#include "cppdefs.h" MODULE p4zrem !!====================================================================== !! *** MODULE p4zrem *** !! TOP : PISCES Compute remineralization/dissolution of organic compounds !!========================================================================= !! 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 !!---------------------------------------------------------------------- #if defined key_pisces !! p4z_rem : Compute remineralization/dissolution of organic compounds !! p4z_rem_init : Initialisation of parameters for remineralisation !! p4z_rem_alloc : Allocate remineralisation variables !!---------------------------------------------------------------------- USE sms_pisces ! PISCES Source Minus Sink variables USE p4zche ! chemical model USE p4zprod ! Growth rate of the 2 phyto groups USE p4zlim ! USE iom ! I/O manager IMPLICIT NONE PRIVATE PUBLIC p4z_rem ! called in p4zbio.F90 PUBLIC p4z_rem_init ! called in trcsms_pisces.F90 PUBLIC p4z_rem_alloc !!* Substitution # include "ocean2pisces.h90" # include "top_substitute.h90" REAL(wp), PUBLIC :: xremikc !: remineralisation rate of DOC REAL(wp), PUBLIC :: xremikn !: remineralisation rate of DON REAL(wp), PUBLIC :: xremikp !: remineralisation rate of DOP REAL(wp), PUBLIC :: xremik !: remineralisation rate of POC REAL(wp), PUBLIC :: nitrif !: NH4 nitrification rate REAL(wp), PUBLIC :: xsirem !: remineralisation rate of POC REAL(wp), PUBLIC :: xsiremlab !: fast remineralisation rate of POC REAL(wp), PUBLIC :: xsilab !: fraction of labile biogenic silica REAL(wp), PUBLIC :: feratb !: Fe/C quota in bacteria REAL(wp), PUBLIC :: xkferb !: Half-saturation constant for bacteria Fe/C REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: denitr !: denitrification array !!---------------------------------------------------------------------- !! NEMO/TOP 4.0 , NEMO Consortium (2018) !! $Id: p4zrem.F90 10425 2018-12-19 21:54:16Z smasson $ !! Software governed by the CeCILL license (see ./LICENSE) !!---------------------------------------------------------------------- CONTAINS SUBROUTINE p4z_rem( kt, knt ) !!--------------------------------------------------------------------- !! *** ROUTINE p4z_rem *** !! !! ** Purpose : Compute remineralization/scavenging of organic compounds !! !! ** Method : - ??? !!--------------------------------------------------------------------- INTEGER, INTENT(in) :: kt, knt ! ocean time step ! INTEGER :: ji, jj, jk REAL(wp) :: zremik, zremikc, zremikn, zremikp, zsiremin, zfact REAL(wp) :: zsatur, zsatur2, znusil, znusil2, zdep, zdepmin, zfactdep REAL(wp) :: zbactfer, zolimit, zrfact2, zmsk REAL(wp) :: zammonic, zoxyremc, zoxyremn, zoxyremp REAL(wp) :: zosil, ztem, zdenitnh4, zolimic, zolimin, zolimip, zdenitrn, zdenitrp CHARACTER (len=25) :: charout REAL(wp), DIMENSION(PRIV_2D_BIOARRAY) :: ztempbac REAL(wp), DIMENSION(PRIV_3D_BIOARRAY) :: zdepbac, zolimi, zonitr, zdepprod, & & zfacsi, zfacsib, zdepeff, zfebact REAL(wp), ALLOCATABLE, DIMENSION(:,:,:) :: zw3d !!--------------------------------------------------------------------- ! ! Initialisation of arrys zdepprod(:,:,:) = 1. zdepeff (:,:,:) = 0.3 ztempbac(:,:) = 0. zfacsib(:,:,:) = xsilab / ( 1.0 - xsilab ) zfebact(:,:,:) = 0. zfacsi(:,:,:) = xsilab ! Computation of the mean phytoplankton concentration as ! a crude estimate of the bacterial biomass ! this parameterization has been deduced from a model version ! that was modeling explicitely bacteria ! ------------------------------------------------------- DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE zdep = MAX( hmld(ji,jj), heup(ji,jj) ) IF( gdept_n(ji,jj,K) < zdep ) THEN zdepbac(ji,jj,jk) = MIN( 0.7 * ( trb(ji,jj,K,jpzoo) & & + 2.* trb(ji,jj,K,jpmes) ), 4.e-6 ) ztempbac(ji,jj) = zdepbac(ji,jj,jk) ELSE zdepmin = MIN( 1., zdep / gdept_n(ji,jj,K) ) zdepbac (ji,jj,jk) = zdepmin**0.683 * ztempbac(ji,jj) zdepprod(ji,jj,jk) = zdepmin**0.273 zdepeff (ji,jj,jk) = zdepeff(ji,jj,jk) * zdepmin**0.3 ENDIF END DO END DO END DO IF( ln_p4z ) THEN DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! DOC ammonification. Depends on depth, phytoplankton biomass ! and a limitation term which is supposed to be a parameterization of the bacterial activity. zremik = xremik * xstep / 1.e-6 * xlimbac(ji,jj,jk) * zdepbac(ji,jj,jk) zremik = MAX( zremik, 2.74e-4 * xstep ) ! Ammonification in oxic waters with oxygen consumption ! ----------------------------------------------------- zolimit = zremik * ( 1.- nitrfac(ji,jj,jk) ) & & * trb(ji,jj,K,jpdoc) zolimi(ji,jj,jk) = MIN( ( trb(ji,jj,K,jpoxy) - rtrn ) / o2ut, zolimit ) ! Ammonification in suboxic waters with denitrification ! ------------------------------------------------------- zammonic = zremik * nitrfac(ji,jj,jk) * trb(ji,jj,K,jpdoc) denitr(ji,jj,jk) = zammonic * ( 1. - nitrfac2(ji,jj,jk) ) denitr(ji,jj,jk) = MIN( ( trb(ji,jj,K,jpno3) - rtrn ) / rdenit, denitr(ji,jj,jk) ) zoxyremc = zammonic - denitr(ji,jj,jk) ! zolimi (ji,jj,jk) = MAX( 0.e0, zolimi (ji,jj,jk) ) denitr (ji,jj,jk) = MAX( 0.e0, denitr (ji,jj,jk) ) zoxyremc = MAX( 0.e0, zoxyremc ) ! tra(ji,jj,jk,jppo4) = tra(ji,jj,jk,jppo4) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) - denitr (ji,jj,jk) * rdenit tra(ji,jj,jk,jpdoc) = tra(ji,jj,jk,jpdoc) - zolimi (ji,jj,jk) - denitr(ji,jj,jk) - zoxyremc tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - zolimi (ji,jj,jk) * o2ut tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) + rno3 * ( zolimi(ji,jj,jk) + zoxyremc & & + ( rdenit + 1.) * denitr(ji,jj,jk) ) END DO END DO END DO ELSE DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! DOC ammonification. Depends on depth, phytoplankton biomass ! and a limitation term which is supposed to be a parameterization of the bacterial activity. ! ----------------------------------------------------------------- zremik = xstep / 1.e-6 * MAX(0.01, xlimbac(ji,jj,jk)) * zdepbac(ji,jj,jk) zremik = MAX( zremik, 2.74e-4 * xstep / xremikc ) zremikc = xremikc * zremik zremikn = xremikn / xremikc zremikp = xremikp / xremikc ! Ammonification in oxic waters with oxygen consumption ! ----------------------------------------------------- zolimit = zremikc * ( 1.- nitrfac(ji,jj,jk) ) * trb(ji,jj,K,jpdoc) zolimic = MAX( 0.e0, MIN( ( trb(ji,jj,K,jpoxy) - rtrn ) / o2ut, zolimit ) ) zolimi(ji,jj,jk) = zolimic zolimin = zremikn * zolimic * trb(ji,jj,K,jpdon) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) zolimip = zremikp * zolimic * trb(ji,jj,K,jpdop) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) ! Ammonification in suboxic waters with denitrification ! ------------------------------------------------------- zammonic = zremikc * nitrfac(ji,jj,jk) * trb(ji,jj,K,jpdoc) denitr(ji,jj,jk) = zammonic * ( 1. - nitrfac2(ji,jj,jk) ) denitr(ji,jj,jk) = MAX(0., MIN( ( trb(ji,jj,K,jpno3) - rtrn ) & & / rdenit, denitr(ji,jj,jk) ) ) zoxyremc = MAX(0., zammonic - denitr(ji,jj,jk)) zdenitrn = zremikn * denitr(ji,jj,jk) * trb(ji,jj,K,jpdon) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) zdenitrp = zremikp * denitr(ji,jj,jk) * trb(ji,jj,K,jpdop) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) zoxyremn = zremikn * zoxyremc * trb(ji,jj,K,jpdon) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) zoxyremp = zremikp * zoxyremc * trb(ji,jj,K,jpdop) & & / ( trb(ji,jj,K,jpdoc) + rtrn ) tra(ji,jj,jk,jppo4) = tra(ji,jj,jk,jppo4) + zolimip + zdenitrp + zoxyremp tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) + zolimin + zdenitrn + zoxyremn tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) - denitr(ji,jj,jk) * rdenit tra(ji,jj,jk,jpdoc) = tra(ji,jj,jk,jpdoc) - zolimic - denitr(ji,jj,jk) - zoxyremc tra(ji,jj,jk,jpdon) = tra(ji,jj,jk,jpdon) - zolimin - zdenitrn - zoxyremn tra(ji,jj,jk,jpdop) = tra(ji,jj,jk,jpdop) - zolimip - zdenitrp - zoxyremp tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - zolimic * o2ut tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) + zolimic + denitr(ji,jj,jk) + zoxyremc tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) + rno3 * ( zolimin + zoxyremn + ( rdenit + 1.) * zdenitrn ) END DO END DO END DO ! ENDIF DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! NH4 nitrification to NO3. Ceased for oxygen concentrations ! below 2 umol/L. Inhibited at strong light ! ---------------------------------------------------------- zonitr(ji,jj,jk) = nitrif * xstep * trb(ji,jj,K,jpnh4) * ( 1.- nitrfac(ji,jj,jk) ) & & / ( 1.+ emoy(ji,jj,jk) ) * ( 1. + fr_i(ji,jj) * emoy(ji,jj,jk) ) zdenitnh4 = nitrif * xstep * trb(ji,jj,K,jpnh4) * nitrfac(ji,jj,jk) zdenitnh4 = MIN( ( trb(ji,jj,K,jpno3) - rtrn ) / rdenita, zdenitnh4 ) ! Update of the tracers trends ! ---------------------------- tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) - zonitr(ji,jj,jk) - zdenitnh4 tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) + zonitr(ji,jj,jk) - rdenita * zdenitnh4 tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - o2nit * zonitr(ji,jj,jk) tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) - 2 * rno3 * zonitr(ji,jj,jk)+ rno3 * ( rdenita - 1. ) * zdenitnh4 END DO END DO END DO IF(ln_ctl) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem1')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc( charout, ltra='tra') ENDIF DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! Bacterial uptake of iron. No iron is available in DOC. So ! Bacteries are obliged to take up iron from the water. Some ! studies (especially at Papa) have shown this uptake to be significant ! ---------------------------------------------------------- zbactfer = feratb * rfact2 * 0.6 / rday * tgfunc(ji,jj,jk) * xlimbacl(ji,jj,jk) & & * trb(ji,jj,K,jpfer) & & / ( xkferb + trb(ji,jj,K,jpfer) ) & & * zdepprod(ji,jj,jk) * zdepeff(ji,jj,jk) * zdepbac(ji,jj,jk) tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) - zbactfer*0.33 tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zbactfer*0.25 tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + zbactfer*0.08 zfebact(ji,jj,jk) = zbactfer * 0.33 blim(ji,jj,jk) = xlimbacl(ji,jj,jk) * zdepbac(ji,jj,jk) / 1.e-6 * zdepprod(ji,jj,jk) END DO END DO END DO IF(ln_ctl) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem2')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc( charout, ltra='tra') ENDIF ! Initialization of the array which contains the labile fraction ! of bSi. Set to a constant in the upper ocean ! --------------------------------------------------------------- DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE zdep = MAX( hmld(ji,jj), heup_01(ji,jj) ) zsatur = MAX( rtrn, ( sio3eq(ji,jj,jk) - trb(ji,jj,K,jpsil) ) & & / ( sio3eq(ji,jj,jk) + rtrn ) ) zsatur2 = ( 1. + tsn(ji,jj,K,jp_tem) / 400.)**37 znusil = 0.225 * ( 1. + tsn(ji,jj,K,jp_tem) / 15.) * zsatur + 0.775 * zsatur2 * zsatur**9.25 ! Remineralization rate of BSi depedant on T and saturation ! --------------------------------------------------------- IF ( gdept_n(ji,jj,K) > zdep ) THEN zfacsib(ji,jj,jk) = zfacsib(ji,jj,jk-1) * EXP( -0.5 * ( xsiremlab - xsirem ) & & * znusil * e3t_n(ji,jj,K) / wsbio4(ji,jj,jk) ) zfacsi(ji,jj,jk) = zfacsib(ji,jj,jk) / ( 1.0 + zfacsib(ji,jj,jk) ) zfacsib(ji,jj,jk) = zfacsib(ji,jj,jk) * EXP( -0.5 * ( xsiremlab - xsirem ) & & * znusil * e3t_n(ji,jj,K) / wsbio4(ji,jj,jk) ) ENDIF zsiremin = ( xsiremlab * zfacsi(ji,jj,jk) + xsirem * ( 1. - zfacsi(ji,jj,jk) ) ) * xstep * znusil zosil = zsiremin * trb(ji,jj,K,jpgsi) ! tra(ji,jj,jk,jpgsi) = tra(ji,jj,jk,jpgsi) - zosil tra(ji,jj,jk,jpsil) = tra(ji,jj,jk,jpsil) + zosil END DO END DO END DO IF(ln_ctl) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem3')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc( charout, ltra='tra') ENDIF #if defined key_iomput IF( lk_iomput ) THEN IF( knt == nrdttrc ) THEN zrfact2 = 1.e3 * rfact2r ALLOCATE( zw3d(PRIV_3D_BIOARRAY) ) zfact = 1.e+3 * rfact2r ! conversion from mol/l/kt to mol/m3/s ! IF( iom_use( "REMIN" ) ) THEN zw3d(:,:,:) = zolimi(:,:,:) * tmask(:,:,:) * zfact ! Remineralisation rate CALL iom_put( "REMIN" , zw3d ) ENDIF IF( iom_use( "DENIT" ) ) THEN zw3d(:,:,:) = denitr(:,:,:) * rdenit * rno3 * tmask(:,:,:) * zfact ! Denitrification CALL iom_put( "DENIT" , zw3d ) ENDIF IF( iom_use( "BACT" ) ) THEN zw3d(:,:,:) = zdepbac(:,:,:) * 1.E6 * tmask(:,:,:) ! Bacterial biomass CALL iom_put( "BACT", zw3d ) ENDIF IF( iom_use( "FEBACT" ) ) THEN zw3d(:,:,:) = zfebact(:,:,:) * 1E9 * tmask(:,:,:) * zrfact2 ! Bacterial iron consumption CALL iom_put( "FEBACT" , zw3d ) ENDIF ! DEALLOCATE( zw3d ) ENDIF ENDIF #endif ! # if defined key_trc_diaadd zrfact2 = 1.e3 * rfact2r DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE zmsk = zrfact2 * tmask(ji,jj,jk) trc3d(ji,jj,K,jp_remino2) = (-o2ut) * zolimi(ji,jj,jk) * zmsk ! O2 consumption by nitrification trc3d(ji,jj,K,jp_nitrifo2) = (-o2nit) * zonitr(ji,jj,jk) * zmsk ! O2 consumption by remin END DO END DO END DO #endif END SUBROUTINE p4z_rem SUBROUTINE p4z_rem_init !!---------------------------------------------------------------------- !! *** ROUTINE p4z_rem_init *** !! !! ** Purpose : Initialization of remineralization parameters !! !! ** Method : Read the nampisrem namelist and check the parameters !! called at the first timestep !! !! ** input : Namelist nampisrem !! !!---------------------------------------------------------------------- NAMELIST/nampisrem/ xremik, nitrif, xsirem, xsiremlab, xsilab, feratb, xkferb, & & xremikc, xremikn, xremikp INTEGER :: ios ! Local integer output status for namelist read !!---------------------------------------------------------------------- ! IF(lwp) THEN WRITE(numout,*) WRITE(numout,*) 'p4z_rem_init : Initialization of remineralization parameters' WRITE(numout,*) '~~~~~~~~~~~~' ENDIF ! REWIND( numnatp_ref ) ! Namelist nampisrem in reference namelist : Pisces remineralization READ ( numnatp_ref, nampisrem, IOSTAT = ios, ERR = 901) 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisrem in reference namelist', lwp ) REWIND( numnatp_cfg ) ! Namelist nampisrem in configuration namelist : Pisces remineralization READ ( numnatp_cfg, nampisrem, IOSTAT = ios, ERR = 902 ) 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisrem in configuration namelist', lwp ) IF(lwm) WRITE( numonp, nampisrem ) IF(lwp) THEN ! control print WRITE(numout,*) ' Namelist parameters for remineralization, nampisrem' IF( ln_p4z ) THEN WRITE(numout,*) ' remineralization rate of DOC xremik =', xremik ELSE WRITE(numout,*) ' remineralization rate of DOC xremikc =', xremikc WRITE(numout,*) ' remineralization rate of DON xremikn =', xremikn WRITE(numout,*) ' remineralization rate of DOP xremikp =', xremikp ENDIF WRITE(numout,*) ' remineralization rate of Si xsirem =', xsirem WRITE(numout,*) ' fast remineralization rate of Si xsiremlab =', xsiremlab WRITE(numout,*) ' fraction of labile biogenic silica xsilab =', xsilab WRITE(numout,*) ' NH4 nitrification rate nitrif =', nitrif WRITE(numout,*) ' Bacterial Fe/C ratio feratb =', feratb WRITE(numout,*) ' Half-saturation constant for bact. Fe/C xkferb =', xkferb ENDIF ! denitr(:,:,:) = 0. ! END SUBROUTINE p4z_rem_init INTEGER FUNCTION p4z_rem_alloc() !!---------------------------------------------------------------------- !! *** ROUTINE p4z_rem_alloc *** !!---------------------------------------------------------------------- ALLOCATE( denitr(PRIV_3D_BIOARRAY), STAT=p4z_rem_alloc ) ! IF( p4z_rem_alloc /= 0 ) CALL ctl_warn( 'p4z_rem_alloc: failed to allocate arrays' ) ! END FUNCTION p4z_rem_alloc #else !!====================================================================== !! Dummy module : No PISCES bio-model !!====================================================================== CONTAINS SUBROUTINE p4z_rem ! Empty routine END SUBROUTINE p4z_rem #endif !!====================================================================== END MODULE p4zrem