MODULE p4zfechem !!====================================================================== !! *** MODULE p4zfechem *** !! TOP : PISCES Compute iron chemistry and scavenging !!====================================================================== !! History : 3.5 ! 2012-07 (O. Aumont, A. Tagliabue, C. Ethe) Original code !! 3.6 ! 2015-05 (O. Aumont) PISCES quota !!---------------------------------------------------------------------- !! p4z_fechem : Compute remineralization/scavenging of iron !! p4z_fechem_init : Initialisation of parameters for remineralisation !! p4z_fechem_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 p4zbc ! Boundary conditions from sediments USE prtctl_trc ! print control for debugging USE iom ! I/O manager IMPLICIT NONE PRIVATE PUBLIC p4z_fechem ! called in p4zbio.F90 PUBLIC p4z_fechem_init ! called in trcsms_pisces.F90 LOGICAL :: ln_ligvar !: boolean for variable ligand concentration following Tagliabue and voelker REAL(wp), PUBLIC :: xlam1 !: scavenging rate of Iron REAL(wp), PUBLIC :: xlamdust !: scavenging rate of Iron by dust REAL(wp), PUBLIC :: ligand !: ligand concentration in the ocean REAL(wp), PUBLIC :: kfep !: rate constant for nanoparticle formation !! * 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_fechem( kt, knt, Kbb, Kmm, Krhs ) !!--------------------------------------------------------------------- !! *** ROUTINE p4z_fechem *** !! !! ** Purpose : Compute remineralization/scavenging of iron !! !! ** Method : A simple chemistry model of iron from Aumont and Bopp (2006) !! based on one ligand and one inorganic form !!--------------------------------------------------------------------- INTEGER, INTENT(in) :: kt, knt ! ocean time step INTEGER, INTENT(in) :: Kbb, Kmm, Krhs ! time level indices ! INTEGER :: ji, jj, jk, jic, jn REAL(wp) :: zdep, zlam1a, zlam1b, zlamfac REAL(wp) :: zkeq, zfeequi, zfesatur, zfecoll, fe3sol REAL(wp) :: zdenom1, zscave, zaggdfea, zaggdfeb, zcoag REAL(wp) :: ztrc, zdust REAL(wp) :: zdenom2 REAL(wp) :: zzFeL1, zzFeL2, zzFe2, zzFeP, zzFe3, zzstrn2 REAL(wp) :: zrum, zcodel, zargu, zlight REAL(wp) :: zkox, zkph1, zkph2, zph, zionic, ztligand REAL(wp) :: za, zb, zc, zkappa1, zkappa2, za0, za1, za2 REAL(wp) :: zxs, zfunc, zp, zq, zd, zr, zphi, zfff, zp3, zq2 REAL(wp) :: ztfe, zoxy, zhplus, zxlam REAL(wp) :: zaggliga, zaggligb REAL(wp) :: dissol, zligco REAL(wp) :: zrfact2 CHARACTER (len=25) :: charout REAL(wp), DIMENSION(jpi,jpj,jpk) :: zTL1, zFe3, ztotlig, precip, zFeL1 REAL(wp), DIMENSION(jpi,jpj,jpk) :: zcoll3d, zscav3d, zlcoll3d !!--------------------------------------------------------------------- ! IF( ln_timing ) CALL timing_start('p4z_fechem') ! ! Total ligand concentration : Ligands can be chosen to be constant or variable ! Parameterization from Tagliabue and Voelker (2011) ! ------------------------------------------------- IF( ln_ligvar ) THEN ztotlig(:,:,:) = 0.09 * tr(:,:,:,jpdoc,Kbb) * 1E6 + ligand * 1E9 ztotlig(:,:,:) = MIN( ztotlig(:,:,:), 10. ) ELSE IF( ln_ligand ) THEN ; ztotlig(:,:,:) = tr(:,:,:,jplgw,Kbb) * 1E9 ELSE ; ztotlig(:,:,:) = ligand * 1E9 ENDIF ENDIF ! ------------------------------------------------------------ ! from Aumont and Bopp (2006) ! This model is based on one ligand and Fe' ! Chemistry is supposed to be fast enough to be at equilibrium ! ------------------------------------------------------------ DO_3D_11_11( 1, jpkm1 ) zTL1(ji,jj,jk) = ztotlig(ji,jj,jk) zkeq = fekeq(ji,jj,jk) zfesatur = zTL1(ji,jj,jk) * 1E-9 ztfe = tr(ji,jj,jk,jpfer,Kbb) ! Fe' is the root of a 2nd order polynom zFe3 (ji,jj,jk) = ( -( 1. + zfesatur * zkeq - zkeq * ztfe ) & & + SQRT( ( 1. + zfesatur * zkeq - zkeq * ztfe )**2 & & + 4. * ztfe * zkeq) ) / ( 2. * zkeq ) zFe3 (ji,jj,jk) = zFe3(ji,jj,jk) * 1E9 zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) * 1E9 - zFe3(ji,jj,jk) ) END_3D ! zdust = 0. ! if no dust available DO_3D_11_11( 1, jpkm1 ) ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water. ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]). ! Scavenging onto dust is also included as evidenced from the DUNE experiments. ! -------------------------------------------------------------------------------------- zhplus = max( rtrn, hi(ji,jj,jk) ) fe3sol = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2 & & + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4) & & + fesol(ji,jj,jk,5) / zhplus ) ! zfeequi = zFe3(ji,jj,jk) * 1E-9 zhplus = max( rtrn, hi(ji,jj,jk) ) fe3sol = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2 & & + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4) & & + fesol(ji,jj,jk,5) / zhplus ) zfecoll = 0.5 * zFeL1(ji,jj,jk) * 1E-9 ! precipitation of Fe3+, creation of nanoparticles precip(ji,jj,jk) = MAX( 0., ( zFe3(ji,jj,jk) * 1E-9 - fe3sol ) ) * kfep * xstep ! ztrc = ( tr(ji,jj,jk,jppoc,Kbb) + tr(ji,jj,jk,jpgoc,Kbb) + tr(ji,jj,jk,jpcal,Kbb) + tr(ji,jj,jk,jpgsi,Kbb) ) * 1.e6 IF( ll_dust ) zdust = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk) & & * EXP( -gdept(ji,jj,jk,Kmm) / 540. ) IF (ln_ligand) THEN zxlam = xlam1 * MAX( 1.E-3, EXP(-2 * etot(ji,jj,jk) / 10. ) * (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) )) ELSE zxlam = xlam1 * 1.0 ENDIF zlam1b = 3.e-5 + xlamdust * zdust + zxlam * ztrc zscave = zfeequi * zlam1b * xstep ! Compute the different ratios for scavenging of iron ! to later allocate scavenged iron to the different organic pools ! --------------------------------------------------------- zdenom1 = zxlam * tr(ji,jj,jk,jppoc,Kbb) / zlam1b zdenom2 = zxlam * tr(ji,jj,jk,jpgoc,Kbb) / zlam1b ! Increased scavenging for very high iron concentrations found near the coasts ! due to increased lithogenic particles and let say it is unknown processes (precipitation, ...) ! ----------------------------------------------------------- zlamfac = MAX( 0.e0, ( gphit(ji,jj) + 55.) / 30. ) zlamfac = MIN( 1. , zlamfac ) zdep = MIN( 1., 1000. / gdept(ji,jj,jk,Kmm) ) zcoag = 1E-4 * ( 1. - zlamfac ) * zdep * xstep * tr(ji,jj,jk,jpfer,Kbb) ! Compute the coagulation of colloidal iron. This parameterization ! could be thought as an equivalent of colloidal pumping. ! It requires certainly some more work as it is very poorly constrained. ! ---------------------------------------------------------------- zlam1a = ( 0.369 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4 * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk) & & + ( 114. * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) ) zaggdfea = zlam1a * xstep * zfecoll ! zlam1b = 3.53E3 * tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk) zaggdfeb = zlam1b * xstep * zfecoll ! tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb & & - zcoag - precip(ji,jj,jk) tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * zdenom1 + zaggdfea tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * zdenom2 + zaggdfeb zscav3d(ji,jj,jk) = zscave zcoll3d(ji,jj,jk) = zaggdfea + zaggdfeb ! END_3D ! ! Define the bioavailable fraction of iron ! ---------------------------------------- biron(:,:,:) = tr(:,:,:,jpfer,Kbb) ! IF( ln_ligand ) THEN ! DO_3D_11_11( 1, jpkm1 ) zlam1a = ( 0.369 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4 * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk) & & + ( 114. * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) ) ! zlam1b = 3.53E3 * tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk) zligco = 0.5 * tr(ji,jj,jk,jplgw,Kmm) zaggliga = zlam1a * xstep * zligco zaggligb = zlam1b * xstep * zligco tr(ji,jj,jk,jplgw,Krhs) = tr(ji,jj,jk,jplgw,Krhs) - zaggliga - zaggligb zlcoll3d(ji,jj,jk) = zaggliga + zaggligb END_3D ! plig(:,:,:) = MAX( 0., ( ( zFeL1(:,:,:) * 1E-9 ) / ( tr(:,:,:,jpfer,Kbb) +rtrn ) ) ) ! ENDIF ! Output of some diagnostics variables ! --------------------------------- IF( lk_iomput ) THEN IF( knt == nrdttrc ) THEN zrfact2 = 1.e3 * rfact2r ! conversion from mol/L/timestep into mol/m3/s IF( iom_use("Fe3") ) THEN zFe3(:,:,jpk) = 0. ; CALL iom_put("Fe3" , zFe3(:,:,:) * tmask(:,:,:) ) ! Fe3+ ENDIF IF( iom_use("FeL1") ) THEN zFeL1(:,:,jpk) = 0. ; CALL iom_put("FeL1", zFeL1(:,:,:) * tmask(:,:,:) ) ! FeL1 ENDIF IF( iom_use("TL1") ) THEN zTL1(:,:,jpk) = 0. ; CALL iom_put("TL1" , zTL1(:,:,:) * tmask(:,:,:) ) ! TL1 ENDIF IF( iom_use("Totlig") ) CALL iom_put("Totlig" , ztotlig(:,:,:) * tmask(:,:,:) ) ! TL IF( iom_use("Biron") ) CALL iom_put("Biron" , biron (:,:,:) * 1e9 * tmask(:,:,:) ) ! biron IF( iom_use("FESCAV") ) THEN zscav3d (:,:,jpk) = 0. ; CALL iom_put("FESCAV" , zscav3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) ENDIF IF( iom_use("FECOLL") ) THEN zcoll3d (:,:,jpk) = 0. ; CALL iom_put("FECOLL" , zcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) ENDIF IF( iom_use("LGWCOLL")) THEN zlcoll3d(:,:,jpk) = 0. ; CALL iom_put("LGWCOLL", zlcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) ENDIF ENDIF ENDIF IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) WRITE(charout, FMT="('fechem')") CALL prt_ctl_trc_info(charout) CALL prt_ctl_trc(tab4d=tr(:,:,:,:,Krhs), mask=tmask, clinfo=ctrcnm) ENDIF ! IF( ln_timing ) CALL timing_stop('p4z_fechem') ! END SUBROUTINE p4z_fechem SUBROUTINE p4z_fechem_init !!---------------------------------------------------------------------- !! *** ROUTINE p4z_fechem_init *** !! !! ** Purpose : Initialization of iron chemistry parameters !! !! ** Method : Read the nampisfer namelist and check the parameters !! called at the first timestep !! !! ** input : Namelist nampisfer !! !!---------------------------------------------------------------------- INTEGER :: ios ! Local integer !! NAMELIST/nampisfer/ ln_ligvar, xlam1, xlamdust, ligand, kfep !!---------------------------------------------------------------------- ! IF(lwp) THEN WRITE(numout,*) WRITE(numout,*) 'p4z_rem_init : Initialization of iron chemistry parameters' WRITE(numout,*) '~~~~~~~~~~~~' ENDIF ! READ ( numnatp_ref, nampisfer, IOSTAT = ios, ERR = 901) 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisfer in reference namelist' ) READ ( numnatp_cfg, nampisfer, IOSTAT = ios, ERR = 902 ) 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisfer in configuration namelist' ) IF(lwm) WRITE( numonp, nampisfer ) IF(lwp) THEN ! control print WRITE(numout,*) ' Namelist : nampisfer' WRITE(numout,*) ' variable concentration of ligand ln_ligvar =', ln_ligvar WRITE(numout,*) ' scavenging rate of Iron xlam1 =', xlam1 WRITE(numout,*) ' scavenging rate of Iron by dust xlamdust =', xlamdust WRITE(numout,*) ' ligand concentration in the ocean ligand =', ligand WRITE(numout,*) ' rate constant for nanoparticle formation kfep =', kfep ENDIF ! END SUBROUTINE p4z_fechem_init !!====================================================================== END MODULE p4zfechem