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p4zfechem.F90 in NEMO/branches/2021/dev_r14383_PISCES_NEWDEV_PISCO/src/TOP/PISCES/P4Z – NEMO

source: NEMO/branches/2021/dev_r14383_PISCES_NEWDEV_PISCO/src/TOP/PISCES/P4Z/p4zfechem.F90 @ 14416

Last change on this file since 14416 was 14416, checked in by cetlod, 4 years ago

dev_r14383_PISCES_NEWDEV_PISCO : minor improvments

  • Property svn:keywords set to Id
File size: 14.0 KB
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1MODULE p4zfechem
2   !!======================================================================
3   !!                         ***  MODULE p4zfechem  ***
4   !! TOP :   PISCES Compute iron chemistry and scavenging
5   !!======================================================================
6   !! History :   3.5  !  2012-07 (O. Aumont, A. Tagliabue, C. Ethe) Original code
7   !!             3.6  !  2015-05  (O. Aumont) PISCES quota
8   !!----------------------------------------------------------------------
9   !!   p4z_fechem       : Compute remineralization/scavenging of iron
10   !!   p4z_fechem_init  : Initialisation of parameters for remineralisation
11   !!   p4z_fechem_alloc : Allocate remineralisation variables
12   !!----------------------------------------------------------------------
13   USE oce_trc         ! shared variables between ocean and passive tracers
14   USE trc             ! passive tracers common variables
15   USE sms_pisces      ! PISCES Source Minus Sink variables
16   USE p4zche          ! chemical model
17   USE p4zbc           ! Boundary conditions from sediments
18   USE prtctl          ! print control for debugging
19   USE iom             ! I/O manager
20
21   IMPLICIT NONE
22   PRIVATE
23
24   PUBLIC   p4z_fechem        ! called in p4zbio.F90
25   PUBLIC   p4z_fechem_init   ! called in trcsms_pisces.F90
26
27   LOGICAL          ::   ln_ligvar    !: boolean for variable ligand concentration following Tagliabue and voelker
28   REAL(wp), PUBLIC ::   xlam1        !: scavenging rate of Iron
29   REAL(wp), PUBLIC ::   xlamdust     !: scavenging rate of Iron by dust
30   REAL(wp), PUBLIC ::   ligand       !: ligand concentration in the ocean
31   REAL(wp), PUBLIC ::   kfep         !: rate constant for nanoparticle formation
32   REAL(wp), PUBLIC ::   scaveff      !: Fraction of scavenged iron that is considered as being subject to solubilization
33
34   !! * Substitutions
35#  include "do_loop_substitute.h90"
36#  include "domzgr_substitute.h90"
37   !!----------------------------------------------------------------------
38   !! NEMO/TOP 4.0 , NEMO Consortium (2018)
39   !! $Id$
40   !! Software governed by the CeCILL license (see ./LICENSE)
41   !!----------------------------------------------------------------------
42CONTAINS
43
44   SUBROUTINE p4z_fechem( kt, knt, Kbb, Kmm, Krhs )
45      !!---------------------------------------------------------------------
46      !!                     ***  ROUTINE p4z_fechem  ***
47      !!
48      !! ** Purpose :   Compute remineralization/scavenging of iron
49      !!
50      !! ** Method  :   A simple chemistry model of iron from Aumont and Bopp (2006)
51      !!                based on one ligand and one inorganic form
52      !!---------------------------------------------------------------------
53      INTEGER, INTENT(in) ::   kt, knt   ! ocean time step
54      INTEGER, INTENT(in) ::   Kbb, Kmm, Krhs  ! time level indices
55      !
56      INTEGER  ::   ji, jj, jk, jic, jn
57      REAL(wp) ::   zlam1a, zlam1b
58      REAL(wp) ::   zkeq, zfesatur, zfecoll, fe3sol, zligco
59      REAL(wp) ::   zscave, zaggdfea, zaggdfeb, ztrc, zdust, zklight
60      REAL(wp) ::   ztfe, zhplus, zxlam, zaggliga, zaggligb
61      REAL(wp) ::   zprecip, zprecipno3, zvar
62      REAL(wp) ::   zrfact2
63      CHARACTER (len=25) :: charout
64      REAL(wp), DIMENSION(jpi,jpj,jpk) ::   zTL1, zFe3, ztotlig, zfeprecip, zFeL1
65      REAL(wp), DIMENSION(jpi,jpj,jpk) ::   zcoll3d, zscav3d, zlcoll3d
66      !!---------------------------------------------------------------------
67      !
68      IF( ln_timing )   CALL timing_start('p4z_fechem')
69      !
70      zFe3     (:,:,jpk) = 0.
71      zFeL1    (:,:,jpk) = 0.
72      zTL1     (:,:,jpk) = 0.
73      zfeprecip(:,:,jpk) = 0.
74      zcoll3d  (:,:,jpk) = 0.
75      zscav3d  (:,:,jpk) = 0.
76      zlcoll3d (:,:,jpk) = 0.
77
78      ! Total ligand concentration : Ligands can be chosen to be constant or variable
79      ! Parameterization from Pham and Ito (2018)
80      ! -------------------------------------------------
81      IF( ln_ligvar ) THEN
82         ztotlig(:,:,:) =  0.09 * 0.667 * tr(:,:,:,jpdoc,Kbb) * 1E6 &
83           &             + ligand * 1E9 &
84           &             + MAX(0., chemo2(:,:,:) - tr(:,:,:,jpoxy,Kbb) ) / 400.E-6
85         ztotlig(:,:,:) =  MIN( ztotlig(:,:,:), 10. )
86      ELSE
87        IF( ln_ligand ) THEN  ;   ztotlig(:,:,:) = tr(:,:,:,jplgw,Kbb) * 1E9
88        ELSE                  ;   ztotlig(:,:,:) = ligand * 1E9 
89        ENDIF
90      ENDIF
91
92      ! ------------------------------------------------------------
93      !  from Aumont and Bopp (2006)
94      ! This model is based on one ligand, Fe2+ and Fe3+
95      ! Chemistry is supposed to be fast enough to be at equilibrium
96      ! ------------------------------------------------------------
97      DO_3D( 1, 1, 1, 1, 1, jpkm1 )
98          zTL1(ji,jj,jk)  = ztotlig(ji,jj,jk)
99          zkeq            = fekeq(ji,jj,jk)
100          zklight         = 4.77E-7 * etot(ji,jj,jk) * 0.5 / 10**-6.3
101          zfesatur        = zTL1(ji,jj,jk) * 1E-9
102          ztfe            = (1.0 + zklight) * tr(ji,jj,jk,jpfer,Kbb) 
103          ! Fe' is the root of a 2nd order polynom
104          zvar =  1. + zfesatur * zkeq + zklight + consfe3(ji,jj,jk)/10**-6.3 - zkeq * tr(ji,jj,jk,jpfer,Kbb)
105          zFe3 (ji,jj,jk) = ( -1 * zvar + SQRT( zvar**2 + 4. * ztfe * zkeq) ) / ( 2. * zkeq + rtrn )
106          zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) - zFe3(ji,jj,jk) )
107      END_3D
108      !
109      plig(:,:,:) =  MAX( 0., ( zFeL1(:,:,:) / ( tr(:,:,:,jpfer,Kbb) + rtrn ) ) )
110      !
111      zdust = 0.         ! if no dust available
112      DO_3D( 1, 1, 1, 1, 1, jpkm1 )
113         ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water.
114         ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]).
115         ! Scavenging onto dust is also included as evidenced from the DUNE experiments.
116         ! --------------------------------------------------------------------------------------
117         zhplus  = max( rtrn, hi(ji,jj,jk) )
118         fe3sol  = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2  &
119         &         + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4)     &
120         &         + fesol(ji,jj,jk,5) / zhplus )
121         !
122         zfecoll = 0.5 * zFeL1(ji,jj,jk) * 1E-9
123         ! precipitation of Fe3+, creation of nanoparticles
124         zprecip = MAX( 0., ( zFe3(ji,jj,jk) - fe3sol ) ) * kfep * xstep * ( 1.0 - nitrfac(ji,jj,jk) ) 
125         ! Precipitation of Fe2+ due to oxidation by NO3 (Croot et al., 2019)
126         ! This occurs in anoxic waters only
127         zprecipno3 = 2.0 * 130.0 * tr(ji,jj,jk,jpno3,Kbb) * nitrfac(ji,jj,jk) * xstep * zFe3(ji,jj,jk)
128         !
129         zfeprecip(ji,jj,jk) = zprecip + zprecipno3
130         !
131         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 
132         ztrc = MAX( rtrn, ztrc )
133         IF( ll_dust )  zdust  = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk)
134         zxlam  = MAX( 1.E-3, (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) ))
135         zlam1b = 3.e-5 + ( xlamdust * zdust + xlam1 * ztrc ) * zxlam
136         zscave = zFe3(ji,jj,jk) * zlam1b * xstep
137
138         !  Compute the coagulation of colloidal iron. This parameterization
139         !  could be thought as an equivalent of colloidal pumping.
140         !  It requires certainly some more work as it is very poorly constrained.
141         !  ----------------------------------------------------------------
142         zlam1a   = ( 12.0  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 9.05  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
143             &    + ( 2.49  * tr(ji,jj,jk,jppoc,Kbb) )     &
144             &    + ( 127.8 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 725.7 * tr(ji,jj,jk,jppoc,Kbb) )
145         zaggdfea = zlam1a * xstep * zfecoll
146               !
147         zlam1b   = ( 1.94 * xdiss(ji,jj,jk) + 1.37 ) * tr(ji,jj,jk,jpgoc,Kbb)
148         zaggdfeb = zlam1b * xstep * zfecoll
149
150         !
151         tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb &
152         &                       - zfeprecip(ji,jj,jk)
153
154         tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc
155         tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * scaveff * tr(ji,jj,jk,jppoc,Kbb) / ztrc
156
157
158          ! Precipitated iron is supposed to be permanently lost.
159          ! Scavenged iron is supposed to be released back to seawater
160          ! when POM is solubilized. This is highly uncertain as probably
161          ! a significant part of it may be rescavenged back onto
162          ! the particles. An efficiency factor is applied that is read
163          ! in the namelist.
164          ! See for instance Tagliabue et al. (2019).
165          ! Aggregated FeL is considered as biogenic Fe as it
166          ! probably remains  complexed when the particle is solubilized.
167          ! -------------------------------------------------------------
168          tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zaggdfea
169          tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zaggdfeb
170          !
171          zscav3d(ji,jj,jk)   = zscave 
172          zcoll3d(ji,jj,jk)   = zaggdfea + zaggdfeb
173         !
174      END_3D
175      !
176      !  Define the bioavailable fraction of iron
177      !  ----------------------------------------
178      biron(:,:,:) = tr(:,:,:,jpfer,Kbb) 
179      !
180      IF( ln_ligand ) THEN
181         !
182         DO_3D( 1, 1, 1, 1, 1, jpkm1 )
183             ! Coagulation of ligands due to various processes (Brownian, shear, diff. sedimentation
184             ! Coefficients are taken from p4zagg
185             ! -------------------------------------------------------------------------------------
186             zlam1a   = ( 12.0  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 9.05  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
187                 &    + ( 2.49  * tr(ji,jj,jk,jppoc,Kbb) )     &
188                 &    + ( 127.8 * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 725.7 * tr(ji,jj,jk,jppoc,Kbb) )
189             !
190             zlam1b   = ( 1.94 * xdiss(ji,jj,jk) + 1.37 ) * tr(ji,jj,jk,jpgoc,Kbb)
191             ! 50% of the ligands are supposed to be in the colloidal size fraction
192             ! as for FeL
193             zligco   = 0.5 * tr(ji,jj,jk,jplgw,Kbb)
194             zaggliga = zlam1a * xstep * zligco 
195             zaggligb = zlam1b * xstep * zligco
196             !
197             tr(ji,jj,jk,jplgw,Krhs) = tr(ji,jj,jk,jplgw,Krhs)  - zaggliga - zaggligb
198             zlcoll3d(ji,jj,jk)  = zaggliga + zaggligb
199         END_3D
200         plig(:,:,:) =  MAX( 0., ( ( zFeL1(:,:,:) * 1E-9 ) / ( tr(:,:,:,jpfer,Kbb) +rtrn ) ) )
201         !
202      ENDIF
203      !  Output of some diagnostics variables
204      !     ---------------------------------
205      IF( lk_iomput .AND. knt == nrdttrc ) THEN
206         zrfact2 = 1.e3 * rfact2r  ! conversion from mol/L/timestep into mol/m3/s
207         IF( iom_use("Fe3")    )  CALL iom_put("Fe3"    , zFe3   (:,:,:)       * tmask(:,:,:) )   ! Fe3+
208         IF( iom_use("FeL1")   )  CALL iom_put("FeL1"   , zFeL1  (:,:,:)       * tmask(:,:,:) )   ! FeL1
209         IF( iom_use("TL1")    )  CALL iom_put("TL1"    , zTL1   (:,:,:)       * tmask(:,:,:) )   ! TL1
210         IF( iom_use("Totlig") )  CALL iom_put("Totlig" , ztotlig(:,:,:)       * tmask(:,:,:) )   ! TL
211         IF( iom_use("Biron")  )  CALL iom_put("Biron"  , biron  (:,:,:)  * 1e9 * tmask(:,:,:) )   ! biron
212         IF( iom_use("FESCAV") )  CALL iom_put("FESCAV" , zscav3d(:,:,:)  * 1e9 * tmask(:,:,:) * zrfact2 )
213         IF( iom_use("FECOLL") )  CALL iom_put("FECOLL" , zcoll3d(:,:,:)  * 1e9 * tmask(:,:,:) * zrfact2 )
214         IF( iom_use("FEPREC") )  CALL iom_put("FEPREC" , zfeprecip(:,:,:) *1e9*tmask(:,:,:)*zrfact2 )
215         IF( iom_use("LGWCOLL"))  CALL iom_put("LGWCOLL", zlcoll3d(:,:,:) * 1e9 * tmask(:,:,:) * zrfact2 )
216      ENDIF
217
218      IF(sn_cfctl%l_prttrc)   THEN  ! print mean trends (used for debugging)
219         WRITE(charout, FMT="('fechem')")
220         CALL prt_ctl_info( charout, cdcomp = 'top' )
221         CALL prt_ctl(tab4d_1=tr(:,:,:,:,Krhs), mask1=tmask, clinfo=ctrcnm)
222      ENDIF
223      !
224      IF( ln_timing )   CALL timing_stop('p4z_fechem')
225      !
226   END SUBROUTINE p4z_fechem
227
228
229   SUBROUTINE p4z_fechem_init
230      !!----------------------------------------------------------------------
231      !!                  ***  ROUTINE p4z_fechem_init  ***
232      !!
233      !! ** Purpose :   Initialization of iron chemistry parameters
234      !!
235      !! ** Method  :   Read the nampisfer namelist and check the parameters
236      !!      called at the first timestep
237      !!
238      !! ** input   :   Namelist nampisfer
239      !!
240      !!----------------------------------------------------------------------
241      INTEGER ::   ios   ! Local integer
242      !!
243      NAMELIST/nampisfer/ ln_ligvar, xlam1, xlamdust, ligand, kfep, scaveff 
244      !!----------------------------------------------------------------------
245      !
246      IF(lwp) THEN
247         WRITE(numout,*)
248         WRITE(numout,*) 'p4z_rem_init : Initialization of iron chemistry parameters'
249         WRITE(numout,*) '~~~~~~~~~~~~'
250      ENDIF
251      !
252      READ  ( numnatp_ref, nampisfer, IOSTAT = ios, ERR = 901)
253901   IF( ios /= 0 )   CALL ctl_nam ( ios , 'nampisfer in reference namelist' )
254      READ  ( numnatp_cfg, nampisfer, IOSTAT = ios, ERR = 902 )
255902   IF( ios >  0 )   CALL ctl_nam ( ios , 'nampisfer in configuration namelist' )
256      IF(lwm) WRITE( numonp, nampisfer )
257
258      IF(lwp) THEN                     ! control print
259         WRITE(numout,*) '   Namelist : nampisfer'
260         WRITE(numout,*) '      variable concentration of ligand          ln_ligvar    =', ln_ligvar
261         WRITE(numout,*) '      scavenging rate of Iron                   xlam1        =', xlam1
262         WRITE(numout,*) '      scavenging rate of Iron by dust           xlamdust     =', xlamdust
263         WRITE(numout,*) '      ligand concentration in the ocean         ligand       =', ligand
264         WRITE(numout,*) '      rate constant for nanoparticle formation  kfep         =', kfep
265         WRITE(numout,*) '      Scavenged iron that is added to POFe      scaveff      =', scaveff
266      ENDIF
267      !
268   END SUBROUTINE p4z_fechem_init
269   
270   !!======================================================================
271END MODULE p4zfechem
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