#include "BLING_OPTIONS.h" CBOP subroutine BLING_BIO( I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP, O G_DIC, G_ALK, G_O2, G_FE, O G_PO4, G_DOP, I bi, bj, imin, imax, jmin, jmax, I myTime, myIter, myThid) C ================================================================= C | subroutine bling_bio_nitrogen C | o Nutrient uptake and partitioning between organic pools. C | - Phytoplankton biomass-specific growth rate is calculated C | as a function of light, nutrient limitation, and C | temperature. C | - A simple relationship between growth rate, C | biomass, and uptake is derived by assuming that growth is C | exactly balanced by losses. C | o Organic matter export and remineralization. C | - Calculate the nutrient flux to depth from bio activity C | - Iron source from sediments C | - Iron scavenging C ================================================================= IMPLICIT NONE C === Global variables === C phyto_sm :: Small phytoplankton biomass C phyto_lg :: Large phytoplankton biomass C phyto_diaz :: Diazotroph phytoplankton biomass C *** if ADVECT_PHYTO, these are fraction of total biomass instead *** #include "SIZE.h" #include "DYNVARS.h" #include "EEPARAMS.h" #include "PARAMS.h" #include "GRID.h" #include "BLING_VARS.h" #include "PTRACERS_SIZE.h" #include "PTRACERS_PARAMS.h" #ifdef ALLOW_AUTODIFF # include "tamc.h" #endif C === Routine arguments === C bi,bj :: tile indices C iMin,iMax :: computation DOPain: 1rst index range C jMin,jMax :: computation DOPain: 2nd index range C myTime :: current time C myIter :: current timestep C myThid :: thread Id. number INTEGER bi, bj, imin, imax, jmin, jmax _RL myTime INTEGER myIter INTEGER myThid C === Input === C PTR_O2 :: oxygen concentration C PTR_FE :: iron concentration C PTR_PO4 :: phosphate concentration C PTR_DOP :: dissolved organic phosphorus concentration _RL PTR_O2 (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL PTR_FE (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL PTR_PO4(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL PTR_DOP(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) C === Output === C G_xxx :: tendency term for tracer xxx _RL G_DIC (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_ALK (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_O2 (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_FE (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_PO4 (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_DOP (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) #ifdef ALLOW_BLING # ifdef USE_BLING_V1 C === Local variables === C i,j,k :: loop indices C Phy_lg_local :: biomass in large phytoplankton C Phy_sm_local :: biomass in small phytoplankton C PO4_lim :: phosphate limitation C Fe_lim :: iron limitation for phytoplankton C FetoP_up :: iron to phosphorus uptake ratio C light_lim :: light limitation C expkT :: temperature function C Pc_m :: light-saturated max photosynthesis rate for phyto C Pc_tot :: carbon-specific photosynthesis rate C theta_Fe :: Chl:C ratio C theta_Fe_inv :: C:Chl ratio C theta_Fe_max :: Fe-replete maximum Chl:C ratio C alpha_Fe :: initial slope of the P-I curve C irrk :: nut-limited efficiency of algal photosystems C irr_inst :: instantaneous light C irr_eff :: effective irradiance C mld :: mixed layer depth C mu :: net carbon-specific growth rate for phyt C biomass_sm :: nutrient concentration in small phyto biomass C biomass_lg :: nutrient concentration in large phyto biomass C P_uptake :: PO4 utilization by phytoplankton C Fe_uptake :: dissolved Fe utilization by phytoplankton C CaCO3_uptake :: Calcium carbonate uptake for shell formation C CaCO3_diss :: Calcium carbonate dissolution C G_CaCO3 :: tendency of calcium carbonate C DOP_prod :: production of dissolved organic phosphorus C DOP_remin :: remineralization of dissolved organic phosphorus C frac_exp :: fraction of sinking particulate organic matter C P_spm :: particulate sinking of phosphorus C Fe_spm :: particulate sinking of iron C P_recycle :: recycling of newly-produced organic phosphorus C Fe_recycle :: recycling of newly-produced organic iron C P_reminp :: remineralization of particulate organic phosphorus C Fe_reminsum :: iron remineralization and adsorption C POC_flux :: particulate organic carbon flux C NPP :: net primary production C NCP :: net community production C depth_l :: depth of lower interface C *flux_u :: "*" flux through upper interface C *flux_l :: "*" flux through lower interface C *_export :: vertically-integrated export of "*" C zremin :: remineralization lengthscale for nutrients C zremin_caco3 :: remineralization lengthscale for CaCO3 C wsink :: speed of sinking particles C POC_sed :: flux of particulate organic carbon to sediment C Fe_sed :: sediment iron efflux C kFe_eq_lig :: iron ligand stability constant C FreeFe :: free (unbound) iron concentration C Fe_ads_inorg :: iron adsorption C Fe_ads_org :: iron adsorption (2nd order) C INTEGER i,j,k INTEGER bottomlayer _RL Phy_lg_local(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Phy_sm_local(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL PO4_lim(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_lim(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL FetoP_up(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL light_lim(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL expkT(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Pc_m _RL Pc_tot _RL theta_Fe(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL theta_Fe_inv(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL theta_Fe_max _RL alpha_Fe _RL irrk(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL irr_inst(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL irr_eff(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL mld(1-OLx:sNx+OLx,1-OLy:sNy+OLy) _RL mu(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL biomass_sm _RL biomass_lg _RL P_uptake(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_uptake(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL CaCO3_uptake(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL CaCO3_diss(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL G_CaCO3(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL DOP_prod(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL DOP_remin(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL frac_exp _RL P_spm(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_spm(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL P_recycle(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_recycle(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL P_reminp(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_reminp(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_reminsum(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL POC_flux(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL NPP(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL NCP(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL depth_l _RL POPflux_u _RL POPflux_l _RL PFEflux_u _RL PFEflux_l _RL CaCO3flux_u _RL CaCO3flux_l _RL POP_export(1-OLx:sNx+OLx,1-OLy:sNy+OLy) _RL PFE_export(1-OLx:sNx+OLx,1-OLy:sNy+OLy) _RL CaCO3_export(1-OLx:sNx+OLx,1-OLy:sNy+OLy) _RL zremin _RL zremin_caco3 _RL wsink _RL POC_sed _RL Fe_sed(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL kFe_eq_lig _RL FreeFe _RL Fe_ads_inorg(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_ads_org(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL Fe_burial(1-OLx:sNx+OLx,1-OLy:sNy+OLy) _RL po4_adj(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL fe_adj(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL o2_adj(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) _RL dop_adj(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) #ifdef ML_MEAN_PHYTO _RL tmp_p_sm_ML _RL tmp_p_lg_ML _RL tmp_p_diaz_ML _RL tmp_ML #endif CEOP c --------------------------------------------------------------------- c Initialize output and diagnostics DO j=jmin,jmax DO i=imin,imax mld(i,j) = 0. _d 0 POP_export(i,j) = 0. _d 0 PFE_export(i,j) = 0. _d 0 CaCO3_export(i,j) = 0. _d 0 ENDDO ENDDO DO k=1,Nr DO j=jmin,jmax DO i=imin,imax G_DIC(i,j,k) = 0. _d 0 G_ALK(i,j,k) = 0. _d 0 G_O2(i,j,k) = 0. _d 0 G_FE(i,j,k) = 0. _d 0 G_PO4(i,j,k) = 0. _d 0 G_DOP(i,j,k) = 0. _d 0 G_CaCO3(i,j,k) = 0. _d 0 Phy_lg_local(i,j,k) = 0. _d 0 Phy_sm_local(i,j,k) = 0. _d 0 PO4_lim(i,j,k) = 0. _d 0 Fe_lim(i,j,k) = 0. _d 0 FetoP_up(i,j,k) = 0. _d 0 light_lim(i,j,k) = 0. _d 0 expkT(i,j,k) = 0. _d 0 theta_Fe(i,j,k) = 0. _d 0 theta_Fe_inv(i,j,k) = 0. _d 0 irrk(i,j,k) = 0. _d 0 irr_inst(i,j,k) = 0. _d 0 irr_eff(i,j,k) = 0. _d 0 mu(i,j,k) = 0. _d 0 P_uptake(i,j,k) = 0. _d 0 Fe_uptake(i,j,k) = 0. _d 0 CaCO3_uptake(i,j,k) = 0. _d 0 CaCO3_diss(i,j,k) = 0. _d 0 DOP_prod(i,j,k) = 0. _d 0 DOP_remin(i,j,k) = 0. _d 0 P_spm(i,j,k) = 0. _d 0 Fe_spm(i,j,k) = 0. _d 0 P_recycle(i,j,k) = 0. _d 0 Fe_recycle(i,j,k) = 0. _d 0 P_reminp(i,j,k) = 0. _d 0 Fe_reminp(i,j,k) = 0. _d 0 Fe_reminsum(i,j,k) = 0. _d 0 POC_flux(i,j,k) = 0. _d 0 NPP(i,j,k) = 0. _d 0 NCP(i,j,k) = 0. _d 0 Fe_sed(i,j,k) = 0. _d 0 Fe_ads_org(i,j,k) = 0. _d 0 Fe_ads_inorg(i,j,k) = 0. _d 0 ENDDO ENDDO ENDDO c----------------------------------------------------------- c avoid negative nutrient concentrations that can result from c advection when low concentrations #ifdef BLING_NO_NEG CALL BLING_MIN_VAL(PTR_O2, 1. _d -11, o2_adj, bi, bj) CALL BLING_MIN_VAL(PTR_FE, 1. _d -11, fe_adj, bi, bj) CALL BLING_MIN_VAL(PTR_PO4, 1. _d -8, po4_adj, bi, bj) CALL BLING_MIN_VAL(PTR_DOP, 1. _d -11, dop_adj, bi, bj) #endif c----------------------------------------------------------- c Phytoplankton size classes DO k=1,Nr DO j=jmin,jmax DO i=imin,imax Phy_lg_local(i,j,k) = phyto_lg(i,j,k,bi,bj) Phy_sm_local(i,j,k) = phyto_sm(i,j,k,bi,bj) ENDDO ENDDO ENDDO c----------------------------------------------------------- c Mixed layer depth calculation for light, phytoplankton and dvm. c Do not need to calculate if not using ML_MEAN_LIGHT, ML_MEAN_PHYTO, c and USE_BLING_DVM c (with BLING_ADJOINT_SAFE flag, USE_BLING_DVM is undefined) #if ( defined (ML_MEAN_LIGHT) || \ defined (ML_MEAN_PHYTO) || \ defined (USE_BLING_DVM) ) CALL BLING_MIXEDLAYER( U mld, I bi, bj, imin, imax, jmin, jmax, I myTime, myIter, myThid) #endif c Phytoplankton mixing c The mixed layer is assumed to homogenize vertical gradients of phytoplankton. c This allows for basic Sverdrup dynamics in a qualitative sense. c This has not been thoroughly tested, and care should be c taken with its interpretation. #ifdef ML_MEAN_PHYTO DO j=jmin,jmax DO i=imin,imax tmp_p_sm_ML = 0. _d 0 tmp_p_lg_ML = 0. _d 0 tmp_ML = 0. _d 0 DO k=1,Nr IF (hFacC(i,j,k,bi,bj).gt.0. _d 0) THEN IF ((-rf(k+1) .le. mld(i,j)).and. & (-rf(k+1).lt.MLmix_max)) THEN tmp_p_sm_ML = tmp_p_sm_ML+Phy_sm_local(i,j,k)*drF(k) & *hFacC(i,j,k,bi,bj) tmp_p_lg_ML = tmp_p_lg_ML+Phy_lg_local(i,j,k)*drF(k) & *hFacC(i,j,k,bi,bj) tmp_ML = tmp_ML + drF(k) ENDIF ENDIF ENDDO DO k=1,Nr IF (hFacC(i,j,k,bi,bj).gt.0. _d 0) THEN IF ((-rf(k+1) .le. mld(i,j)).and. & (-rf(k+1).lt.MLmix_max)) THEN Phy_lg_local(i,j,k) = max(1. _d -8,tmp_p_lg_ML/tmp_ML) Phy_sm_local(i,j,k) = max(1. _d -8,tmp_p_sm_ML/tmp_ML) ENDIF ENDIF ENDDO ENDDO ENDDO #endif c----------------------------------------------------------- c light availability for biological production CALL BLING_LIGHT( I mld, U irr_inst, irr_eff, I bi, bj, imin, imax, jmin, jmax, I myTime, myIter, myThid ) c phytoplankton photoadaptation to local light level c This represents the fact that phytoplankton cells are adapted c to the averaged light field to which they've been exposed over c their lifetimes, rather than the instantaneous light. The c timescale is set by gamma_irr_mem. DO k=1,Nr DO j=jmin,jmax DO i=imin,imax irr_mem(i,j,k,bi,bj) = irr_mem(i,j,k,bi,bj) + & (irr_eff(i,j,k) - irr_mem(i,j,k,bi,bj))* & min( 1. _d 0, gamma_irr_mem*PTRACERS_dTLev(k) ) ENDDO ENDDO ENDDO c --------------------------------------------------------------------- c Nutrient uptake and partitioning between organic pools c Phytoplankton are assumed to grow according to the general properties c described in Geider (1997). This formulation gives a biomass-specific c growthrate as a function of light, nutrient limitation, and c temperature. We modify this relationship slightly here, as described c below, and also use the assumption of steady state growth vs. loss to c derive a simple relationship between growth rate, biomass and uptake. DO k=1,Nr DO j=jmin,jmax DO i=imin,imax IF (hFacC(i,j,k,bi,bj) .gt. 0. _d 0) THEN c --------------------------------------------------------------------- c First, calculate the limitation terms for PO4 and Fe, and the c Fe-limited Chl:C maximum. The light-saturated maximal photosynthesis c rate term (Pc_m) is simply the product of a prescribed maximal c photosynthesis rate (Pc_0), the Eppley temperature dependence, and a c resource limitation term. The iron limitation term has a lower limit c of Fe_lim_min and is scaled by (k_Fe2P + Fe2P_max) / Fe2P_max so that c it approaches 1 as Fe approaches infinity. Thus, it is of comparable c magnitude to the macro-nutrient limitation term. c Macro-nutrient limitation PO4_lim(i,j,k) = PTR_PO4(i,j,k)/(PTR_PO4(i,j,k)+k_PO4) c Iron to macro-nutrient uptake. More iron is utilized relative c to macro-nutrient under iron-replete conditions. FetoP_up(i,j,k) = FetoP_max*PTR_FE(i,j,k)/(k_Fe+PTR_FE(i,j,k)) c Iron limitation Fe_lim(i,j,k) = Fe_lim_min + (1-Fe_lim_min)* & (FetoP_up(i,j,k)/(k_FetoP + FetoP_up(i,j,k)))* & (k_FetoP+FetoP_max)/FetoP_max c --------------------------------------------------------------------- c Light-saturated maximal photosynthesis rate c NB: The temperature effect of Eppley (1972) is used instead of that in c Geider et al (1997) for both simplicity and to incorporate combined c effects on uptake, incorporation into organic matter and photorespiration. c Values of PCc_m are normalized to 0C rather than 20C in Geider et al. (1997) expkT(i,j,k) = exp(kappa_eppley * theta(i,j,k,bi,bj)) c For the effective resource limitation, there is an option to replace c the default Liebig limitation (the minimum of Michaelis-Menton c PO4-limitation, or iron-limitation) by the product (safer for adjoint) #ifdef MULT_NUT_LIM Pc_m = Pc_0*expkT(i,j,k) & *PO4_lim(i,j,k)*Fe_lim(i,j,k)*maskC(i,j,k,bi,bj) #else Pc_m = Pc_0*expkT(i,j,k) & *min(PO4_lim(i,j,k), Fe_lim(i,j,k))*maskC(i,j,k,bi,bj) #endif c --------------------------------------------------------------------- c Fe limitation 1) reduces photosynthetic efficiency (alpha_Fe) c and 2) reduces the maximum achievable Chl:C ratio (theta_Fe) c below a prescribed, Fe-replete maximum value (theta_Fe_max), c to approach a prescribed minimum Chl:C (theta_Fe_min) under extreme c Fe-limitation. alpha_Fe = alpha_min + (alpha_max-alpha_min)*Fe_lim(i,j,k) theta_Fe_max = theta_Fe_max_lo+ & (theta_Fe_max_hi-theta_Fe_max_lo)*Fe_lim(i,j,k) theta_Fe(i,j,k) = theta_Fe_max/(1. _d 0 + alpha_Fe & *theta_Fe_max*irr_mem(i,j,k,bi,bj)/ & (2. _d 0*Pc_m)) c for diagnostics: C:Chl ratio in g C / g Chl IF ( theta_Fe(i,j,k) .EQ.0. ) THEN theta_Fe_inv(i,j,k) = 0. ELSE theta_Fe_inv(i,j,k) = 1./theta_Fe(i,j,k) ENDIF c --------------------------------------------------------------------- c Nutrient-limited efficiency of algal photosystems, irrk, is calculated c with the iron limitation term included as a multiplier of the c theta_Fe_max to represent the importance of Fe in forming chlorophyll c accessory antennae, which do not affect the Chl:C but still affect the c phytoplankton ability to use light (eg Stzrepek & Harrison, Nature 2004). irrk(i,j,k) = Pc_m/(epsln + alpha_Fe*theta_Fe_max) + & irr_mem(i,j,k,bi,bj)/2. _d 0 light_lim(i,j,k) = ( 1. _d 0 - exp(-irr_eff(i,j,k) & /(epsln + irrk(i,j,k)))) c Carbon-specific photosynthesis rate Pc_tot = Pc_m * light_lim(i,j,k) c --------------------------------------------------------------------- c Account for the maintenance effort that phytoplankton must exert in c order to combat decay. This is prescribed as a fraction of the c light-saturated photosynthesis rate, resp_frac. The result of this c is to set a level of energy availability below which net growth c (and therefore nutrient uptake) is zero, given by resp_frac * Pc_m. mu(i,j,k) = max(0. _d 0, Pc_tot - resp_frac*Pc_m) c --------------------------------------------------------------------- c In order to convert this net carbon-specific growth rate to nutrient c uptake rates, the quantities we are interested in, a biomass is required. c This is determined by the balance between growth and grazing. c Since there is no explicit biomass tracer, use the result of Dunne c et al. (GBC, 2005) to calculate an implicit biomass from the uptake c rate through the application of a simple idealized grazing law. c instantaneous nutrient concentration in phyto biomass biomass_lg = pivotal*(mu(i,j,k)/(lambda_0 & *expkT(i,j,k)))**3 biomass_sm = pivotal*(mu(i,j,k)/(lambda_0 & *expkT(i,j,k))) c phytoplankton biomass diagnostic c for no lag: set gamma_biomass to 0 phy_sm_local(i,j,k) = phy_sm_local(i,j,k) + & (biomass_sm - phy_sm_local(i,j,k)) & *min(1., gamma_biomass*PTRACERS_dTLev(k)) phy_lg_local(i,j,k) = phy_lg_local(i,j,k) + & (biomass_lg - phy_lg_local(i,j,k)) & *min(1., gamma_biomass*PTRACERS_dTLev(k)) c use the diagnostic biomass to calculate the chl concentration c in mg/m3 (carbon = 12.01 g/mol) chl(i,j,k,bi,bj) = max(chl_min, CtoP * 12.01 * 1. _d 3 * & theta_Fe(i,j,k) * & (Phy_lg_local(i,j,k) + Phy_sm_local(i,j,k))) c Nutrient uptake P_uptake(i,j,k) = mu(i,j,k)*(phy_sm_local(i,j,k) & + phy_lg_local(i,j,k)) c Iron is then taken up as a function of nutrient uptake and iron c limitation, with a maximum Fe:P uptake ratio of Fe2p_max Fe_uptake(i,j,k) = P_uptake(i,j,k)*FetoP_up(i,j,k) ENDIF ENDDO ENDDO ENDDO c Separate loop for adjoint stores CADJ STORE Phy_sm_local = comlev1, key = ikey_dynamics, kind=isbyte CADJ STORE Phy_lg_local = comlev1, key = ikey_dynamics, kind=isbyte DO k=1,Nr DO j=jmin,jmax DO i=imin,imax IF (hFacC(i,j,k,bi,bj) .gt. 0. _d 0) THEN c update biomass phyto_lg(i,j,k,bi,bj) = Phy_lg_local(i,j,k) phyto_sm(i,j,k,bi,bj) = Phy_sm_local(i,j,k) ENDIF ENDDO ENDDO ENDDO c --------------------------------------------------------------------- c Partitioning between organic pools c The uptake of nutrients is assumed to contribute to the growth of c phytoplankton, which subsequently die and are consumed by heterotrophs. c This can involve the transfer of nutrient elements between many c organic pools, both particulate and dissolved, with complex histories. c We take a simple approach here, partitioning the total uptake into two c fractions - sinking and non-sinking - as a function of temperature, c following Dunne et al. (2005). c Then, the non-sinking fraction is further subdivided, such that the c majority is recycled instantaneously to the inorganic nutrient pool, c representing the fast turnover of labile dissolved organic matter via c the microbial loop, and the remainder is converted to semi-labile c dissolved organic matter. Iron and macro-nutrient are treated c identically for the first step, but all iron is recycled c instantaneously in the second step (i.e. there is no dissolved organic c iron pool). DO k=1,Nr DO j=jmin,jmax DO i=imin,imax IF (hFacC(i,j,k,bi,bj) .gt. 0. _d 0) THEN c sinking particulate organic matter frac_exp = (phi_sm + phi_lg * & (mu(i,j,k)/(lambda_0*expkT(i,j,k)))**2.)/ & (1. + (mu(i,j,k)/(lambda_0*expkT(i,j,k)))**2.)* & exp(kappa_remin * theta(i,j,k,bi,bj)) P_spm(i,j,k) = frac_exp * P_uptake(i,j,k) Fe_spm(i,j,k) = P_spm(i,j,k)*FetoP_up(i,j,k) c the remainder is divided between instantaneously recycled and c long-lived dissolved organic matter. c (recycling = P_uptake - P_spm - DOP_prod) DOP_prod(i,j,k) = phi_DOM*(P_uptake(i,j,k) & - P_spm(i,j,k)) P_recycle(i,j,k) = P_uptake(i,j,k) - P_spm(i,j,k) & - DOP_prod(i,j,k) Fe_recycle(i,j,k) = Fe_uptake(i,j,k) - Fe_spm(i,j,k) c Carbon flux diagnostic POC_flux(i,j,k) = CtoP*P_spm(i,j,k) c --------------------------------------------------------------------- c Calcium carbonate production c Alkalinity is consumed through the production of CaCO3. Here, this is c simply a linear function of the implied growth rate of small c phytoplankton, which gave a reasonably good fit to the global c observational synthesis of Dunne (2009). This is consistent c with the findings of Jin et al. (GBC,2006). CaCO3_uptake(i,j,k) = phy_sm_local(i,j,k)*phi_sm & *expkT(i,j,k)*mu(i,j,k)*CatoP ENDIF ENDDO ENDDO ENDDO c --------------------------------------------------------------------- c Nutrients export/remineralization, CaCO3 export/dissolution c c The flux at the bottom of a grid cell equals C Fb = (Ft + prod*dz) / (1 + zremin*dz) C where Ft is the flux at the top, and prod*dz is the integrated C production of new sinking particles within the layer. C Ft = 0 in the first layer. C$TAF LOOP = parallel DO j=jmin,jmax C$TAF LOOP = parallel DO i=imin,imax C Initialize upper flux POPflux_u = 0. _d 0 PFEflux_u = 0. _d 0 CaCO3flux_u = 0. _d 0 DO k=1,Nr C Initialization here helps taf Fe_ads_org(i,j,k) = 0. _d 0 c check if we are at a bottom cell bottomlayer = 1 IF (k.LT.Nr) THEN IF (hFacC(i,j,k+1,bi,bj).GT.0) THEN c not a bottom cell bottomlayer = 0 ENDIF ENDIF IF ( hFacC(i,j,k,bi,bj).gt.0. _d 0 ) THEN C Sinking speed is evaluated at the bottom of the cell depth_l=-rF(k+1) IF (depth_l .LE. wsink0z) THEN wsink = wsink0_2d(i,j,bi,bj) ELSE wsink = wsinkacc * (depth_l - wsink0z) + wsink0_2d(i,j,bi,bj) ENDIF C Nutrient remineralization lengthscale C Not an e-folding scale: this term increases with remineralization. zremin = gamma_POM_2d(i,j,bi,bj) * ( PTR_O2(i,j,k)**2 / & (k_O2**2 + PTR_O2(i,j,k)**2) * (1-remin_min) & + remin_min )/(wsink + epsln) C Calcium remineralization relaxed toward the inverse of the C ca_remin_depth constant value as the calcite saturation approaches 0. zremin_caco3 = 1. _d 0/ca_remin_depth*(1. _d 0 - min(1. _d 0, & omegaC(i,j,k,bi,bj) + epsln )) C POM flux leaving the cell POPflux_l = (POPflux_u+P_spm(i,j,k)*drF(k) & *hFacC(i,j,k,bi,bj))/(1+zremin*drF(k) & *hFacC(i,j,k,bi,bj)) C CaCO3 flux leaving the cell CaCO3flux_l = (caco3flux_u+CaCO3_uptake(i,j,k)*drF(k) & *hFacC(i,j,k,bi,bj))/(1+zremin_caco3*drF(k) & *hFacC(i,j,k,bi,bj)) C Begin iron uptake calculations by determining ligand bound and free iron. C Both forms are available for biology, but only free iron is scavenged C onto particles and forms colloids. kFe_eq_lig = kFe_eq_lig_max-(kFe_eq_lig_max-kFe_eq_lig_min) & *(irr_inst(i,j,k)**2 & /(kFe_eq_lig_irr**2+irr_inst(i,j,k)**2)) & *max(epsln,min(1. _d 0,(PTR_FE(i,j,k) & -kFe_eq_lig_Femin)/ & (PTR_FE(i,j,k)+epsln)*1.2 _d 0)) C Use the quadratic equation to solve for binding between iron and ligands FreeFe = (-(1+kFe_eq_lig*(ligand-PTR_FE(i,j,k))) & +((1+kFe_eq_lig*(ligand-PTR_FE(i,j,k)))**2+4* & kFe_eq_lig*PTR_FE(i,j,k))**(0.5))/(2* & kFe_eq_lig) C Iron scavenging does not occur in anoxic water (Fe2+ is soluble), so set C FreeFe = 0 when anoxic. FreeFe should be interpreted the free iron that C participates in scavenging. IF (PTR_O2(i,j,k) .LT. oxic_min) THEN FreeFe = 0. _d 0 ENDIF C Two mechanisms for iron uptake, in addition to biological production: C colloidal scavenging and scavenging by organic matter. Fe_ads_inorg(i,j,k) = & kFe_inorg*(max(1. _d -8,FreeFe))**(1.5) C Scavenging of iron by organic matter: C The POM value used is the bottom boundary flux. This does not occur in C oxic waters, but FreeFe is set to 0 in such waters earlier. IF ( POPflux_l .GT. 0. _d 0 ) THEN Fe_ads_org(i,j,k) = & kFE_org*(POPflux_l/(epsln + wsink) & * MasstoN*NtoP)**(0.58)*FreeFe ENDIF C If water is oxic then the iron is remineralized normally. Otherwise C it is completely remineralized (fe 2+ is soluble, but unstable C in oxidizing environments). IF ( PTR_O2(i,j,k) .LT. oxic_min ) THEN PFEflux_l = 0. _d 0 ELSE PFEflux_l = (PFEflux_u+(Fe_spm(i,j,k)+Fe_ads_inorg(i,j,k) & +Fe_ads_org(i,j,k))*drF(k) & *hFacC(i,j,k,bi,bj))/(1+zremin*drF(k) & *hFacC(i,j,k,bi,bj)) ENDIF C Nutrient accumulation in a cell is given by the biological production C (and instant remineralization) of particulate organic matter C plus flux thought upper interface minus flux through lower interface. C If this layer is adjacent to bottom topography or it is the deepest C cell of the domain, then remineralize/dissolve in this grid cell C i.e. do not subtract off lower boundary fluxes when calculating remin C For the deepest cells: IF (bottomlayer.EQ.1) THEN POPflux_l = 0. _d 0 CACO3flux_l = 0. _d 0 C Efflux Fed out of sediments C The phosphate flux hitting the bottom boundary C is used to scale the return of iron to the water column. C Maximum value added for numerical stability. POC_sed = POPflux_l * CtoP Fe_sed(i,j,k) = max(epsln, FetoC_sed * POC_sed * recip_drF(k) & * recip_hFacC(i,j,k,bi,bj)) ELSE Fe_sed(i,j,k) = 0. _d 0 ENDIF P_reminp(i,j,k) = (POPflux_u + P_spm(i,j,k) * drF(k) & * hFacC(i,j,k,bi,bj) - POPflux_l) & * recip_drF(k) * recip_hFacC(i,j,k,bi,bj) CaCO3_diss(i,j,k) = (CaCO3flux_u + CaCO3_uptake(i,j,k) & * drF(k) * hFacC(i,j,k,bi,bj) - CaCO3flux_l) & * recip_drF(k) * recip_hFacC(i,j,k,bi,bj) Fe_sed(i,j,k) = 0. _d 0 Fe_reminp(i,j,k) = (PFEflux_u + (Fe_spm(i,j,k) & + Fe_ads_inorg(i,j,k) + Fe_ads_org(i,j,k)) & * drF(k) * hFacC(i,j,k,bi,bj) - PFEflux_l) & * recip_drF(k) * recip_hFacC(i,j,k,bi,bj) Fe_reminsum(i,j,k) = Fe_reminp(i,j,k) + Fe_sed(i,j,k) & - Fe_ads_org(i,j,k) - Fe_ads_inorg(i,j,k) C Added the burial flux of sinking particulate iron here as a C diagnostic, needed to calculate mass balance of iron. C this is calculated last for the deepest cell Fe_burial(i,j) = PFEflux_l C Prepare the tracers for the next layer down POPflux_u = POPflux_l PFEflux_u = PFEflux_l CaCO3flux_u = CaCO3flux_l ENDIF ENDDO ENDDO ENDDO C----------------------------------------------------------- C add all tendencies DO k=1,Nr DO j=jmin,jmax DO i=imin,imax C Dissolved organic matter slow remineralization #ifdef BLING_NO_NEG DOP_remin(i,j,k) = MAX(maskC(i,j,k,bi,bj)*gamma_DOP & *PTR_DOP(i,j,k),0. _d 0) #else DOP_remin(i,j,k) = maskC(i,j,k,bi,bj)*gamma_DOP & *PTR_DOP(i,j,k) #endif c Tendencies G_PO4(i,j,k) = -P_uptake(i,j,k) + P_recycle(i,j,k) & + DOP_remin(i,j,k) & + (1-phi_DOM) * P_reminp(i,j,k) G_DOP(i,j,k) = DOP_prod(i,j,k) - DOP_remin(i,j,k) & + phi_DOM * P_reminp(i,j,k) if ( PTR_O2(i,j,k) .GT. oxic_min ) then G_O2(i,j,k) = -O2toP*G_PO4(i,j,k) else G_O2(i,j,k) = 0. _d 0 endif G_FE(i,j,k) = - Fe_uptake(i,j,k) + Fe_reminsum(i,j,k) & + Fe_recycle(i,j,k) C Carbon system diagnostics C Change in DIC from primary production, from recycling and C remineralization, change in carbonate ions concentration C from biological activity: G_CaCO3(i,j,k) = CaCO3_diss(i,j,k) - CaCO3_uptake(i,j,k) NPP(i,j,k) = P_uptake(i,j,k) * CtoP NCP(i,j,k) = -G_PO4(i,j,k)*CtoP G_ALK(i,j,k) = 2. _d 0*G_CaCO3(i,j,k) - NtoP*G_PO4(i,j,k) G_DIC(i,j,k) = -NCP(i,j,k) + G_CaCO3(i,j,k) c Carbon flux diagnostic POC_flux(i,j,k) = CtoP * P_spm(i,j,k) c for diagnostics: convert to mol C/m3 Phy_lg_local(i,j,k) = Phy_lg_local(i,j,k) * CtoP Phy_sm_local(i,j,k) = Phy_sm_local(i,j,k) * CtoP c for constraints determine POC, assuming that phytoplankton carbon c is 30% of POC poc(i,j,k,bi,bj) = (Phy_lg_local(i,j,k) + & Phy_sm_local(i,j,k)) * 3.33333 _d 0 ENDDO ENDDO ENDDO c --------------------------------------------------------------------- #ifdef ALLOW_DIAGNOSTICS IF ( useDiagnostics ) THEN c 3d global variables CALL DIAGNOSTICS_FILL(chl, 'BLGCHL ',0,Nr,1,bi,bj,myThid) CALL DIAGNOSTICS_FILL(poc, 'BLGPOC ',0,Nr,1,bi,bj,myThid) CALL DIAGNOSTICS_FILL(irr_mem,'BLGIMEM ',0,Nr,1,bi,bj,myThid) c 3d local variables CALL DIAGNOSTICS_FILL(G_DIC ,'BLGBIOC ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(G_ALK ,'BLGBIOAL',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(G_O2 ,'BLGBIOO2',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(G_Fe ,'BLGBIOFE',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(G_PO4 ,'BLGBIOP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(Phy_sm_local,'BLGPSM ',0,Nr,2,bi,bj, & myThid) CALL DIAGNOSTICS_FILL(Phy_lg_local,'BLGPLG ',0,Nr,2,bi,bj, & myThid) CALL DIAGNOSTICS_FILL(irrk, 'BLGIRRK ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(irr_eff, 'BLGIEFF ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(theta_Fe,'BLGCHL2C',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(theta_Fe_inv,'BLGC2CHL',0,Nr,2,bi,bj, & myThid) CALL DIAGNOSTICS_FILL(Fe_lim, 'BLGFELIM',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(PO4_lim, 'BLGPLIM ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(light_lim,'BLGLLIM ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(POC_flux,'BLGPOCF ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(NPP, 'BLGNPP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(NCP, 'BLGNCP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(Fe_spm, 'BLGFESPM',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(Fe_recycle,'BLGFEREC',0,Nr,2,bi,bj, & myThid) CALL DIAGNOSTICS_FILL(Fe_uptake,'BLGFEUP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(DOP_prod, 'BLGDOPP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(DOP_remin,'BLGDOPR ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(P_spm, 'BLGPSPM ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(P_recycle,'BLGPREC ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(P_reminp, 'BLGPREM ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(P_uptake, 'BLGPUP ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(mu, 'BLGMU ',0,Nr,2,bi,bj,myThid) CALL DIAGNOSTICS_FILL(CaCO3_diss,'BLGCCdis',0,Nr,2,bi,bj, & myThid) CALL DIAGNOSTICS_FILL(CaCO3_uptake,'BLGCCpro',0,Nr,2,bi,bj, & myThid) c 2d local variables CALL DIAGNOSTICS_FILL(mld, 'BLGMLD ',0,1,1,bi,bj,myThid) ENDIF #endif /* ALLOW_DIAGNOSTICS */ #endif /* USE_BLING_V1 */ #endif /* ALLOW_BLING */ RETURN END