        enddo   !} n
@@ -2946,9 +2947,8 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
        ! Note that this is si_2_n in large phytoplankton pool, not in diatoms themselves (q_si_2_n_lg_diatoms)
        phyto(LARGE)%q_si_2_n(i,j,k) = cobalt%f_silg(i,j,k)/(phyto(LARGE)%f_n(i,j,k)+epsln)
        phyto(MEDIUM)%q_si_2_n(i,j,k) = cobalt%f_simd(i,j,k)/(phyto(MEDIUM)%f_n(i,j,k)+epsln)
-
     enddo; enddo ; enddo !} i,j,k
-!
+
     call mpp_clock_end(id_clock_phyto_growth)
 !
 !-----------------------------------------------------------------------
@@ -5092,7 +5092,6 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
        cobalt%wc_vert_int_o2(i,j) = 0.0
        cobalt%wc_vert_int_alk(i,j) = 0.0
        cobalt%wc_vert_int_chemoautopp(i,j) = 0.0
-       cobalt%wc_vert_int_net_phyto_resp(i,j) = 0.0
        cobalt%wc_vert_int_npp(i,j) = 0.0
        cobalt%wc_vert_int_jdiss_sidet(i,j) = 0.0
        cobalt%wc_vert_int_jdiss_cadet(i,j) = 0.0
@@ -5122,8 +5121,6 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
           cobalt%wc_vert_int_alk(i,j) = cobalt%wc_vert_int_alk(i,j) + cobalt%tot_layer_int_alk(i,j,k)*grid_tmask(i,j,k)
           cobalt%wc_vert_int_chemoautopp(i,j) = cobalt%wc_vert_int_chemoautopp(i,j) +                 &
              (bact(1)%jprod_n_nitrif(i,j,k) + bact(1)%jprod_n_amx(i,j,k)) * rho_dzt(i,j,k) * grid_tmask(i,j,k)
-          cobalt%wc_vert_int_net_phyto_resp(i,j) = cobalt%wc_vert_int_net_phyto_resp(i,j) +                 &
-             cobalt%net_phyto_resp(i,j,k) * rho_dzt(i,j,k) * grid_tmask(i,j,k)
           cobalt%wc_vert_int_npp(i,j) = cobalt%wc_vert_int_npp(i,j) + (phyto(SMALL)%jprod_n(i,j,k) +  &
               phyto(MEDIUM)%jprod_n(i,j,k) + phyto(LARGE)%jprod_n(i,j,k) + phyto(DIAZO)%jprod_n(i,j,k))* &
               rho_dzt(i,j,k)*grid_tmask(i,j,k)
@@ -6511,7 +6508,6 @@ subroutine user_allocate_arrays
     allocate(cobalt%jprod_nh4(isd:ied, jsd:jed, 1:nk))    ; cobalt%jprod_nh4=0.0
     allocate(cobalt%jprod_nh4_plus_btm(isd:ied, jsd:jed, 1:nk))    ; cobalt%jprod_nh4_plus_btm=0.0
     allocate(cobalt%jprod_po4(isd:ied, jsd:jed, 1:nk))    ; cobalt%jprod_po4=0.0
-    allocate(cobalt%net_phyto_resp(isd:ied, jsd:jed, 1:nk)) ; cobalt%net_phyto_resp=0.0
     allocate(cobalt%det_jzloss_n(isd:ied, jsd:jed, 1:nk)) ; cobalt%det_jzloss_n=0.0
     allocate(cobalt%det_jzloss_p(isd:ied, jsd:jed, 1:nk)) ; cobalt%det_jzloss_p=0.0
     allocate(cobalt%det_jzloss_fe(isd:ied, jsd:jed, 1:nk)); cobalt%det_jzloss_fe=0.0
@@ -6640,7 +6636,6 @@ subroutine user_allocate_arrays
     allocate(cobalt%wc_vert_int_o2(isd:ied, jsd:jed))         ; cobalt%wc_vert_int_o2=0.0
     allocate(cobalt%wc_vert_int_alk(isd:ied, jsd:jed))        ; cobalt%wc_vert_int_alk=0.0
     allocate(cobalt%wc_vert_int_chemoautopp(isd:ied, jsd:jed)) ; cobalt%wc_vert_int_chemoautopp=0.0
-    allocate(cobalt%wc_vert_int_net_phyto_resp(isd:ied, jsd:jed))  ; cobalt%wc_vert_int_net_phyto_resp=0.0
     allocate(cobalt%wc_vert_int_npp(isd:ied, jsd:jed))     ; cobalt%wc_vert_int_npp=0.0
     allocate(cobalt%wc_vert_int_jdiss_sidet(isd:ied, jsd:jed))  ; cobalt%wc_vert_int_jdiss_sidet=0.0
     allocate(cobalt%wc_vert_int_jdiss_cadet(isd:ied, jsd:jed))  ; cobalt%wc_vert_int_jdiss_cadet=0.0
@@ -7079,7 +7074,6 @@ subroutine user_deallocate_arrays
     deallocate(cobalt%jprod_nh4)
     deallocate(cobalt%jprod_nh4_plus_btm)
     deallocate(cobalt%jprod_po4)
-    deallocate(cobalt%net_phyto_resp)
     deallocate(cobalt%det_jzloss_n)
     deallocate(cobalt%det_jzloss_p)
     deallocate(cobalt%det_jzloss_fe)
@@ -7275,7 +7269,6 @@ subroutine user_deallocate_arrays
     deallocate(cobalt%wc_vert_int_o2)
     deallocate(cobalt%wc_vert_int_alk)
     deallocate(cobalt%wc_vert_int_chemoautopp)
-    deallocate(cobalt%wc_vert_int_net_phyto_resp)
     deallocate(cobalt%wc_vert_int_npp)
     deallocate(cobalt%wc_vert_int_jdiss_sidet)
     deallocate(cobalt%wc_vert_int_jdiss_cadet)