[3443] | 1 | MODULE p4zfechem |
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| 2 | !!====================================================================== |
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| 3 | !! *** MODULE p4zfechem *** |
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| 4 | !! TOP : PISCES Compute iron chemistry and scavenging |
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| 5 | !!====================================================================== |
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[3461] | 6 | !! History : 3.5 ! 2012-07 (O. Aumont, A. Tagliabue, C. Ethe) Original code |
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[7646] | 7 | !! 3.6 ! 2015-05 (O. Aumont) PISCES quota |
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[3443] | 8 | !!---------------------------------------------------------------------- |
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[9169] | 9 | !! p4z_fechem : Compute remineralization/scavenging of iron |
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| 10 | !! p4z_fechem_init : Initialisation of parameters for remineralisation |
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| 11 | !! p4z_fechem_alloc : Allocate remineralisation variables |
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[3443] | 12 | !!---------------------------------------------------------------------- |
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[9169] | 13 | USE oce_trc ! shared variables between ocean and passive tracers |
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| 14 | USE trc ! passive tracers common variables |
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| 15 | USE sms_pisces ! PISCES Source Minus Sink variables |
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| 16 | USE p4zche ! chemical model |
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[12377] | 17 | USE p4zbc ! Boundary conditions from sediments |
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[13286] | 18 | USE prtctl ! print control for debugging |
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[9169] | 19 | USE iom ! I/O manager |
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[3443] | 20 | |
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| 21 | IMPLICIT NONE |
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| 22 | PRIVATE |
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| 23 | |
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[9169] | 24 | PUBLIC p4z_fechem ! called in p4zbio.F90 |
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| 25 | PUBLIC p4z_fechem_init ! called in trcsms_pisces.F90 |
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[3443] | 26 | |
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[9169] | 27 | LOGICAL :: ln_ligvar !: boolean for variable ligand concentration following Tagliabue and voelker |
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| 28 | REAL(wp), PUBLIC :: xlam1 !: scavenging rate of Iron |
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| 29 | REAL(wp), PUBLIC :: xlamdust !: scavenging rate of Iron by dust |
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| 30 | REAL(wp), PUBLIC :: ligand !: ligand concentration in the ocean |
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| 31 | REAL(wp), PUBLIC :: kfep !: rate constant for nanoparticle formation |
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[15459] | 32 | REAL(wp), PUBLIC :: scaveff !: Fraction of scavenged iron that is considered as being subject to solubilization |
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[3443] | 33 | |
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[12377] | 34 | !! * Substitutions |
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| 35 | # include "do_loop_substitute.h90" |
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[13237] | 36 | # include "domzgr_substitute.h90" |
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[3443] | 37 | !!---------------------------------------------------------------------- |
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[10067] | 38 | !! NEMO/TOP 4.0 , NEMO Consortium (2018) |
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[10069] | 39 | !! $Id$ |
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[10068] | 40 | !! Software governed by the CeCILL license (see ./LICENSE) |
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[3443] | 41 | !!---------------------------------------------------------------------- |
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| 42 | CONTAINS |
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| 43 | |
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[12377] | 44 | SUBROUTINE p4z_fechem( kt, knt, Kbb, Kmm, Krhs ) |
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[3443] | 45 | !!--------------------------------------------------------------------- |
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| 46 | !! *** ROUTINE p4z_fechem *** |
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| 47 | !! |
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| 48 | !! ** Purpose : Compute remineralization/scavenging of iron |
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| 49 | !! |
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[10401] | 50 | !! ** Method : A simple chemistry model of iron from Aumont and Bopp (2006) |
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| 51 | !! based on one ligand and one inorganic form |
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[3443] | 52 | !!--------------------------------------------------------------------- |
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[9169] | 53 | INTEGER, INTENT(in) :: kt, knt ! ocean time step |
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[12377] | 54 | INTEGER, INTENT(in) :: Kbb, Kmm, Krhs ! time level indices |
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[3443] | 55 | ! |
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[7646] | 56 | INTEGER :: ji, jj, jk, jic, jn |
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[15459] | 57 | REAL(wp) :: zlam1a, zlam1b |
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| 58 | REAL(wp) :: zkeq, zfesatur, fe3sol, zligco |
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| 59 | REAL(wp) :: zscave, zaggdfea, zaggdfeb, ztrc, zdust, zklight |
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| 60 | REAL(wp) :: ztfe, zhplus, zxlam, zaggliga, zaggligb |
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| 61 | REAL(wp) :: zprecip, zprecipno3, zconsfe, za1 |
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| 62 | REAL(wp) :: zrfact2 |
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[7646] | 63 | CHARACTER (len=25) :: charout |
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[15459] | 64 | REAL(wp), DIMENSION(jpi,jpj,jpk) :: zTL1, zFe3, ztotlig, zfeprecip, zFeL1, zfecoll |
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[10362] | 65 | REAL(wp), DIMENSION(jpi,jpj,jpk) :: zcoll3d, zscav3d, zlcoll3d |
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[3443] | 66 | !!--------------------------------------------------------------------- |
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| 67 | ! |
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[9124] | 68 | IF( ln_timing ) CALL timing_start('p4z_fechem') |
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[3443] | 69 | ! |
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[15459] | 70 | zFe3 (:,:,jpk) = 0. |
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| 71 | zFeL1 (:,:,jpk) = 0. |
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| 72 | zTL1 (:,:,jpk) = 0. |
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| 73 | zfeprecip(:,:,jpk) = 0. |
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| 74 | zcoll3d (:,:,jpk) = 0. |
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| 75 | zscav3d (:,:,jpk) = 0. |
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| 76 | zlcoll3d (:,:,jpk) = 0. |
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| 77 | zfecoll (:,:,jpk) = 0. |
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| 78 | xfecolagg(:,:,jpk) = 0. |
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| 79 | xcoagfe (:,:,jpk) = 0. |
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| 80 | ! |
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[3443] | 81 | ! Total ligand concentration : Ligands can be chosen to be constant or variable |
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[15459] | 82 | ! Parameterization from Pham and Ito (2018) |
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[3443] | 83 | ! ------------------------------------------------- |
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[15459] | 84 | xfecolagg(:,:,:) = ligand * 1E9 + MAX(0., chemo2(:,:,:) - tr(:,:,:,jpoxy,Kbb) ) / 400.E-6 |
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[3443] | 85 | IF( ln_ligvar ) THEN |
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[15459] | 86 | ztotlig(:,:,:) = 0.09 * 0.667 * tr(:,:,:,jpdoc,Kbb) * 1E6 + xfecolagg(:,:,:) |
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[7753] | 87 | ztotlig(:,:,:) = MIN( ztotlig(:,:,:), 10. ) |
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[3443] | 88 | ELSE |
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[12377] | 89 | IF( ln_ligand ) THEN ; ztotlig(:,:,:) = tr(:,:,:,jplgw,Kbb) * 1E9 |
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[15459] | 90 | ELSE ; ztotlig(:,:,:) = ligand * 1E9 |
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[7646] | 91 | ENDIF |
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[3443] | 92 | ENDIF |
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| 93 | |
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[10401] | 94 | ! ------------------------------------------------------------ |
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| 95 | ! from Aumont and Bopp (2006) |
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[15459] | 96 | ! This model is based on one ligand, Fe2+ and Fe3+ |
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[10401] | 97 | ! Chemistry is supposed to be fast enough to be at equilibrium |
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| 98 | ! ------------------------------------------------------------ |
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[15090] | 99 | DO_3D( nn_hls, nn_hls, nn_hls, nn_hls, 1, jpkm1) |
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[15459] | 100 | zTL1(ji,jj,jk) = ztotlig(ji,jj,jk) |
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| 101 | zkeq = fekeq(ji,jj,jk) |
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| 102 | zklight = 4.77E-7 * etot(ji,jj,jk) * 0.5 / ( 10**(-6.3) ) |
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| 103 | zconsfe = consfe3(ji,jj,jk) / ( 10**(-6.3) ) |
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| 104 | zfesatur = zTL1(ji,jj,jk) * 1E-9 |
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| 105 | ztfe = (1.0 + zklight) * tr(ji,jj,jk,jpfer,Kbb) |
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| 106 | ! Fe' is the root of a 2nd order polynom |
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| 107 | za1 = 1. + zfesatur * zkeq + zklight + zconsfe - zkeq * tr(ji,jj,jk,jpfer,Kbb) |
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| 108 | zFe3 (ji,jj,jk) = ( -1 * za1 + SQRT( za1**2 + 4. * ztfe * zkeq) ) / ( 2. * zkeq + rtrn ) |
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| 109 | zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) - zFe3(ji,jj,jk) ) |
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[12377] | 110 | END_3D |
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[15459] | 111 | ! |
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| 112 | plig(:,:,:) = MAX( 0., ( zFeL1(:,:,:) / ( tr(:,:,:,jpfer,Kbb) + rtrn ) ) ) |
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| 113 | ! |
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| 114 | zdust = 0. ! if no dust available |
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[7646] | 115 | |
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[15459] | 116 | ! Computation of the colloidal fraction that is subjecto to coagulation |
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| 117 | ! The assumption is that 50% of complexed iron is colloidal. Furthermore |
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| 118 | ! The refractory part is supposed to be non sticky. The refractory |
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| 119 | ! fraction is supposed to equal to the background concentration + |
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| 120 | ! the fraction that accumulates in the deep ocean. AOU is taken as a |
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| 121 | ! proxy of that accumulation following numerous studies showing |
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| 122 | ! some relationship between weak ligands and AOU. |
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| 123 | ! An issue with that parameterization is that when ligands are not |
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| 124 | ! prognostic or non variable, all the colloidal fraction is supposed |
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| 125 | ! to coagulate |
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| 126 | ! ---------------------------------------------------------------------- |
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| 127 | IF (ln_ligand) THEN |
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| 128 | zfecoll(:,:,:) = 0.5 * zFeL1(:,:,:) * MAX(0., tr(:,:,:,jplgw,Kbb) - xfecolagg(:,:,:) * 1.0E-9 ) / ( tr(:,:,:,jplgw,Kbb) + rtrn ) |
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| 129 | ELSE |
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| 130 | IF (ln_ligvar) THEN |
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| 131 | zfecoll(:,:,:) = 0.5 * zFeL1(:,:,:) * MAX(0., tr(:,:,:,jplgw,Kbb) - xfecolagg(:,:,:) * 1.0E-9 ) / ( tr(:,:,:,jplgw,Kbb) + rtrn ) |
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| 132 | ELSE |
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| 133 | zfecoll(:,:,:) = 0.5 * zFeL1(:,:,:) |
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| 134 | ENDIF |
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| 135 | ENDIF |
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| 136 | |
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[15090] | 137 | DO_3D( nn_hls, nn_hls, nn_hls, nn_hls, 1, jpkm1) |
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[12377] | 138 | ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water. |
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| 139 | ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]). |
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| 140 | ! Scavenging onto dust is also included as evidenced from the DUNE experiments. |
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| 141 | ! -------------------------------------------------------------------------------------- |
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| 142 | zhplus = max( rtrn, hi(ji,jj,jk) ) |
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| 143 | fe3sol = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2 & |
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| 144 | & + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4) & |
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| 145 | & + fesol(ji,jj,jk,5) / zhplus ) |
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| 146 | ! |
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| 147 | ! precipitation of Fe3+, creation of nanoparticles |
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[15459] | 148 | zprecip = MAX( 0., ( zFe3(ji,jj,jk) - fe3sol ) ) * kfep * xstep * ( 1.0 - nitrfac(ji,jj,jk) ) |
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| 149 | ! Precipitation of Fe2+ due to oxidation by NO3 (Croot et al., 2019) |
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| 150 | ! This occurs in anoxic waters only |
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| 151 | zprecipno3 = 2.0 * 130.0 * tr(ji,jj,jk,jpno3,Kbb) * nitrfac(ji,jj,jk) * xstep * zFe3(ji,jj,jk) |
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[12377] | 152 | ! |
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[15459] | 153 | zfeprecip(ji,jj,jk) = zprecip + zprecipno3 |
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| 154 | ! |
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[12377] | 155 | 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 |
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[15459] | 156 | ztrc = MAX( rtrn, ztrc ) |
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| 157 | IF( ll_dust ) zdust = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk) |
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| 158 | zxlam = MAX( 1.E-3, (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) )) |
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| 159 | zlam1b = 3.e-5 + ( xlamdust * zdust + xlam1 * ztrc ) * zxlam |
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| 160 | zscave = zFe3(ji,jj,jk) * zlam1b * xstep |
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[3443] | 161 | |
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[12377] | 162 | ! Compute the coagulation of colloidal iron. This parameterization |
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| 163 | ! could be thought as an equivalent of colloidal pumping. |
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| 164 | ! It requires certainly some more work as it is very poorly constrained. |
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| 165 | ! ---------------------------------------------------------------- |
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[15459] | 166 | zlam1a = ( 12.0 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 9.05 * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk) & |
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| 167 | & + ( 2.49 * tr(ji,jj,jk,jppoc,Kbb) ) & |
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| 168 | & + ( 127.8 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 725.7 * tr(ji,jj,jk,jppoc,Kbb) ) |
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| 169 | zaggdfea = zlam1a * xstep * zfecoll(ji,jj,jk) |
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| 170 | ! |
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| 171 | zlam1b = ( 1.94 * xdiss(ji,jj,jk) + 1.37 ) * tr(ji,jj,jk,jpgoc,Kbb) |
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| 172 | zaggdfeb = zlam1b * xstep * zfecoll(ji,jj,jk) |
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| 173 | xcoagfe(ji,jj,jk) = zlam1a + zlam1b |
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[12377] | 174 | ! |
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| 175 | tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb & |
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[15459] | 176 | & - zfeprecip(ji,jj,jk) |
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| 177 | |
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| 178 | tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc |
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| 179 | tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc |
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| 180 | |
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| 181 | |
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| 182 | ! Precipitated iron is supposed to be permanently lost. |
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| 183 | ! Scavenged iron is supposed to be released back to seawater |
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| 184 | ! when POM is solubilized. This is highly uncertain as probably |
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| 185 | ! a significant part of it may be rescavenged back onto |
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| 186 | ! the particles. An efficiency factor is applied that is read |
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| 187 | ! in the namelist. |
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| 188 | ! See for instance Tagliabue et al. (2019). |
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| 189 | ! Aggregated FeL is considered as biogenic Fe as it |
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| 190 | ! probably remains complexed when the particle is solubilized. |
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| 191 | ! ------------------------------------------------------------- |
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| 192 | tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zaggdfea |
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| 193 | tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zaggdfeb |
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| 194 | ! |
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| 195 | zscav3d(ji,jj,jk) = zscave |
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| 196 | zcoll3d(ji,jj,jk) = zaggdfea + zaggdfeb |
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[12377] | 197 | ! |
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| 198 | END_3D |
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[3443] | 199 | ! |
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[3446] | 200 | ! Define the bioavailable fraction of iron |
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| 201 | ! ---------------------------------------- |
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[12377] | 202 | biron(:,:,:) = tr(:,:,:,jpfer,Kbb) |
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[7646] | 203 | ! |
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[3443] | 204 | ! Output of some diagnostics variables |
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| 205 | ! --------------------------------- |
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[15459] | 206 | IF( lk_iomput .AND. knt == nrdttrc ) THEN |
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| 207 | zrfact2 = 1.e3 * rfact2r ! conversion from mol/L/timestep into mol/m3/s |
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| 208 | IF( iom_use("Fe3") ) CALL iom_put("Fe3" , zFe3 (:,:,:) * tmask(:,:,:) ) ! Fe3+ |
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| 209 | IF( iom_use("FeL1") ) CALL iom_put("FeL1" , zFeL1 (:,:,:) * tmask(:,:,:) ) ! FeL1 |
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| 210 | IF( iom_use("TL1") ) CALL iom_put("TL1" , zTL1 (:,:,:) * tmask(:,:,:) ) ! TL1 |
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| 211 | IF( iom_use("Totlig") ) CALL iom_put("Totlig" , ztotlig(:,:,:) * tmask(:,:,:) ) ! TL |
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| 212 | IF( iom_use("Biron") ) CALL iom_put("Biron" , biron (:,:,:) * 1e9 * tmask(:,:,:) ) ! biron |
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| 213 | IF( iom_use("FESCAV") ) CALL iom_put("FESCAV" , zscav3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) |
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| 214 | IF( iom_use("FECOLL") ) CALL iom_put("FECOLL" , zcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) |
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| 215 | IF( iom_use("FEPREC") ) CALL iom_put("FEPREC" , zfeprecip(:,:,:) *1e9*tmask(:,:,:)*zrfact2 ) |
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[3443] | 216 | ENDIF |
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| 217 | |
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[12377] | 218 | IF(sn_cfctl%l_prttrc) THEN ! print mean trends (used for debugging) |
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[3449] | 219 | WRITE(charout, FMT="('fechem')") |
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[13286] | 220 | CALL prt_ctl_info( charout, cdcomp = 'top' ) |
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| 221 | CALL prt_ctl(tab4d_1=tr(:,:,:,:,Krhs), mask1=tmask, clinfo=ctrcnm) |
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[3443] | 222 | ENDIF |
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| 223 | ! |
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[9124] | 224 | IF( ln_timing ) CALL timing_stop('p4z_fechem') |
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[3443] | 225 | ! |
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| 226 | END SUBROUTINE p4z_fechem |
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| 227 | |
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| 228 | |
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| 229 | SUBROUTINE p4z_fechem_init |
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| 230 | !!---------------------------------------------------------------------- |
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| 231 | !! *** ROUTINE p4z_fechem_init *** |
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| 232 | !! |
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| 233 | !! ** Purpose : Initialization of iron chemistry parameters |
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| 234 | !! |
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| 235 | !! ** Method : Read the nampisfer namelist and check the parameters |
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| 236 | !! called at the first timestep |
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| 237 | !! |
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| 238 | !! ** input : Namelist nampisfer |
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| 239 | !! |
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| 240 | !!---------------------------------------------------------------------- |
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[9124] | 241 | INTEGER :: ios ! Local integer |
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| 242 | !! |
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[15459] | 243 | NAMELIST/nampisfer/ ln_ligvar, xlam1, xlamdust, ligand, kfep, scaveff |
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[9124] | 244 | !!---------------------------------------------------------------------- |
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[9169] | 245 | ! |
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| 246 | IF(lwp) THEN |
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| 247 | WRITE(numout,*) |
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| 248 | WRITE(numout,*) 'p4z_rem_init : Initialization of iron chemistry parameters' |
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| 249 | WRITE(numout,*) '~~~~~~~~~~~~' |
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| 250 | ENDIF |
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| 251 | ! |
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[4147] | 252 | READ ( numnatp_ref, nampisfer, IOSTAT = ios, ERR = 901) |
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[11536] | 253 | 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisfer in reference namelist' ) |
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[4147] | 254 | READ ( numnatp_cfg, nampisfer, IOSTAT = ios, ERR = 902 ) |
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[11536] | 255 | 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisfer in configuration namelist' ) |
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[9169] | 256 | IF(lwm) WRITE( numonp, nampisfer ) |
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[4147] | 257 | |
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[9169] | 258 | IF(lwp) THEN ! control print |
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| 259 | WRITE(numout,*) ' Namelist : nampisfer' |
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| 260 | WRITE(numout,*) ' variable concentration of ligand ln_ligvar =', ln_ligvar |
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| 261 | WRITE(numout,*) ' scavenging rate of Iron xlam1 =', xlam1 |
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| 262 | WRITE(numout,*) ' scavenging rate of Iron by dust xlamdust =', xlamdust |
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| 263 | WRITE(numout,*) ' ligand concentration in the ocean ligand =', ligand |
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| 264 | WRITE(numout,*) ' rate constant for nanoparticle formation kfep =', kfep |
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[15459] | 265 | WRITE(numout,*) ' Scavenged iron that is added to POFe scaveff =', scaveff |
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[3443] | 266 | ENDIF |
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[15459] | 267 | ! |
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[3443] | 268 | END SUBROUTINE p4z_fechem_init |
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[9124] | 269 | |
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[3443] | 270 | !!====================================================================== |
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| 271 | END MODULE p4zfechem |
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