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 !!---------------------------------------------------------------------- !! p4z_rem : Compute remineralization/dissolution of organic compounds !! p4z_rem_init : Initialisation of parameters for remineralisation !! p4z_rem_alloc : Allocate remineralisation variables !!---------------------------------------------------------------------- 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 p4zche ! chemical model USE p4zprod ! Growth rate of the 2 phyto groups USE p4zlim USE prtctl_trc ! print control for debugging 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 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 !! * 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_rem( kt, knt, Kbb, Kmm, Krhs ) !!--------------------------------------------------------------------- !! *** ROUTINE p4z_rem *** !! !! ** Purpose : Compute remineralization/scavenging of organic compounds !! !! ** Method : - ??? !!--------------------------------------------------------------------- INTEGER, INTENT(in) :: kt, knt ! ocean time step INTEGER, INTENT(in) :: Kbb, Kmm, Krhs ! time level indices ! 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, zonitr, zrfact2 REAL(wp) :: zammonic, zoxyremc, zoxyremn, zoxyremp REAL(wp) :: zosil, ztem, zdenitnh4, zolimic, zolimin, zolimip, zdenitrn, zdenitrp CHARACTER (len=25) :: charout REAL(wp), DIMENSION(jpi,jpj ) :: ztempbac REAL(wp), DIMENSION(jpi,jpj,jpk) :: zdepbac, zolimi, zdepprod, zfacsi, zfacsib, zdepeff, zfebact !!--------------------------------------------------------------------- ! IF( ln_timing ) CALL timing_start('p4z_rem') ! ! Initialisation of arrys zdepprod(:,:,:) = 1._wp zdepeff (:,:,:) = 0.3_wp ztempbac(:,:) = 0._wp zfacsib(:,:,:) = xsilab / ( 1.0 - xsilab ) zfebact(:,:,:) = 0._wp 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_3D_11_11( 1, jpkm1 ) zdep = MAX( hmld(ji,jj), heup(ji,jj) ) IF( gdept(ji,jj,jk,Kmm) < zdep ) THEN zdepbac(ji,jj,jk) = MIN( 0.7 * ( tr(ji,jj,jk,jpzoo,Kbb) + 2.* tr(ji,jj,jk,jpmes,Kbb) ), 4.e-6 ) ztempbac(ji,jj) = zdepbac(ji,jj,jk) ELSE zdepmin = MIN( 1., zdep / gdept(ji,jj,jk,Kmm) ) 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_3D IF( ln_p4z ) THEN DO_3D_11_11( 1, jpkm1 ) ! 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) ) * tr(ji,jj,jk,jpdoc,Kbb) zolimi(ji,jj,jk) = MIN( ( tr(ji,jj,jk,jpoxy,Kbb) - rtrn ) / o2ut, zolimit ) ! Ammonification in suboxic waters with denitrification ! ------------------------------------------------------- zammonic = zremik * nitrfac(ji,jj,jk) * tr(ji,jj,jk,jpdoc,Kbb) denitr(ji,jj,jk) = zammonic * ( 1. - nitrfac2(ji,jj,jk) ) denitr(ji,jj,jk) = MIN( ( tr(ji,jj,jk,jpno3,Kbb) - 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 ) ! tr(ji,jj,jk,jppo4,Krhs) = tr(ji,jj,jk,jppo4,Krhs) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tr(ji,jj,jk,jpno3,Krhs) = tr(ji,jj,jk,jpno3,Krhs) - denitr (ji,jj,jk) * rdenit tr(ji,jj,jk,jpdoc,Krhs) = tr(ji,jj,jk,jpdoc,Krhs) - zolimi (ji,jj,jk) - denitr(ji,jj,jk) - zoxyremc tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - zolimi (ji,jj,jk) * o2ut tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyremc tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + rno3 * ( zolimi(ji,jj,jk) + zoxyremc & & + ( rdenit + 1.) * denitr(ji,jj,jk) ) END_3D ELSE DO_3D_11_11( 1, jpkm1 ) ! 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) ) * tr(ji,jj,jk,jpdoc,Kbb) zolimic = MAX( 0.e0, MIN( ( tr(ji,jj,jk,jpoxy,Kbb) - rtrn ) / o2ut, zolimit ) ) zolimi(ji,jj,jk) = zolimic zolimin = zremikn * zolimic * tr(ji,jj,jk,jpdon,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) zolimip = zremikp * zolimic * tr(ji,jj,jk,jpdop,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) ! Ammonification in suboxic waters with denitrification ! ------------------------------------------------------- zammonic = zremikc * nitrfac(ji,jj,jk) * tr(ji,jj,jk,jpdoc,Kbb) denitr(ji,jj,jk) = zammonic * ( 1. - nitrfac2(ji,jj,jk) ) denitr(ji,jj,jk) = MAX(0., MIN( ( tr(ji,jj,jk,jpno3,Kbb) - rtrn ) / rdenit, denitr(ji,jj,jk) ) ) zoxyremc = MAX(0., zammonic - denitr(ji,jj,jk)) zdenitrn = zremikn * denitr(ji,jj,jk) * tr(ji,jj,jk,jpdon,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) zdenitrp = zremikp * denitr(ji,jj,jk) * tr(ji,jj,jk,jpdop,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) zoxyremn = zremikn * zoxyremc * tr(ji,jj,jk,jpdon,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) zoxyremp = zremikp * zoxyremc * tr(ji,jj,jk,jpdop,Kbb) / ( tr(ji,jj,jk,jpdoc,Kbb) + rtrn ) tr(ji,jj,jk,jppo4,Krhs) = tr(ji,jj,jk,jppo4,Krhs) + zolimip + zdenitrp + zoxyremp tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) + zolimin + zdenitrn + zoxyremn tr(ji,jj,jk,jpno3,Krhs) = tr(ji,jj,jk,jpno3,Krhs) - denitr(ji,jj,jk) * rdenit tr(ji,jj,jk,jpdoc,Krhs) = tr(ji,jj,jk,jpdoc,Krhs) - zolimic - denitr(ji,jj,jk) - zoxyremc tr(ji,jj,jk,jpdon,Krhs) = tr(ji,jj,jk,jpdon,Krhs) - zolimin - zdenitrn - zoxyremn tr(ji,jj,jk,jpdop,Krhs) = tr(ji,jj,jk,jpdop,Krhs) - zolimip - zdenitrp - zoxyremp tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - zolimic * o2ut tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zolimic + denitr(ji,jj,jk) + zoxyremc tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + rno3 * ( zolimin + zoxyremn + ( rdenit + 1.) * zdenitrn ) END_3D ! ENDIF DO_3D_11_11( 1, jpkm1 ) ! NH4 nitrification to NO3. Ceased for oxygen concentrations ! below 2 umol/L. Inhibited at strong light ! ---------------------------------------------------------- zonitr = nitrif * xstep * tr(ji,jj,jk,jpnh4,Kbb) * ( 1.- nitrfac(ji,jj,jk) ) & & / ( 1.+ emoy(ji,jj,jk) ) * ( 1. + fr_i(ji,jj) * emoy(ji,jj,jk) ) zdenitnh4 = nitrif * xstep * tr(ji,jj,jk,jpnh4,Kbb) * nitrfac(ji,jj,jk) zdenitnh4 = MIN( ( tr(ji,jj,jk,jpno3,Kbb) - rtrn ) / rdenita, zdenitnh4 ) ! Update of the tracers trends ! ---------------------------- tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) - zonitr - zdenitnh4 tr(ji,jj,jk,jpno3,Krhs) = tr(ji,jj,jk,jpno3,Krhs) + zonitr - rdenita * zdenitnh4 tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - o2nit * zonitr tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) - 2 * rno3 * zonitr + rno3 * ( rdenita - 1. ) * zdenitnh4 END_3D IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem1')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc(tab4d=tr(:,:,:,:,Krhs), mask=tmask, clinfo=ctrcnm) ENDIF DO_3D_11_11( 1, jpkm1 ) ! 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_wp / rday * tgfunc(ji,jj,jk) * xlimbacl(ji,jj,jk) & & * tr(ji,jj,jk,jpfer,Kbb) / ( xkferb + tr(ji,jj,jk,jpfer,Kbb) ) & & * zdepprod(ji,jj,jk) * zdepeff(ji,jj,jk) * zdepbac(ji,jj,jk) tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zbactfer*0.33 tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zbactfer*0.25 tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + 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_3D IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem2')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc(tab4d=tr(:,:,:,:,Krhs), mask=tmask, clinfo=ctrcnm) ENDIF ! Initialization of the array which contains the labile fraction ! of bSi. Set to a constant in the upper ocean ! --------------------------------------------------------------- DO_3D_11_11( 1, jpkm1 ) zdep = MAX( hmld(ji,jj), heup_01(ji,jj) ) zsatur = MAX( rtrn, ( sio3eq(ji,jj,jk) - tr(ji,jj,jk,jpsil,Kbb) ) / ( sio3eq(ji,jj,jk) + rtrn ) ) zsatur2 = ( 1. + ts(ji,jj,jk,jp_tem,Kmm) / 400.)**37 znusil = 0.225 * ( 1. + ts(ji,jj,jk,jp_tem,Kmm) / 15.) * zsatur + 0.775 * zsatur2 * zsatur**9.25 ! Remineralization rate of BSi depedant on T and saturation ! --------------------------------------------------------- IF ( gdept(ji,jj,jk,Kmm) > zdep ) THEN zfacsib(ji,jj,jk) = zfacsib(ji,jj,jk-1) * EXP( -0.5 * ( xsiremlab - xsirem ) & & * znusil * e3t(ji,jj,jk,Kmm) / 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(ji,jj,jk,Kmm) / wsbio4(ji,jj,jk) ) ENDIF zsiremin = ( xsiremlab * zfacsi(ji,jj,jk) + xsirem * ( 1. - zfacsi(ji,jj,jk) ) ) * xstep * znusil zosil = zsiremin * tr(ji,jj,jk,jpgsi,Kbb) ! tr(ji,jj,jk,jpgsi,Krhs) = tr(ji,jj,jk,jpgsi,Krhs) - zosil tr(ji,jj,jk,jpsil,Krhs) = tr(ji,jj,jk,jpsil,Krhs) + zosil END_3D IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('rem3')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc(tab4d=tr(:,:,:,:,Krhs), mask=tmask, clinfo=ctrcnm) ENDIF IF( knt == nrdttrc ) THEN zrfact2 = 1.e+3 * rfact2r ! conversion from mol/l/kt to mol/m3/s ! IF( iom_use( "REMIN" ) ) THEN ! Remineralisation rate zolimi(:,:,jpk) = 0. ; CALL iom_put( "REMIN" , zolimi(:,:,:) * tmask(:,:,:) * zrfact2 ) ENDIF CALL iom_put( "DENIT" , denitr(:,:,:) * rdenit * rno3 * tmask(:,:,:) * zrfact2 ) ! Denitrification IF( iom_use( "BACT" ) ) THEN ! Bacterial biomass zdepbac(:,:,jpk) = 0. ; CALL iom_put( "BACT", zdepbac(:,:,:) * 1.E6 * tmask(:,:,:) ) ENDIF CALL iom_put( "FEBACT" , zfebact(:,:,:) * 1E9 * tmask(:,:,:) * zrfact2 ) ENDIF ! IF( ln_timing ) CALL timing_stop('p4z_rem') ! 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 ! READ ( numnatp_ref, nampisrem, IOSTAT = ios, ERR = 901) 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisrem in reference namelist' ) READ ( numnatp_cfg, nampisrem, IOSTAT = ios, ERR = 902 ) 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisrem in configuration namelist' ) 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._wp ! END SUBROUTINE p4z_rem_init INTEGER FUNCTION p4z_rem_alloc() !!---------------------------------------------------------------------- !! *** ROUTINE p4z_rem_alloc *** !!---------------------------------------------------------------------- ALLOCATE( denitr(jpi,jpj,jpk), STAT=p4z_rem_alloc ) ! IF( p4z_rem_alloc /= 0 ) CALL ctl_stop( 'STOP', 'p4z_rem_alloc: failed to allocate arrays' ) ! END FUNCTION p4z_rem_alloc !!====================================================================== END MODULE p4zrem