MODULE p4zmicro !!====================================================================== !! *** MODULE p4zmicro *** !! TOP : PISCES Compute the sources/sinks for microzooplankton !!====================================================================== !! History : 1.0 ! 2004 (O. Aumont) Original code !! 2.0 ! 2007-12 (C. Ethe, G. Madec) F90 !! 3.4 ! 2011-06 (O. Aumont, C. Ethe) Quota model for iron !!---------------------------------------------------------------------- !! p4z_micro : Compute the sources/sinks for microzooplankton !! p4z_micro_init : Initialize and read the appropriate namelist !!---------------------------------------------------------------------- USE oce_trc ! shared variables between ocean and passive tracers USE trc ! passive tracers common variables USE sms_pisces ! PISCES Source Minus Sink variables USE p4zlim ! Co-limitations USE p4zprod ! production USE iom ! I/O manager USE prtctl ! print control for debugging IMPLICIT NONE PRIVATE !! * Shared module variables PUBLIC p4z_micro ! called in p4zbio.F90 PUBLIC p4z_micro_init ! called in trcsms_pisces.F90 REAL(wp), PUBLIC :: part !: part of calcite not dissolved in microzoo guts REAL(wp), PUBLIC :: xprefc !: microzoo preference for POC REAL(wp), PUBLIC :: xprefn !: microzoo preference for nanophyto REAL(wp), PUBLIC :: xprefd !: microzoo preference for diatoms REAL(wp), PUBLIC :: xthreshdia !: diatoms feeding threshold for microzooplankton REAL(wp), PUBLIC :: xthreshphy !: nanophyto threshold for microzooplankton REAL(wp), PUBLIC :: xthreshpoc !: poc threshold for microzooplankton REAL(wp), PUBLIC :: xthresh !: feeding threshold for microzooplankton REAL(wp), PUBLIC :: resrat !: exsudation rate of microzooplankton REAL(wp), PUBLIC :: mzrat !: microzooplankton mortality rate REAL(wp), PUBLIC :: grazrat !: maximal microzoo grazing rate REAL(wp), PUBLIC :: xkgraz !: Half-saturation constant of assimilation REAL(wp), PUBLIC :: unass !: Non-assimilated part of food REAL(wp), PUBLIC :: sigma1 !: Fraction of microzoo excretion as DOM REAL(wp), PUBLIC :: epsher !: growth efficiency for grazing 1 REAL(wp), PUBLIC :: epshermin !: minimum growth efficiency for grazing 1 REAL(wp), PUBLIC :: xsigma !: Width of the grazing window REAL(wp), PUBLIC :: xsigmadel !: Maximum additional width of the grazing window at low food density !! * Substitutions # include "do_loop_substitute.h90" !!---------------------------------------------------------------------- !! NEMO/TOP 4.0 , NEMO Consortium (2018) !! $Id$ !! Software governed by the CeCILL license (see ./LICENSE) !!---------------------------------------------------------------------- CONTAINS SUBROUTINE p4z_micro( kt, knt, Kbb, Krhs ) !!--------------------------------------------------------------------- !! *** ROUTINE p4z_micro *** !! !! ** Purpose : Compute the sources/sinks for microzooplankton !! This includes ingestion and assimilation, flux feeding !! and mortality. We use a passive prey switching !! parameterization. !! All living compartments smaller than microzooplankton !! are potential preys of microzooplankton !! !! ** Method : - ??? !!--------------------------------------------------------------------- INTEGER, INTENT(in) :: kt ! ocean time step INTEGER, INTENT(in) :: knt ! ??? INTEGER, INTENT(in) :: Kbb, Krhs ! time level indices ! INTEGER :: ji, jj, jk REAL(wp) :: zcompadi, zcompaz , zcompaph, zcompapoc REAL(wp) :: zgraze , zdenom, zdenom2, zfact, zfood, zfoodlim, zbeta REAL(wp) :: zepsherf, zepshert, zepsherq, zepsherv, zgrarsig, zgraztotc, zgraztotn, zgraztotf REAL(wp) :: zgrarem, zgrafer, zgrapoc, zprcaca, zmortz REAL(wp) :: zrespz, ztortz, zgrasratf, zgrasratn REAL(wp) :: zgraznc, zgrazpoc, zgrazdc, zgrazpof, zgrazdf, zgraznf REAL(wp) :: zsigma, zdiffdn, ztmp1, ztmp2, ztmp3, ztmptot, zproport REAL(wp), DIMENSION(jpi,jpj,jpk) :: zgrazing, zfezoo REAL(wp), DIMENSION(:,:,:), ALLOCATABLE :: zzligprod CHARACTER (len=25) :: charout !!--------------------------------------------------------------------- ! IF( ln_timing ) CALL timing_start('p4z_micro') ! IF (ln_ligand) THEN ALLOCATE( zzligprod(jpi,jpj,jpk) ) zzligprod(:,:,:) = 0._wp ENDIF ! DO_3D( nn_hls, nn_hls, nn_hls, nn_hls, 1, jpkm1) zcompaz = MAX( ( tr(ji,jj,jk,jpzoo,Kbb) - 1.e-9 ), 0.e0 ) zfact = xstep * tgfunc2(ji,jj,jk) * zcompaz ! Proportion of diatoms that are within the size range ! accessible to microzooplankton. zproport = min(1.0, exp(-1.1 * MAX(0., ( sized(ji,jj,jk) - 1.8 ))**0.8 )) ! linear mortality of mesozooplankton ! A michaelis menten modulation term is used to avoid extinction of ! microzooplankton at very low food concentrations. Mortality is ! enhanced in low O2 waters ! ----------------------------------------------------------------- zrespz = resrat * zfact * tr(ji,jj,jk,jpzoo,Kbb) / ( xkmort + tr(ji,jj,jk,jpzoo,Kbb) ) & & + resrat * zfact * 3. * nitrfac(ji,jj,jk) ! Zooplankton quadratic mortality. A square function has been selected with ! to mimic predation and disease (density dependent mortality). It also tends ! to stabilise the model ! ------------------------------------------------------------------------- ztortz = mzrat * 1.e6 * zfact * tr(ji,jj,jk,jpzoo,Kbb) * (1. - nitrfac(ji,jj,jk)) ! Computation of the abundance of the preys ! A threshold can be specified in the namelist ! Diatoms have a specific treatment. WHen concentrations ! exceed a certain value, diatoms are suppposed to be too ! big for microzooplankton. ! -------------------------------------------------------- zcompadi = zproport * MAX( ( tr(ji,jj,jk,jpdia,Kbb) - xthreshdia ), 0.e0 ) zcompaph = MAX( ( tr(ji,jj,jk,jpphy,Kbb) - xthreshphy ), 0.e0 ) zcompapoc = MAX( ( tr(ji,jj,jk,jppoc,Kbb) - xthreshpoc ), 0.e0 ) ! Microzooplankton grazing ! The total amount of food is the sum of all preys accessible to mesozooplankton ! multiplied by their food preference ! A threshold can be specified in the namelist (xthresh). However, when food ! concentration is close to this threshold, it is decreased to avoid the ! accumulation of food in the mesozoopelagic domain ! ------------------------------------------------------------------------------- zfood = xprefn * zcompaph + xprefc * zcompapoc + xprefd * zcompadi zfoodlim = MAX( 0. , zfood - min(xthresh,0.5*zfood) ) zdenom = zfoodlim / ( xkgraz + zfoodlim ) zdenom2 = zdenom / ( zfood + rtrn ) zgraze = grazrat * xstep * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jpzoo,Kbb) * (1. - nitrfac(ji,jj,jk)) ! An active switching parameterization is used here. ! We don't use the KTW parameterization proposed by ! Vallina et al. because it tends to produce too steady biomass ! composition and the variance of Chl is too low as it grazes ! too strongly on winning organisms. We use a generalized ! switching parameterization proposed by Morozov and ! Petrovskii (2013) ! ------------------------------------------------------------ ! The width of the selection window is increased when preys ! have low abundance, .i.e. zooplankton become less specific ! to avoid starvation. ! ---------------------------------------------------------- zsigma = 1.0 - zdenom**2/(0.05**2+zdenom**2) zsigma = xsigma + xsigmadel * zsigma zdiffdn = exp( -ABS(log(1.67 * sizen(ji,jj,jk) / (5.0 * sized(ji,jj,jk) + rtrn )) )**2 / zsigma**2) ztmp1 = xprefn * zcompaph * ( zcompaph + zdiffdn * zcompadi ) / ( 1.0 + zdiffdn ) ztmp2 = xprefd * zcompadi * ( zdiffdn * zcompaph + zcompadi ) / ( 1.0 + zdiffdn ) ztmp3 = xprefc * zcompapoc**2 ztmptot = ztmp1 + ztmp2 + ztmp3 + rtrn ztmp1 = ztmp1 / ztmptot ztmp2 = ztmp2 / ztmptot ztmp3 = ztmp3 / ztmptot ! Ingestion terms on the different preys of microzooplankton zgraznc = zgraze * ztmp1 * zdenom ! Nanophytoplankton zgrazdc = zgraze * ztmp2 * zdenom ! Diatoms zgrazpoc = zgraze * ztmp3 * zdenom ! POC ! Ingestion terms on the iron content of the different preys zgraznf = zgraznc * tr(ji,jj,jk,jpnfe,Kbb) / (tr(ji,jj,jk,jpphy,Kbb) + rtrn) zgrazpof = zgrazpoc * tr(ji,jj,jk,jpsfe,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) zgrazdf = zgrazdc * tr(ji,jj,jk,jpdfe,Kbb) / (tr(ji,jj,jk,jpdia,Kbb) + rtrn) ! ! Total ingestion rate in C, Fe, N units zgraztotc = zgraznc + zgrazpoc + zgrazdc zgraztotf = zgraznf + zgrazdf + zgrazpof zgraztotn = zgraznc * quotan(ji,jj,jk) + zgrazpoc + zgrazdc * quotad(ji,jj,jk) ! Grazing by microzooplankton zgrazing(ji,jj,jk) = zgraztotc ! Microzooplankton efficiency. ! We adopt a formulation proposed by Mitra et al. (2007) ! The gross growth efficiency is controled by the most limiting nutrient. ! Growth is also further decreased when the food quality is poor. This is currently ! hard coded : it can be decreased by up to 50% (zepsherq) ! GGE can also be decreased when food quantity is high, zepsherf (Montagnes and ! Fulton, 2012) ! ----------------------------------------------------------------------------- zgrasratf = ( zgraztotf + rtrn ) / ( zgraztotc + rtrn ) zgrasratn = ( zgraztotn + rtrn ) / ( zgraztotc + rtrn ) zepshert = MIN( 1., zgrasratn, zgrasratf / feratz) zbeta = MAX(0., (epsher - epshermin) ) ! Food quantity deprivation of the GGE zepsherf = epshermin + zbeta / ( 1.0 + 0.04E6 * 12. * zfood * zbeta ) ! Food quality deprivation of the GGE zepsherq = 0.5 + (1.0 - 0.5) * zepshert * ( 1.0 + 1.0 ) / ( zepshert + 1.0 ) ! Actual GGE of microzooplankton zepsherv = zepsherf * zepshert * zepsherq ! Excretion of Fe zgrafer = zgraztotc * MAX( 0. , ( 1. - unass ) * zgrasratf - feratz * zepsherv ) ! Excretion of C, N, P zgrarem = zgraztotc * ( 1. - zepsherv - unass ) ! Egestion of C, N, P zgrapoc = zgraztotc * unass ! Update of the TRA arrays ! ------------------------ ! Fraction of excretion as inorganic nutrients and DIC zgrarsig = zgrarem * sigma1 tr(ji,jj,jk,jppo4,Krhs) = tr(ji,jj,jk,jppo4,Krhs) + zgrarsig tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) + zgrarsig tr(ji,jj,jk,jpdoc,Krhs) = tr(ji,jj,jk,jpdoc,Krhs) + zgrarem - zgrarsig ! IF( ln_ligand ) THEN tr(ji,jj,jk,jplgw,Krhs) = tr(ji,jj,jk,jplgw,Krhs) + (zgrarem - zgrarsig) * ldocz zzligprod(ji,jj,jk) = (zgrarem - zgrarsig) * ldocz ENDIF ! tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - o2ut * zgrarsig tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) + zgrafer zfezoo(ji,jj,jk) = zgrafer tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) + zgrapoc prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + zgrapoc tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zgraztotf * unass tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zgrarsig tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + rno3 * zgrarsig ! Update the arrays TRA which contain the biological sources and sinks ! -------------------------------------------------------------------- zmortz = ztortz + zrespz tr(ji,jj,jk,jpzoo,Krhs) = tr(ji,jj,jk,jpzoo,Krhs) - zmortz + zepsherv * zgraztotc tr(ji,jj,jk,jpphy,Krhs) = tr(ji,jj,jk,jpphy,Krhs) - zgraznc tr(ji,jj,jk,jpdia,Krhs) = tr(ji,jj,jk,jpdia,Krhs) - zgrazdc tr(ji,jj,jk,jpnch,Krhs) = tr(ji,jj,jk,jpnch,Krhs) - zgraznc * tr(ji,jj,jk,jpnch,Kbb)/(tr(ji,jj,jk,jpphy,Kbb)+rtrn) tr(ji,jj,jk,jpdch,Krhs) = tr(ji,jj,jk,jpdch,Krhs) - zgrazdc * tr(ji,jj,jk,jpdch,Kbb)/(tr(ji,jj,jk,jpdia,Kbb)+rtrn) tr(ji,jj,jk,jpdsi,Krhs) = tr(ji,jj,jk,jpdsi,Krhs) - zgrazdc * tr(ji,jj,jk,jpdsi,Kbb)/(tr(ji,jj,jk,jpdia,Kbb)+rtrn) tr(ji,jj,jk,jpgsi,Krhs) = tr(ji,jj,jk,jpgsi,Krhs) + zgrazdc * tr(ji,jj,jk,jpdsi,Kbb)/(tr(ji,jj,jk,jpdia,Kbb)+rtrn) tr(ji,jj,jk,jpnfe,Krhs) = tr(ji,jj,jk,jpnfe,Krhs) - zgraznf tr(ji,jj,jk,jpdfe,Krhs) = tr(ji,jj,jk,jpdfe,Krhs) - zgrazdf tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) + zmortz - zgrazpoc prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + zmortz conspoc(ji,jj,jk) = conspoc(ji,jj,jk) - zgrazpoc tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + feratz * zmortz - zgrazpof ! ! Calcite remineralization due to zooplankton activity ! part of the ingested calcite is not dissolving in the acidic gut ! ---------------------------------------------------------------- zprcaca = xfracal(ji,jj,jk) * zgraznc prodcal(ji,jj,jk) = prodcal(ji,jj,jk) + zprcaca ! prodcal=prodcal(nanophy)+prodcal(microzoo)+prodcal(mesozoo) ! zprcaca = part * zprcaca tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) - zprcaca tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) - 2. * zprcaca tr(ji,jj,jk,jpcal,Krhs) = tr(ji,jj,jk,jpcal,Krhs) + zprcaca END_3D ! IF( lk_iomput .AND. knt == nrdttrc ) THEN IF( iom_use("GRAZ1") ) THEN ! Total grazing of phyto by zooplankton zgrazing(:,:,jpk) = 0._wp ; CALL iom_put( "GRAZ1" , zgrazing(:,:,:) * 1.e+3 * rfact2r * tmask(:,:,:) ) ENDIF IF( iom_use("FEZOO") ) THEN zfezoo (:,:,jpk) = 0._wp ; CALL iom_put( "FEZOO", zfezoo(:,:,:) * 1e9 * 1.e+3 * rfact2r * tmask(:,:,:) ) ENDIF IF( ln_ligand ) THEN zzligprod(:,:,jpk) = 0._wp ; CALL iom_put( "LPRODZ", zzligprod(:,:,:) * 1e9 * 1.e+3 * rfact2r * tmask(:,:,:)) ENDIF ENDIF ! IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('micro')") CALL prt_ctl_info( charout, cdcomp = 'top' ) CALL prt_ctl(tab4d_1=tr(:,:,:,:,Krhs), mask1=tmask, clinfo=ctrcnm) ENDIF ! IF( ln_timing ) CALL timing_stop('p4z_micro') ! END SUBROUTINE p4z_micro SUBROUTINE p4z_micro_init !!---------------------------------------------------------------------- !! *** ROUTINE p4z_micro_init *** !! !! ** Purpose : Initialization of microzooplankton parameters !! !! ** Method : Read the namp4zzoo namelist and check the parameters !! called at the first timestep (nittrc000) !! !! ** input : Namelist namp4zzoo !! !!---------------------------------------------------------------------- INTEGER :: ios ! Local integer ! NAMELIST/namp4zzoo/ part, grazrat, resrat, mzrat, xprefn, xprefc, & & xprefd, xthreshdia, xthreshphy, xthreshpoc, & & xthresh, xkgraz, epsher, epshermin, sigma1, unass, & & xsigma, xsigmadel !!---------------------------------------------------------------------- ! IF(lwp) THEN WRITE(numout,*) WRITE(numout,*) 'p4z_micro_init : Initialization of microzooplankton parameters' WRITE(numout,*) '~~~~~~~~~~~~~~' ENDIF ! READ ( numnatp_ref, namp4zzoo, IOSTAT = ios, ERR = 901) 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namp4zzoo in reference namelist' ) READ ( numnatp_cfg, namp4zzoo, IOSTAT = ios, ERR = 902 ) 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'namp4zzoo in configuration namelist' ) IF(lwm) WRITE( numonp, namp4zzoo ) ! IF(lwp) THEN ! control print WRITE(numout,*) ' Namelist : namp4zzoo' WRITE(numout,*) ' part of calcite not dissolved in microzoo guts part =', part WRITE(numout,*) ' microzoo preference for POC xprefc =', xprefc WRITE(numout,*) ' microzoo preference for nano xprefn =', xprefn WRITE(numout,*) ' microzoo preference for diatoms xprefd =', xprefd WRITE(numout,*) ' diatoms feeding threshold for microzoo xthreshdia =', xthreshdia WRITE(numout,*) ' nanophyto feeding threshold for microzoo xthreshphy =', xthreshphy WRITE(numout,*) ' poc feeding threshold for microzoo xthreshpoc =', xthreshpoc WRITE(numout,*) ' feeding threshold for microzooplankton xthresh =', xthresh WRITE(numout,*) ' exsudation rate of microzooplankton resrat =', resrat WRITE(numout,*) ' microzooplankton mortality rate mzrat =', mzrat WRITE(numout,*) ' maximal microzoo grazing rate grazrat =', grazrat WRITE(numout,*) ' non assimilated fraction of P by microzoo unass =', unass WRITE(numout,*) ' Efficicency of microzoo growth epsher =', epsher WRITE(numout,*) ' Minimum efficicency of microzoo growth epshermin =', epshermin WRITE(numout,*) ' Fraction of microzoo excretion as DOM sigma1 =', sigma1 WRITE(numout,*) ' half saturation constant for grazing 1 xkgraz =', xkgraz WRITE(numout,*) ' Width of the grazing window xsigma =', xsigma WRITE(numout,*) ' Maximum additional width of the grazing window xsigmadel =', xsigmadel ENDIF ! END SUBROUTINE p4z_micro_init !!====================================================================== END MODULE p4zmicro