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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 ! 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
REAL(wp), PUBLIC :: scaveff !: Fraction of scavenged iron that is considered as being subject to solubilization
!! * Substitutions
# include "do_loop_substitute.h90"
# include "domzgr_substitute.h90"
!!----------------------------------------------------------------------
!! NEMO/TOP 4.0 , NEMO Consortium (2018)
!! $Id: p4zfechem.F90 15459 2021-10-29 08:19:18Z cetlod $
!! 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) :: zlam1a, zlam1b
REAL(wp) :: zkeq, zfesatur, fe3sol, zligco
REAL(wp) :: zscave, zaggdfea, zaggdfeb, ztrc, zdust, zklight
REAL(wp) :: ztfe, zhplus, zxlam, zaggliga, zaggligb
REAL(wp) :: zprecip, zprecipno3, zconsfe, za1
REAL(wp) :: zrfact2
CHARACTER (len=25) :: charout
REAL(wp), DIMENSION(A2D(0),jpk) :: zTL1, zFe3, ztotlig, zfeprecip, zFeL1, zfecoll
REAL(wp), DIMENSION(A2D(0),jpk) :: zcoll3d, zscav3d, zlcoll3d
REAL(wp), ALLOCATABLE, DIMENSION(:,:,:) :: zw3d
!!---------------------------------------------------------------------
!
IF( ln_timing ) CALL timing_start('p4z_fechem')
!
! zFe3 (:,:,jpk) = 0.
! zFeL1 (:,:,jpk) = 0.
! zTL1 (:,:,jpk) = 0.
! zfeprecip(:,:,jpk) = 0.
! zcoll3d (:,:,jpk) = 0.
! zscav3d (:,:,jpk) = 0.
! zlcoll3d (:,:,jpk) = 0.
! zfecoll (:,:,jpk) = 0.
! xfecolagg(:,:,jpk) = 0.
! xcoagfe (:,:,jpk) = 0.
!
! Total ligand concentration : Ligands can be chosen to be constant or variable
! Parameterization from Pham and Ito (2018)
! -------------------------------------------------
DO_3D( 0, 0, 0, 0, 1, jpkm1)
xfecolagg(ji,jj,jk) = ligand * 1E9 + MAX(0., chemo2(ji,jj,jk) - tr(ji,jj,jk,jpoxy,Kbb) ) / 400.E-6
END_3D
DO_3D( 0, 0, 0, 0, 1, jpkm1)
ztotlig(ji,jj,jk) = 0.09 * 0.667 * tr(ji,jj,jk,jpdoc,Kbb) * 1E6 + xfecolagg(ji,jj,jk)
ztotlig(ji,jj,jk) = MIN( ztotlig(ji,jj,jk), 10. )
END_3D
IF( ln_ligand ) THEN
DO_3D( 0, 0, 0, 0, 1, jpkm1)
ztotlig(ji,jj,jk) = tr(ji,jj,jk,jplgw,Kbb) * 1E9
END_3D
ELSE
ztotlig(:,:,:) = ligand * 1E9
ENDIF
ENDIF
! ------------------------------------------------------------
! from Aumont and Bopp (2006)
! This model is based on one ligand, Fe2+ and Fe3+
! Chemistry is supposed to be fast enough to be at equilibrium
! ------------------------------------------------------------
DO_3D( 0, 0, 0, 0, 1, jpkm1)
zTL1(ji,jj,jk) = ztotlig(ji,jj,jk)
zkeq = fekeq(ji,jj,jk)
zklight = 4.77E-7 * etot(ji,jj,jk) * 0.5 / ( 10**(-6.3) )
zconsfe = consfe3(ji,jj,jk) / ( 10**(-6.3) )
zfesatur = zTL1(ji,jj,jk) * 1E-9
ztfe = (1.0 + zklight) * tr(ji,jj,jk,jpfer,Kbb)
! Fe' is the root of a 2nd order polynom
za1 = 1. + zfesatur * zkeq + zklight + zconsfe - zkeq * tr(ji,jj,jk,jpfer,Kbb)
zFe3 (ji,jj,jk) = ( -1 * za1 + SQRT( za1**2 + 4. * ztfe * zkeq) ) / ( 2. * zkeq + rtrn )
zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) - zFe3(ji,jj,jk) )
END_3D
!
DO_3D( 0, 0, 0, 0, 1, jpkm1)
plig(ji,jj,jk) = MAX( 0., ( zFeL1(ji,jj,jk) / ( tr(ji,jj,jk,jpfer,Kbb) + rtrn ) ) )
END_3D
!
zdust = 0. ! if no dust available
! Computation of the colloidal fraction that is subjecto to coagulation
! The assumption is that 50% of complexed iron is colloidal. Furthermore
! The refractory part is supposed to be non sticky. The refractory
! fraction is supposed to equal to the background concentration +
! the fraction that accumulates in the deep ocean. AOU is taken as a
! proxy of that accumulation following numerous studies showing
! some relationship between weak ligands and AOU.
! An issue with that parameterization is that when ligands are not
! prognostic or non variable, all the colloidal fraction is supposed
! to coagulate
! ----------------------------------------------------------------------
IF (ln_ligand) THEN
DO_3D( 0, 0, 0, 0, 1, jpkm1)
zfecoll(ji,jj,jk) = 0.5 * zFeL1(ji,jj,jk) * MAX(0., tr(ji,jj,jk,jplgw,Kbb) - xfecolagg(ji,jj,jk) * 1.0E-9 ) &
& / ( tr(ji,jj,jk,jplgw,Kbb) + rtrn )
END_3D
DO_3D( 0, 0, 0, 0, 1, jpkm1)
!Ch Buguuuugggggggg : tr(ji,jj,jk,jplgw ?????????
zfecoll(ji,jj,jk) = 0.5 * zFeL1(ji,jj,jk) * MAX(0., tr(ji,jj,jk,jplgw,Kbb) - xfecolagg(ji,jj,jk) * 1.0E-9 ) &
& / ( tr(ji,jj,jk,jplgw,Kbb) + rtrn )
END_3D
DO_3D( 0, 0, 0, 0, 1, jpkm1)
zfecoll(ji,jj,jk) = 0.5 * zFeL1(ji,jj,jk)
END_3D
DO_3D( 0, 0, 0, 0, 1, jpkm1)
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! 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 )
!
! precipitation of Fe3+, creation of nanoparticles
zprecip = MAX( 0., ( zFe3(ji,jj,jk) - fe3sol ) ) * kfep * xstep * ( 1.0 - nitrfac(ji,jj,jk) )
! Precipitation of Fe2+ due to oxidation by NO3 (Croot et al., 2019)
! This occurs in anoxic waters only
zprecipno3 = 2.0 * 130.0 * tr(ji,jj,jk,jpno3,Kbb) * nitrfac(ji,jj,jk) * xstep * zFe3(ji,jj,jk)
!
zfeprecip(ji,jj,jk) = zprecip + zprecipno3
!
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
ztrc = MAX( rtrn, ztrc )
IF( ll_dust ) zdust = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk)
zxlam = MAX( 1.E-3, (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) ))
zlam1b = 3.e-5 + ( xlamdust * zdust + xlam1 * ztrc ) * zxlam
zscave = zFe3(ji,jj,jk) * zlam1b * xstep
! 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 = ( 12.0 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 9.05 * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk) &
& + ( 2.49 * tr(ji,jj,jk,jppoc,Kbb) ) &
& + ( 127.8 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 725.7 * tr(ji,jj,jk,jppoc,Kbb) )
zaggdfea = zlam1a * xstep * zfecoll(ji,jj,jk)
!
zlam1b = ( 1.94 * xdiss(ji,jj,jk) + 1.37 ) * tr(ji,jj,jk,jpgoc,Kbb)
zaggdfeb = zlam1b * xstep * zfecoll(ji,jj,jk)
xcoagfe(ji,jj,jk) = zlam1a + zlam1b
!
tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb &
& - zfeprecip(ji,jj,jk)
tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc
tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc
! Precipitated iron is supposed to be permanently lost.
! Scavenged iron is supposed to be released back to seawater
! when POM is solubilized. This is highly uncertain as probably
! a significant part of it may be rescavenged back onto
! the particles. An efficiency factor is applied that is read
! in the namelist.
! See for instance Tagliabue et al. (2019).
! Aggregated FeL is considered as biogenic Fe as it
! probably remains complexed when the particle is solubilized.
! -------------------------------------------------------------
tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zaggdfea
tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zaggdfeb
!
zscav3d(ji,jj,jk) = zscave
zcoll3d(ji,jj,jk) = zaggdfea + zaggdfeb
!
END_3D
!
! Define the bioavailable fraction of iron
! ----------------------------------------
DO_3D( 0, 0, 0, 0, 1, jpkm1)
biron(ji,jj,jk) = tr(ji,jj,jk,jpfer,Kbb)
END_3D
!
! Output of some diagnostics variables
! ---------------------------------
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IF( lk_iomput .AND. knt == nrdttrc ) THEN
!
ALLOCATE( zw3d(A2D(0),jpk) ) ; zw3d(A2D(0),jpk) = 0._wp
zrfact2 = 1.e3 * rfact2r ! conversion from mol/L/timestep into mol/m3/s
!
IF( iom_use ( "Fe3" ) ) THEN ! Fe3+
zw3d(A2D(0),1:jpkm1) = zFe3(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1)
CALL iom_put( "Fe3", zw3d )
ENDIF
!
IF( iom_use ( "FeL1" ) ) THEN ! FeL1
zw3d(A2D(0),1:jpkm1) = zFeL1(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1)
CALL iom_put( "FeL1", zw3d )
ENDIF
!
IF( iom_use ( "TL1" ) ) THEN ! TL1
zw3d(A2D(0),1:jpkm1) = zTL1(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1)
CALL iom_put( "TL1", zw3d )
ENDIF
!
IF( iom_use ( "Totlig" ) ) THEN ! Totlig
zw3d(A2D(0),1:jpkm1) = ztotlig(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1)
CALL iom_put( "Totlig", zw3d )
ENDIF
!
IF( iom_use ( "Biron" ) ) THEN ! biron
zw3d(A2D(0),1:jpkm1) = biron(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1)
CALL iom_put( "Biron", zw3d )
ENDIF
!
IF( iom_use ( "FESCAV" ) ) THEN ! FESCAV
zw3d(A2D(0),1:jpkm1) = zscav3d(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1) * zrfact2
CALL iom_put( "FESCAV", zw3d )
ENDIF
!
IF( iom_use ( "FECOLL" ) ) THEN ! FECOLL
zw3d(A2D(0),1:jpkm1) = zcoll3d(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1) * zrfact2
CALL iom_put( "FECOLL", zw3d )
ENDIF
!
IF( iom_use ( "FEPREC" ) ) THEN ! FEPREC
zw3d(A2D(0),1:jpkm1) = zfeprecip(A2D(0),1:jpkm1) * tmask(A2D(0),1:jpkm1) * zrfact2
CALL iom_put( "FEPREC", zw3d )
ENDIF
!
DEALLOCATE( zw3d )
!
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ENDIF
IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging)
WRITE(charout, FMT="('fechem')")
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_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, scaveff
!!----------------------------------------------------------------------
!
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
WRITE(numout,*) ' Scavenged iron that is added to POFe scaveff =', scaveff
ENDIF
!
END SUBROUTINE p4z_fechem_init
!!======================================================================
END MODULE p4zfechem