[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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| 17 | USE p4zsbc ! Boundary conditions from sediments |
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| 18 | USE prtctl_trc ! print control for debugging |
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| 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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[3443] | 32 | |
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| 33 | !!---------------------------------------------------------------------- |
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[10067] | 34 | !! NEMO/TOP 4.0 , NEMO Consortium (2018) |
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[10069] | 35 | !! $Id$ |
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[10068] | 36 | !! Software governed by the CeCILL license (see ./LICENSE) |
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[3443] | 37 | !!---------------------------------------------------------------------- |
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| 38 | CONTAINS |
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| 39 | |
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[5385] | 40 | SUBROUTINE p4z_fechem( kt, knt ) |
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[3443] | 41 | !!--------------------------------------------------------------------- |
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| 42 | !! *** ROUTINE p4z_fechem *** |
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| 43 | !! |
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| 44 | !! ** Purpose : Compute remineralization/scavenging of iron |
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| 45 | !! |
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[10401] | 46 | !! ** Method : A simple chemistry model of iron from Aumont and Bopp (2006) |
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| 47 | !! based on one ligand and one inorganic form |
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[3443] | 48 | !!--------------------------------------------------------------------- |
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[9169] | 49 | INTEGER, INTENT(in) :: kt, knt ! ocean time step |
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[3443] | 50 | ! |
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[7646] | 51 | INTEGER :: ji, jj, jk, jic, jn |
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[3446] | 52 | REAL(wp) :: zdep, zlam1a, zlam1b, zlamfac |
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[13200] | 53 | REAL(wp) :: zkeq, zfeequi, zfesatur, zfecoll, fe3sol, zligco |
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| 54 | REAL(wp) :: zdenom1, zscave, zaggdfea, zaggdfeb, zcoag, ztrc, zdust |
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| 55 | REAL(wp) :: zdenom2, ztfe, zhplus, zxlam, zaggliga, zaggligb |
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| 56 | REAL(wp) :: zrfact2 |
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[7646] | 57 | CHARACTER (len=25) :: charout |
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[9169] | 58 | REAL(wp), DIMENSION(jpi,jpj,jpk) :: zTL1, zFe3, ztotlig, precip, zFeL1 |
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[10362] | 59 | REAL(wp), DIMENSION(jpi,jpj,jpk) :: zcoll3d, zscav3d, zlcoll3d |
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[3443] | 60 | !!--------------------------------------------------------------------- |
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| 61 | ! |
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[9124] | 62 | IF( ln_timing ) CALL timing_start('p4z_fechem') |
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[3443] | 63 | ! |
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[13200] | 64 | zFe3 (:,:,:) = 0. ; zFeL1(:,:,:) = 0. |
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[7753] | 65 | zTL1 (:,:,:) = 0. |
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[3461] | 66 | |
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[3443] | 67 | ! Total ligand concentration : Ligands can be chosen to be constant or variable |
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| 68 | ! Parameterization from Tagliabue and Voelker (2011) |
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| 69 | ! ------------------------------------------------- |
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| 70 | IF( ln_ligvar ) THEN |
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[7753] | 71 | ztotlig(:,:,:) = 0.09 * trb(:,:,:,jpdoc) * 1E6 + ligand * 1E9 |
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| 72 | ztotlig(:,:,:) = MIN( ztotlig(:,:,:), 10. ) |
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[3443] | 73 | ELSE |
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[7753] | 74 | IF( ln_ligand ) THEN ; ztotlig(:,:,:) = trb(:,:,:,jplgw) * 1E9 |
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| 75 | ELSE ; ztotlig(:,:,:) = ligand * 1E9 |
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[7646] | 76 | ENDIF |
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[3443] | 77 | ENDIF |
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| 78 | |
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[10401] | 79 | ! ------------------------------------------------------------ |
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| 80 | ! from Aumont and Bopp (2006) |
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| 81 | ! This model is based on one ligand and Fe' |
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| 82 | ! Chemistry is supposed to be fast enough to be at equilibrium |
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| 83 | ! ------------------------------------------------------------ |
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| 84 | DO jk = 1, jpkm1 |
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[7646] | 85 | DO jj = 1, jpj |
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| 86 | DO ji = 1, jpi |
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[10401] | 87 | zTL1(ji,jj,jk) = ztotlig(ji,jj,jk) |
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| 88 | zkeq = fekeq(ji,jj,jk) |
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| 89 | zfesatur = zTL1(ji,jj,jk) * 1E-9 |
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| 90 | ztfe = trb(ji,jj,jk,jpfer) |
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| 91 | ! Fe' is the root of a 2nd order polynom |
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| 92 | zFe3 (ji,jj,jk) = ( -( 1. + zfesatur * zkeq - zkeq * ztfe ) & |
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| 93 | & + SQRT( ( 1. + zfesatur * zkeq - zkeq * ztfe )**2 & |
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| 94 | & + 4. * ztfe * zkeq) ) / ( 2. * zkeq ) |
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| 95 | zFe3 (ji,jj,jk) = zFe3(ji,jj,jk) * 1E9 |
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| 96 | zFeL1(ji,jj,jk) = MAX( 0., trb(ji,jj,jk,jpfer) * 1E9 - zFe3(ji,jj,jk) ) |
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| 97 | END DO |
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[7646] | 98 | END DO |
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[10401] | 99 | END DO |
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[3443] | 100 | ! |
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[7646] | 101 | |
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[3531] | 102 | zdust = 0. ! if no dust available |
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[3443] | 103 | DO jk = 1, jpkm1 |
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| 104 | DO jj = 1, jpj |
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| 105 | DO ji = 1, jpi |
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| 106 | ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water. |
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| 107 | ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]). |
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| 108 | ! Scavenging onto dust is also included as evidenced from the DUNE experiments. |
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| 109 | ! -------------------------------------------------------------------------------------- |
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[10362] | 110 | zhplus = max( rtrn, hi(ji,jj,jk) ) |
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| 111 | fe3sol = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2 & |
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| 112 | & + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4) & |
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| 113 | & + fesol(ji,jj,jk,5) / zhplus ) |
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[10401] | 114 | ! |
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| 115 | zfeequi = zFe3(ji,jj,jk) * 1E-9 |
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| 116 | zfecoll = 0.5 * zFeL1(ji,jj,jk) * 1E-9 |
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| 117 | ! precipitation of Fe3+, creation of nanoparticles |
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| 118 | precip(ji,jj,jk) = MAX( 0., ( zFe3(ji,jj,jk) * 1E-9 - fe3sol ) ) * kfep * xstep |
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[7646] | 119 | ! |
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[5385] | 120 | ztrc = ( trb(ji,jj,jk,jppoc) + trb(ji,jj,jk,jpgoc) + trb(ji,jj,jk,jpcal) + trb(ji,jj,jk,jpgsi) ) * 1.e6 |
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[13200] | 121 | IF( ln_dust ) zdust = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk) |
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[10362] | 122 | IF (ln_ligand) THEN |
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| 123 | zxlam = xlam1 * MAX( 1.E-3, EXP(-2 * etot(ji,jj,jk) / 10. ) * (1. - EXP(-2 * trb(ji,jj,jk,jpoxy) / 100.E-6 ) )) |
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| 124 | ELSE |
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| 125 | zxlam = xlam1 * 1.0 |
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| 126 | ENDIF |
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| 127 | zlam1b = 3.e-5 + xlamdust * zdust + zxlam * ztrc |
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[7646] | 128 | zscave = zfeequi * zlam1b * xstep |
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[3443] | 129 | |
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| 130 | ! Compute the different ratios for scavenging of iron |
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| 131 | ! to later allocate scavenged iron to the different organic pools |
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| 132 | ! --------------------------------------------------------- |
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[10362] | 133 | zdenom1 = zxlam * trb(ji,jj,jk,jppoc) / zlam1b |
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| 134 | zdenom2 = zxlam * trb(ji,jj,jk,jpgoc) / zlam1b |
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[3443] | 135 | |
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[13200] | 136 | ! Increased scavenging for very high iron concentrations found near the coasts |
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| 137 | ! due to increased lithogenic particles and let say it is unknown processes (precipitation, ...) |
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[3443] | 138 | ! ----------------------------------------------------------- |
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[3475] | 139 | zlamfac = MAX( 0.e0, ( gphit(ji,jj) + 55.) / 30. ) |
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| 140 | zlamfac = MIN( 1. , zlamfac ) |
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[6140] | 141 | zdep = MIN( 1., 1000. / gdept_n(ji,jj,jk) ) |
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[10362] | 142 | zcoag = 1E-4 * ( 1. - zlamfac ) * zdep * xstep * trb(ji,jj,jk,jpfer) |
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[3443] | 143 | |
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[13200] | 144 | ! Compute the coagulation of colloidal iron. This parameterization |
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| 145 | ! could be thought as an equivalent of colloidal pumping. |
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| 146 | ! It requires certainly some more work as it is very poorly constrained. |
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| 147 | ! ---------------------------------------------------------------- |
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[10362] | 148 | zlam1a = ( 0.369 * 0.3 * trb(ji,jj,jk,jpdoc) + 102.4 * trb(ji,jj,jk,jppoc) ) * xdiss(ji,jj,jk) & |
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[13200] | 149 | & + ( 114. * 0.3 * trb(ji,jj,jk,jpdoc) ) |
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[7646] | 150 | zaggdfea = zlam1a * xstep * zfecoll |
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[3446] | 151 | ! |
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[10362] | 152 | zlam1b = 3.53E3 * trb(ji,jj,jk,jpgoc) * xdiss(ji,jj,jk) |
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[7646] | 153 | zaggdfeb = zlam1b * xstep * zfecoll |
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[3446] | 154 | ! |
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[7646] | 155 | tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) - zscave - zaggdfea - zaggdfeb & |
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| 156 | & - zcoag - precip(ji,jj,jk) |
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[3446] | 157 | tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zscave * zdenom1 + zaggdfea |
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| 158 | tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + zscave * zdenom2 + zaggdfeb |
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[10362] | 159 | zscav3d(ji,jj,jk) = zscave |
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| 160 | zcoll3d(ji,jj,jk) = zaggdfea + zaggdfeb |
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[7646] | 161 | ! |
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[3443] | 162 | END DO |
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| 163 | END DO |
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| 164 | END DO |
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| 165 | ! |
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[3446] | 166 | ! Define the bioavailable fraction of iron |
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| 167 | ! ---------------------------------------- |
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[10401] | 168 | biron(:,:,:) = trb(:,:,:,jpfer) |
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[7646] | 169 | ! |
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| 170 | IF( ln_ligand ) THEN |
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| 171 | ! |
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| 172 | DO jk = 1, jpkm1 |
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| 173 | DO jj = 1, jpj |
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| 174 | DO ji = 1, jpi |
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[13200] | 175 | |
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| 176 | ! Coagulation of ligands due to various processes (Brownian, shear, diff. sedimentation |
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| 177 | ! Coefficients are taken from the p4zagg |
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| 178 | ! ------------------------------------------------------------------------------------- |
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[7646] | 179 | zlam1a = ( 0.369 * 0.3 * trb(ji,jj,jk,jpdoc) + 102.4 * trb(ji,jj,jk,jppoc) ) * xdiss(ji,jj,jk) & |
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| 180 | & + ( 114. * 0.3 * trb(ji,jj,jk,jpdoc) ) |
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| 181 | ! |
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| 182 | zlam1b = 3.53E3 * trb(ji,jj,jk,jpgoc) * xdiss(ji,jj,jk) |
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[13200] | 183 | |
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| 184 | ! 50% of the ligands are supposed to be in the colloidal size fraction |
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[10362] | 185 | zligco = 0.5 * trn(ji,jj,jk,jplgw) |
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[7646] | 186 | zaggliga = zlam1a * xstep * zligco |
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| 187 | zaggligb = zlam1b * xstep * zligco |
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| 188 | tra(ji,jj,jk,jplgw) = tra(ji,jj,jk,jplgw) - zaggliga - zaggligb |
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[10362] | 189 | zlcoll3d(ji,jj,jk) = zaggliga + zaggligb |
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[7646] | 190 | END DO |
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| 191 | END DO |
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| 192 | END DO |
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| 193 | ! |
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[10401] | 194 | plig(:,:,:) = MAX( 0., ( ( zFeL1(:,:,:) * 1E-9 ) / ( trb(:,:,:,jpfer) +rtrn ) ) ) |
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[7646] | 195 | ! |
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| 196 | ENDIF |
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[3443] | 197 | ! Output of some diagnostics variables |
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| 198 | ! --------------------------------- |
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[13200] | 199 | IF( lk_iomput .AND. knt == nrdttrc ) THEN |
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| 200 | zrfact2 = 1.e3 * rfact2r ! conversion from mol/L/timestep into mol/m3/s |
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| 201 | IF( iom_use("Fe3") ) CALL iom_put("Fe3" , zFe3 (:,:,:) * tmask(:,:,:) ) ! Fe3+ |
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| 202 | IF( iom_use("FeL1") ) CALL iom_put("FeL1" , zFeL1 (:,:,:) * tmask(:,:,:) ) ! FeL1 |
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| 203 | IF( iom_use("TL1") ) CALL iom_put("TL1" , zTL1 (:,:,:) * tmask(:,:,:) ) ! TL1 |
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| 204 | IF( iom_use("Totlig") ) CALL iom_put("Totlig" , ztotlig(:,:,:) * tmask(:,:,:) ) ! TL |
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| 205 | IF( iom_use("Biron") ) CALL iom_put("Biron" , biron (:,:,:) * 1e9 * tmask(:,:,:) ) ! biron |
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| 206 | IF( iom_use("FESCAV") ) CALL iom_put("FESCAV" , zscav3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) |
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| 207 | IF( iom_use("FECOLL") ) CALL iom_put("FECOLL" , zcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) |
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| 208 | IF( iom_use("LGWCOLL")) CALL iom_put("LGWCOLL", zlcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 ) |
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[3443] | 209 | ENDIF |
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| 210 | |
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| 211 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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[3449] | 212 | WRITE(charout, FMT="('fechem')") |
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[3443] | 213 | CALL prt_ctl_trc_info(charout) |
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| 214 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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| 215 | ENDIF |
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| 216 | ! |
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[9124] | 217 | IF( ln_timing ) CALL timing_stop('p4z_fechem') |
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[3443] | 218 | ! |
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| 219 | END SUBROUTINE p4z_fechem |
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| 220 | |
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| 221 | |
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| 222 | SUBROUTINE p4z_fechem_init |
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| 223 | !!---------------------------------------------------------------------- |
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| 224 | !! *** ROUTINE p4z_fechem_init *** |
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| 225 | !! |
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| 226 | !! ** Purpose : Initialization of iron chemistry parameters |
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| 227 | !! |
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| 228 | !! ** Method : Read the nampisfer namelist and check the parameters |
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| 229 | !! called at the first timestep |
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| 230 | !! |
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| 231 | !! ** input : Namelist nampisfer |
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| 232 | !! |
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| 233 | !!---------------------------------------------------------------------- |
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[9124] | 234 | INTEGER :: ios ! Local integer |
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| 235 | !! |
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[10401] | 236 | NAMELIST/nampisfer/ ln_ligvar, xlam1, xlamdust, ligand, kfep |
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[9124] | 237 | !!---------------------------------------------------------------------- |
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[9169] | 238 | ! |
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| 239 | IF(lwp) THEN |
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| 240 | WRITE(numout,*) |
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| 241 | WRITE(numout,*) 'p4z_rem_init : Initialization of iron chemistry parameters' |
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| 242 | WRITE(numout,*) '~~~~~~~~~~~~' |
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| 243 | ENDIF |
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| 244 | ! |
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| 245 | REWIND( numnatp_ref ) ! Namelist nampisfer in reference namelist : Pisces iron chemistry |
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[4147] | 246 | READ ( numnatp_ref, nampisfer, IOSTAT = ios, ERR = 901) |
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[11536] | 247 | 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisfer in reference namelist' ) |
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[9169] | 248 | REWIND( numnatp_cfg ) ! Namelist nampisfer in configuration namelist : Pisces iron chemistry |
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[4147] | 249 | READ ( numnatp_cfg, nampisfer, IOSTAT = ios, ERR = 902 ) |
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[11536] | 250 | 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisfer in configuration namelist' ) |
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[9169] | 251 | IF(lwm) WRITE( numonp, nampisfer ) |
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[4147] | 252 | |
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[9169] | 253 | IF(lwp) THEN ! control print |
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| 254 | WRITE(numout,*) ' Namelist : nampisfer' |
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| 255 | WRITE(numout,*) ' variable concentration of ligand ln_ligvar =', ln_ligvar |
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| 256 | WRITE(numout,*) ' scavenging rate of Iron xlam1 =', xlam1 |
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| 257 | WRITE(numout,*) ' scavenging rate of Iron by dust xlamdust =', xlamdust |
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| 258 | WRITE(numout,*) ' ligand concentration in the ocean ligand =', ligand |
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| 259 | WRITE(numout,*) ' rate constant for nanoparticle formation kfep =', kfep |
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[3443] | 260 | ENDIF |
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[10362] | 261 | ! |
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[3443] | 262 | END SUBROUTINE p4z_fechem_init |
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[9124] | 263 | |
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[3443] | 264 | !!====================================================================== |
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| 265 | END MODULE p4zfechem |
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