! source file: /Users/nmengis/Documents/UVic_ESCM/2.10/updates/02_CE_permafrost_merge_CMIP6forcing/source/mom/npzd_src.F subroutine npzd_src (bioin, ntsb, tsb, gl, bct, impo, dzt &, dayfrac, wwd, rkw, nud, bioout, expoout &, grazout, morpout, morzout, graz_Det_out &, graz_Zout &, nppout, morptout, remiout, excrout &, npp_Dout, graz_Dout, morp_Dout, nfixout &, felimit, felimit_D &, bctz & ) !======================================================================= ! computes source terms of the NPZD model ! initial version of code adapted from Xavier Giraud: ! Giraud et al. 2000, J Mar Res, 58, 609-630 ! original model reference: ! Oeschlies and Garcon 1999, Global Biogeochem. Cycles 13, 135-160 ! Schmittner et al. 2005, Global Biogeochem. Cycles 19, GB3004, ! doi:10.1029/2004GB002283. ! Schmittner et al. 2008, Global Biogeochem. Cycles 22, GB1013 ! ! This version was modified by David Keller and corrects the zooplankton ! grazing formulation. Note that zooplankton are now allowed to graze ! on themselves and detritus, in addition to phyt. and diazotrophs. ! The calculation of light has also been corrected. ! ! Note that nutrient now represents phosphate ! input variables: ! bioin(1:4) = N,P,Z,D [mmol m-3] ! bioin(5) = nitrate [mmol m-3] ! bioin(6) = diazotrophs [mmol m-3] ! gl = 2.*light at top of grid box ! ntsb = number of time steps ! tsb = time step [s] ! bct = bbio**(cbio*temperature) ! impo = import of detritus from above [mmol m-3] ! dzt = depth of grid box [cm] ! dayfrac = day length (fraction: 0 < dayfrac < 1) ! wwd = sinking speed of detritus/dzt ! rkw = reciprical of kw*dzt(k) ! nud = remineralisation rate of detritus [s-1] ! output variables: ! bioout = change from bioin [mmol m-3] ! nppout = net primary production [mmol m-3] ! grazout = grazing [mmol m-3] ! morpout = quadratic mortality of phytoplankton [mmol m-3] ! morptout = specific mortality of phytoplankton [mmol m-3] ! morzout = mortality of zooplankton [mmol m-3] ! remiout = remineralisation [mmol m-3] ! excrout = excretion [mmol m-3] ! expoout = detrital export [mmol m-3] ! npp_Dout = NPP of diazotrophs ! graz_Dout = grazing of diazotrophs ! morp_Dout = mortality of diazotrophs ! nfixout = rate of N2 fixation ! graz_Det_out = grazing of detritus ! graz_Zout = grazing on othe zooplankton ! avej_out = light-depend phyt. growth rate ! avej_D_out = light-depend Diaz growth rate ! gmax_out = temp-depend. zoo growth rate ! no3P_out = no3 depend. phyt growth rate ! po4P_out = po4 depend. phyt growth rate ! po4_D_out = po4 depend. Diaz growth rate ! New grazing formulation variables and parameters ! The following terms determine ingestion according to a ! a Holling II curve (i.e. Michaelis Menten): ! ! Ingestion = max_graz_rate * (Ft/(Ft + kzoo)) ! ! where Ft is the weighted measure of the total food available ! and equals the sum of the different prey types times the ! preference of Z for that type of prey ! ! zprefP = Z preference for P ! zprefD = Z preference for Diaz ! zprefDet = Z preference for detritus ! zprefZ = Z preference for other Z ! kzoo = half saturation coefficienct for Z ingestion mmol N m-3 ! ing_P = zooplankton ingestion of phytoplankon ! ing_D = zooplankton ingestion of diazotrophs ! ing_Det = zooplankton ingestion of detritus ! ing_Z = zooplankton ingestion of other zooplankton ! thetaZ = Michaelis-Menten denominator ! ! felimit = Fe limitation parameter ! felmit_D = Fe limitation parameter for diazotrophs ! !======================================================================= implicit none integer n, ntsb real gl, f1, bion, biop, bioz, biod, jmax, u_P, g_P, npp, graz real morp, morpt, morz, remi, excr, expo, impo, nppout, grazout real morpout, morptout, morzout, remiout, excrout, expoout, tsb real avej_out, avej_D_out, gmax_out, no3P_out, po4P_out, po4_D_out real dzt, nflag, pflag, zflag, dflag, wwd, rkw, gd, dayfrac, bct real nupt, nud, biono3, u_D,npp_D, npp_Dout, no3flag, biodiaz real diazflag, g_D,graz_D, morp_D, jmax_D, gd_D, avej_D, no3upt_D real morp_Dout, graz_Dout, nfixout, biop2, u1, u2, phi1, phi2 real avej, graz_Det_out, graz_Zout, thetaZ, ing_P, ing_D real ing_Det, ing_Z, g_Z, g_Det, graz_Z, graz_Det, gmax real no3P, po4P, po4_D, felimit, bctz, felimit_D include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "calendar.h" include "npzd.h" real bioin(ntnpzd), bioout(ntnpzd) ! photosynthesis after Evans & Parslow (1985) ! notation as in JGOFS report No. 23 p. 6 f1 = exp((-kw - kc*(bioin(2)+bioin(6)))*dzt) ! In the following "felimit" is determined by an iron mask and ! is used to limit phytoplankton growth in HNLC regions jmax = abio*bct*felimit gd = jmax*dayfrac u1 = max(gl/gd,1.e-6) u2 = u1*f1 ! for the following approximation ensure that u1 < 20 phi1 = log(u1+sqrt(1.+u1**2.))-(sqrt(1.+u1**2.)-1.)/u1 phi2 = log(u2+sqrt(1.+u2**2.))-(sqrt(1.+u2**2.)-1.)/u2 avej = gd*(phi1 - phi2)/((kw+kc*(bioin(2)+bioin(6)))*dzt) ! Make the max grazing rate a function of temperature gmax = gbio*bctz ! Note bctz, which sets an upper limit on the effects of temp on the ! grazing rate, is set in tracers.F jmax_D = max(0.,abio*(bct - 2.6)*felimit_D)*jdiar gd_D = max(1.e-14,jmax_D*dayfrac) u1 = max(gl/gd_D,1.e-6) u2 = u1*f1 ! for the following approximation ensure that u1 < 20 phi1 = log(u1+sqrt(1.+u1**2.))-(sqrt(1.+u1**2.)-1.)/u1 phi2 = log(u2+sqrt(1.+u2**2.))-(sqrt(1.+u2**2.)-1.)/u2 avej_D = gd_D*(phi1 - phi2)/((kw+kc*(bioin(2)+bioin(6)))*dzt) ! check grazing preferences = 1 for N case IF ((zprefP + zprefDet + zprefZ + zprefD).ne.1) THEN zprefP = 0.30 zprefZ = 0.30 zprefDet = 0.30 zprefD = 0.10 END IF nupt = nupt0*bct bioout(:) = 0.0 bion = bioin(1) biop = bioin(2) bioz = bioin(3) biod = bioin(4) biono3 = bioin(5) biodiaz = bioin(6) expoout = 0.0 grazout = 0.0 morpout = 0.0 morzout = 0.0 graz_Det_out = 0.0 graz_Zout = 0.0 nppout = 0.0 morptout = 0.0 remiout = 0.0 excrout = 0.0 npp_Dout = 0.0 graz_Dout = 0.0 morp_Dout = 0.0 nfixout = 0.0 do n=1,ntsb ! growth rate of phytoplankton u_P = min(avej, jmax*bion/(k1p + bion)) po4P = jmax*bion/(k1p + bion) ! nitrate limitation u_P = min(u_P, jmax*biono3/(k1n + biono3)) no3P = jmax*biono3/(k1n + biono3) ! growth rate of diazotrophs smaller than other phytoplankton and ! not nitrate limited u_D = min(avej_D, jmax_D*bion/(k1p + bion)) po4_D = jmax_D*bion/(k1p + bion) ! Set the grazing coefficients for the N case thetaZ = zprefP*biop+zprefDet*biod+zprefZ*bioz+zprefD*biodiaz & + kzoo ing_P = zprefP/thetaZ ing_Det = zprefDet/thetaZ ing_Z = zprefZ/thetaZ ing_D = zprefD/thetaZ npp = u_P*biop npp_D = max(0.,u_D*biodiaz) ! grazing on diazotrophs g_D = gmax*ing_D*biodiaz graz_D = g_D*bioz morp_D = nupt*biodiaz ! linear mortality no3upt_D = biono3/(k1n + biono3)*npp_D ! nitrate uptake ! grazing on P g_P = gmax*ing_P*biop graz = g_P*bioz ! grazing on Z g_Z = gmax*ing_Z*bioz graz_Z = g_Z*bioz ! grazing on Detritus g_Det = gmax*ing_Det*biod graz_Det = g_Det*bioz ! morp = nup*biop morpt = nupt*biop morz = nuz*bioz*bioz remi = nud*bct*biod expo = wwd*biod ! flags prevent negative values by setting outgoing fluxes to ! zero if tracers are lower than trcmin nflag = 0.5 + sign(0.5,bion - trcmin) pflag = 0.5 + sign(0.5,biop - trcmin) zflag = 0.5 + sign(0.5,bioz - trcmin) dflag = 0.5 + sign(0.5,biod - trcmin) no3flag = 0.5 + sign(0.5,biono3 - trcmin) diazflag = 0.5 + sign(0.5,biodiaz - trcmin) graz = graz*pflag*zflag graz_Z = graz_Z*zflag graz_Det = graz_Det*dflag*zflag morp = morp*pflag morpt = morpt*pflag morz = morz*zflag remi = remi*dflag expo = expo*dflag npp = npp*nflag*no3flag npp_D = npp_D*nflag graz_D = graz_D*diazflag*zflag morp_D = morp_D*diazflag no3upt_D = no3upt_D*no3flag ! Excretion is the difference between ! the zooplankton assimilation and growth efficiencies excr = (gamma1-geZ)*(graz+graz_Z+graz_Det+graz_D) ! nutrients equation bion = bion + tsb*redptn*(remi + excr - (npp + npp_D) + morpt) ! phytoplankton equation biop = biop + tsb*(npp - morp - graz - morpt) ! zooplankton equation bioz = bioz + tsb*(geZ*(graz + graz_D + graz_Det + graz_Z) & - morz - graz_Z) ! detritus equation biod = biod + tsb*((1.-gamma1)*(graz + graz_D + graz_Det & + graz_Z) + morp + morp_D + morz - remi - graz_Det & - expo + impo) ! nitrate (NO3) equation biono3 = biono3 + tsb*(remi + excr - npp + morpt - no3upt_D) ! diazotroph equation biodiaz = biodiaz + tsb*(npp_D - morp_D - graz_D) expoout = expoout + expo grazout = grazout + graz morpout = morpout + morp morzout = morzout + morz graz_Det_out = graz_Det_out + graz_Det graz_Zout = graz_Zout + graz_Z nppout = nppout + npp morptout = morptout + morpt remiout = remiout + remi excrout = excrout + excr npp_Dout = npp_Dout + npp_D graz_Dout = graz_Dout + graz_D morp_Dout = morp_Dout + morp_D nfixout = nfixout + npp_D - no3upt_D enddo bioout(1) = bion - max(bioin(1),trcmin) bioout(2) = biop - max(bioin(2),trcmin) bioout(3) = bioz - max(bioin(3),trcmin) bioout(4) = biod - max(bioin(4),trcmin) bioout(5) = biono3 - max(bioin(5),trcmin) bioout(6) = biodiaz - max(bioin(6),trcmin) return end